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1
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Wang Z, Ferreira Rodrigues C, Jurt S, Domínguez-Martín A, Johannsen S, Sigel RKO. Elucidating the solution structure of the monomolecular BCL2 RNA G-quadruplex: a new robust NMR assignment approach. Chem Sci 2025:d5sc01416f. [PMID: 40181818 PMCID: PMC11962745 DOI: 10.1039/d5sc01416f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Accepted: 03/26/2025] [Indexed: 04/05/2025] Open
Abstract
5' untranslated regions (UTRs) of mRNA commonly feature G-quadruplexes (G4s), crucial for translational regulation and promising as drug targets to modulate gene expression. While NMR spectroscopy is well-suited for studying these motifs' structure and dynamics, their guanine-rich nature complicates resonance assignment due to high signal overlap. Exploiting the inherent rigidity of G4 cores, we developed a universally applicable assignment strategy for uniformly isotopically enriched G4 structures, relying solely on through-bond correlations to establish the G-tetrads. Applying this approach, we resolved the solution structures of two triple mutants of the RNA G4 in the 5' UTR of the human BCL2 proto-oncogene, one of the first natural monomolecular RNA G4 structures available to date. Comparative analysis with other RNA and DNA G4s reveals their notably compact and well-defined cores. Moreover, the sugar pucker geometries of the tetrad guanines are far less stringent than previously assumed, adeptly accommodating specific structural features. This contrasts with the canonical base pairing in RNA and DNA, in which the sugar pucker dictates the type of the double-helical structure. The strategy presented provides a direct path to uncovering G4 structural intricacies, advancing our grasp of their biological roles, and paving the way for RNA-targeted therapeutics.
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Affiliation(s)
- Zenghui Wang
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
| | | | - Simon Jurt
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
| | - Alicia Domínguez-Martín
- Department of Inorganic Chemistry, Faculty of Pharmacy, University of Granada 18071 Granada Spain
| | - Silke Johannsen
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
| | - Roland K O Sigel
- Department of Chemistry, University of Zürich 8057 Zürich Switzerland
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2
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Cueny R, Voter A, McKenzie A, Morgenstern M, Myers K, Place M, Peters J, Coon J, Keck J. Altering translation allows E. coli to overcome G-quadruplex stabilizers. Nucleic Acids Res 2025; 53:gkaf264. [PMID: 40193707 PMCID: PMC11975287 DOI: 10.1093/nar/gkaf264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Revised: 03/14/2025] [Accepted: 03/21/2025] [Indexed: 04/09/2025] Open
Abstract
G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of translation elongation factor Tu or slowing translation initiation or elongation with kasugamycin, chloramphenicol, or spectinomycin suppress the effects of G4-stabilizing compounds. In contrast, reducing the expression of specific translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses reveal decreased protein and transcript levels, respectively, for ribosome assembly factors and proteins associated with translation in the presence of G4 stabilizer. Our results support a model in which reducing the rate of translation by altering translation initiation, translation elongation, or ribosome assembly can compensate for G4-related stress in E. coli.
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Affiliation(s)
- Rachel R Cueny
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706 United States
| | - Andrew F Voter
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706 United States
| | - Aidan M McKenzie
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706 United States
| | - Marcel Morgenstern
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706 United States
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, 53706 United States
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726 United States
| | - Michael M Place
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726 United States
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53706 United States
| | - Joshua J Coon
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706 United States
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI, 53706 United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706 United States
- Morgridge Institute for Research, Madison, WI, 53715 United States
| | - James L Keck
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53706 United States
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3
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Song D, Luo J, Duan X, Jin F, Lu YJ. Identification of G-quadruplex nucleic acid structures by high-throughput sequencing: A review. Int J Biol Macromol 2025; 297:139896. [PMID: 39818384 DOI: 10.1016/j.ijbiomac.2025.139896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Revised: 01/04/2025] [Accepted: 01/13/2025] [Indexed: 01/18/2025]
Abstract
G-quadruplexes (G4s) are non-canonical nucleic acid secondary structures formed by guanine-rich DNA or RNA sequences. These structures play pivotal roles in cellular processes, including DNA replication, transcription, RNA splicing, and protein translation. High-throughput sequencing has significantly advanced the study of G4s by enabling genome-wide mapping and detailed characterization. This review provides a comprehensive overview of current methods for G4 identification using high-throughput sequencing, focusing on key techniques such as G4-seq, G4-ChIP-seq, G4-CUT&Tag, LiveG4ID-seq, G4assess, HepG4-seq, rG4-seq, RT-stop profiling with DMS-m7G footprinting, G4RP-seq, Keth-seq, and SHALIPE-seq. We discuss the principles, advantages, limitations, and applications of these methods, highlighting their contribution to our understanding of G4 biology. The review also emphasizes the need for improved tools to explore the dynamic behavior of G4s, particularly in living organisms.
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Affiliation(s)
- Delong Song
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Junren Luo
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Xuan Duan
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China
| | - Fujun Jin
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China.
| | - Yu-Jing Lu
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China; Smart Medical Innovation Technology Center, Guangdong University of Technology, Guangzhou 510006, China.
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4
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Barr J, Cadoni E, Schellinck S, Laudadio E, Martins JC, Madder A. Locking up G-Quadruplexes with Light-Triggered Staples Leads to Increased Topological, Thermodynamic, and Metabolic Stability. Angew Chem Int Ed Engl 2025; 64:e202420592. [PMID: 39585944 DOI: 10.1002/anie.202420592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2024] [Revised: 11/19/2024] [Accepted: 11/22/2024] [Indexed: 11/27/2024]
Abstract
G-quadruplexes (G4 s) are secondary, tetraplexed DNA structures abundant in non-coding regions of the genome, implicated in gene transcription processes and currently firmly recognised as important potential therapeutic targets. Given their affinity for human proteins, G4 structures are investigated as potential decoys and aptamers. However, G4 s tend to adopt different conformations depending on the exact environmental conditions, and often only one displays the specifically desired biological activity. Their less intensively studied counterparts, the elusive tetraplexed intercalated-motifs (IMs) are typically unstable at neutral pH, hampering the investigation of their potential involvement in a biological context. We herein report on a photochemical method for "stapling" such tetraplexed-structures, to increase their stability, lock their topology and enhance their enzymatic resistance, while maintaining biological activity. The chemical structure and topology of the stapled Thrombin Binding Aptamer (TBA) was spectroscopically characterised and rationalised in silico. The method was then extended to other biologically relevant G4- and IM-prone sequences, hinting towards potential application of such stapled structures in a therapeutic context.
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Affiliation(s)
- Jack Barr
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000, Gent, Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000, Gent, Belgium
| | - Sofie Schellinck
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000, Gent, Belgium
| | - Emiliano Laudadio
- Department of Science and Engineering of Matter, Environment and Urban Planning, Polytechnic University of Marche, Via Brecce Bianche 12, 60131, Ancona, Italy
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000, Gent, Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281-S4, 9000, Gent, Belgium
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5
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Lin X, Zhang J, Liang J, Ji D, Huang ZS, Li D. Selective Up-Regulation of Tumor Suppressor Gene Retinoblastoma by Bisacridine Derivative Through Gene Promoter Quadruplex Structures for Cancer Treatment. Int J Mol Sci 2025; 26:1417. [PMID: 40003883 PMCID: PMC11855212 DOI: 10.3390/ijms26041417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2024] [Revised: 01/31/2025] [Accepted: 02/04/2025] [Indexed: 02/27/2025] Open
Abstract
The retinoblastoma (RB) gene is an important tumor suppressor gene with a higher mutation frequency than other tumor suppressor genes. The mutation or inactivation of RB has been found in various cancers. The discovery of small molecules to promote RB expression is an effective anti-cancer strategy. Special DNA secondary structures with G-quadruplex and i-motif on the RB promoter could act as "molecular switches" for gene transcriptional regulation and are potentially important targets for the development of new anti-cancer drugs. After extensive screening, we found that the bisacridine derivative A06 had selective binding and destabilization for both the G-quadruplex and i-motif on the RB promoter, which significantly up-regulated RB gene transcription and translation, resulting in the inhibition of tumor cell proliferation and metastasis. A06 exhibited potent anti-tumor activity on Hela cells and strongly suppressed tumor growth on the Hela xenograft mice model without significant toxicity. In comparison, A02 exhibited strong binding and destabilization to the RB promoter G-quadruplex only, which showed a much weaker effect than A06 on regulating RB expression and producing anti-tumor activity. As we know, this is the first study for up-regulating a tumor suppressor gene through destabilization of both the G-quadruplex and i-motif on the gene promoter, which provides a new strategy for innovative anti-cancer drug discovery and development.
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Affiliation(s)
| | | | | | | | | | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou University City, Guangzhou 510006, China; (X.L.); (J.Z.); (J.L.); (D.J.); (Z.-S.H.)
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Obermann T, Sakshaug T, Kanagaraj VV, Abentung A, Sousa MMLD, Hagen L, Sarno A, Bjørås M, Scheffler K. Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH. Redox Biol 2025; 79:103461. [PMID: 39662289 PMCID: PMC11697278 DOI: 10.1016/j.redox.2024.103461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 12/03/2024] [Accepted: 12/05/2024] [Indexed: 12/13/2024] Open
Abstract
8-oxo-7,8-dihydroguanine (OG) is one of the most abundant oxidative lesions in the genome and is associated with genome instability. Its mutagenic potential is counteracted by a concerted action of 8-oxoguanine DNA glycosylase (OGG1) and mutY homolog DNA glycosylase (MUTYH). It has been suggested that OG and its repair has epigenetic-like properties and mediates transcription, but genome-wide evidence of this interdependence is lacking. Here, we applied an improved OG-sequencing approach reducing artificial background oxidation and RNA-sequencing to correlate genome-wide distribution of OG with gene transcription in OGG1 and/or MUTYH-deficient cells. Our data identified moderate enrichment of OG in the genome that is mainly dependent on the genomic context and not affected by DNA glycosylase-initiated repair. Interestingly, no association was found between genomic OG deposition and gene expression changes upon loss of OGG1 and MUTYH. Regardless of DNA glycosylase activity, OG in promoter regions correlated with expression of genes related to metabolic processes and damage response pathways indicating that OG functions as a cellular stress sensor to regulate transcription. Our work provides novel insights into the mechanism underlying transcriptional regulation by OG and DNA glycosylases OGG1 and MUTYH and suggests that oxidative DNA damage accumulation and its repair utilize different pathways.
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Affiliation(s)
- Tobias Obermann
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Teri Sakshaug
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Vishnu Vignesh Kanagaraj
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Andreas Abentung
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, 7006, Trondheim, Norway
| | - Mirta Mittelstedt Leal de Sousa
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, N-7491, Trondheim, Norway
| | - Lars Hagen
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Proteomics and Modomics Experimental Core (PROMEC), NTNU and the Central Norway Regional Health Authority, N-7491, Trondheim, Norway
| | - Antonio Sarno
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491 Trondheim, Norway; Centre for Embryology and Healthy Development, University of Oslo, Oslo, 0373, Norway; Department of Microbiology, Oslo University Hospital and University of Oslo, Oslo, 0424, Norway
| | - Katja Scheffler
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, 7491, Trondheim, Norway; Department of Neurology and Clinical Neurophysiology, University Hospital of Trondheim, 7006, Trondheim, Norway.
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7
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Bisoi A, Majumdar T, Sarkar S, Singh PC. Flanking Effect on the Folding of Telomeric DNA Sequences into G-Quadruplex Induced by Antimalarial Drugs. J Phys Chem B 2025; 129:835-843. [PMID: 39807525 DOI: 10.1021/acs.jpcb.4c05133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
Abstract
The folding of the guanine repetitive region in the telomere unit into G-quadruplex (G4) by drugs has been suggested as an alternative approach for cancer therapy. Hydroxychloroquine (HCQ) and chloroquine (CQ) are two important drugs in the trial stage for cancer. Both drugs can induce the folding of telomere-guanine-rich sequences into G4 even in the absence of salt. However, the guanine repetitive telomeric sequences are always flanked by other nucleobases at both the terminal (5' or 3') that can affect the drug-induced folding pathways and stability of the G4 significantly. Hence, in this study, the HCQ and CQ drug-induced folding of the guanine repetitive telomeric sequences into G4 and its stability by varying the chemical nature, number, and positions of the flanking nucleobases has been explored using several biophysical techniques and docking studies. It has been found that the drug-induced folding of telomere with single flanking nucleobases is similar to that without flanking nucleobases irrespective of the chemical nature and position of the flanking nucleobase. However, the propensity of the folding and the stability of the telomeric G4 induced by drugs decrease significantly with the increase of the flanking nucleobases more than one of any chemical nature and position. The data suggest that the number of flanking nucleobases rather than their chemical nature and location is a critical factor in the folding of the telomere into G4 induced by both drugs. Further, it has been observed that both drugs mainly interact with the G-tract and thymine of the loop region rather than the flanking nucleobases of the telomeric sequences without or with one flanking nucleobase. In contrast, the flanking nucleobases also participate in the interaction with the HCQ and CQ along with the core guanine repeat telomeric unit in the case of the telomeric sequences with more than one flanking nucleobases. The participation of the flanking nucleobases in the interaction with the HCQ and CQ affects the hydrogen bonding of the positively charged side chain of drugs with G quartet and loop nucleobases of telomere along with the with π···π and C-H···π weak interactions between the quinoline part of the drugs with the core telomeric guanine repeat unit which affects the folding pattern of the telomere sequences with more than one flanking nucleobases into G4.
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Affiliation(s)
- Asim Bisoi
- School of the Chemical Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Trideep Majumdar
- School of the Chemical Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of the Chemical Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of the Chemical Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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8
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Iskandar M, Xiao Barbero M, Jaber M, Chen R, Gomez-Guevara R, Cruz E, Westerheide S. A Review of Telomere Attrition in Cancer and Aging: Current Molecular Insights and Future Therapeutic Approaches. Cancers (Basel) 2025; 17:257. [PMID: 39858038 PMCID: PMC11764024 DOI: 10.3390/cancers17020257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2024] [Revised: 01/09/2025] [Accepted: 01/11/2025] [Indexed: 01/27/2025] Open
Abstract
BACKGROUND/OBJECTIVES As cells divide, telomeres shorten through a phenomenon known as telomere attrition, which leads to unavoidable senescence of cells. Unprotected DNA exponentially increases the odds of mutations, which can evolve into premature aging disorders and tumorigenesis. There has been growing academic and clinical interest in exploring this duality and developing optimal therapeutic strategies to combat telomere attrition in aging and cellular immortality in cancer. The purpose of this review is to provide an updated overview of telomere biology and therapeutic tactics to address aging and cancer. METHODS We used the Rayyan platform to review the PubMed database and examined the ClinicalTrial.gov registry to gain insight into clinical trials and their results. RESULTS Cancer cells activate telomerase or utilize alternative lengthening of telomeres to escape telomere shortening, leading to near immortality. Contrarily, normal cells experience telomeric erosion, contributing to premature aging disorders, such as Werner syndrome and Hutchinson-Gilford Progeria, and (2) aging-related diseases, such as neurodegenerative and cardiovascular diseases. CONCLUSIONS The literature presents several promising therapeutic approaches to potentially balance telomere maintenance in aging and shortening in cancer. This review highlights gaps in knowledge and points to the potential of these optimal interventions in preclinical and clinical studies to inform future research in cancer and aging.
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Affiliation(s)
| | | | | | | | | | | | - Sandy Westerheide
- Department of Molecular Biosciences, University of South Florida, 4202 East Fowler Avenue, ISA2015, Tampa, FL 33620, USA; (M.I.); (M.X.B.); (M.J.); (R.C.); (R.G.-G.); (E.C.)
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9
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Seth P, Xing E, Hendrickson AD, Li K, Monsen R, Chaires J, Neidle S, Yatsunyk LA. Interaction of N-methylmesoporphyrin IX with a hybrid left-/right-handed G-quadruplex motif from the promoter of the SLC2A1 gene. Nucleic Acids Res 2025; 53:gkae1208. [PMID: 39704129 PMCID: PMC11754737 DOI: 10.1093/nar/gkae1208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 11/18/2024] [Accepted: 11/21/2024] [Indexed: 12/21/2024] Open
Abstract
Left-handed G-quadruplexes (LHG4s) belong to a class of recently discovered noncanonical DNA structures under the larger umbrella of G-quadruplex DNAs (G4s). The biological relevance of these structures and their ability to be targeted with classical G4 ligands is underexplored. Here, we explore whether the putative LHG4 DNA sequence from the SLC2A1 oncogene promoter maintains its left-handed characteristics upon addition of nucleotides in the 5'- and 3'-direction from its genomic context. We also investigate whether this sequence interacts with a well-established G4 binder, N-methylmesoporphyrin IX (NMM). We employed biophysical and X-ray structural studies to address these questions. Our results indicate that the sequence d[G(TGG)3TGA(TGG)4] (termed here as SLC) adopts a two-subunit, four-tetrad hybrid left-/right-handed G4 (LH/RHG4) topology. Addition of 5'-G or 5'-GG abolishes the left-handed fold in one subunit, while the addition of 3'-C or 3'-CA maintains the original fold. X-ray crystal structure analyses show that SLC maintains the same hybrid LH/RHG4 fold in the solid state and that NMM stacks onto the right-handed subunit of SLC. NMM binds to SLC with a 1:1 stoichiometry and a moderate-to-tight binding constant of 15 μM-1. This work deepens our understanding of LHG4 structures and their binding with traditional G4 ligands.
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Affiliation(s)
- Paul Seth
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081USA
| | - Eric Xing
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081USA
| | - Andrew D Hendrickson
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081USA
| | - Kevin Li
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081USA
| | - Robert Monsen
- UofL Health, Brown Cancer Center, University of Louisville, 529 S. Jackson Street Louisville, KY, 40202USA
| | - Jonathan B Chaires
- UofL Health, Brown Cancer Center, University of Louisville, 529 S. Jackson Street Louisville, KY, 40202USA
| | - Stephen Neidle
- School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA, 19081USA
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10
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Cordero J, Swaminathan G, Rogel-Ayala DG, Rubio K, Elsherbiny A, Mahmood S, Szymanski W, Graumann J, Braun T, Günther S, Dobreva G, Barreto G. Nuclear microRNA 9 mediates G-quadruplex formation and 3D genome organization during TGF-β-induced transcription. Nat Commun 2024; 15:10711. [PMID: 39706840 DOI: 10.1038/s41467-024-54740-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 11/20/2024] [Indexed: 12/23/2024] Open
Abstract
The dynamics of three-dimensional (3D) genome organization are essential to transcriptional regulation. While enhancers regulate spatiotemporal gene expression, chromatin looping is a means for enhancer-promoter interactions yielding cell-type-specific gene expression. Further, non-canonical DNA secondary structures, such as G-quadruplexes (G4s), are related to increased gene expression. However, the role of G4s in promoter-distal regulatory elements, such as super-enhancers (SE), and in chromatin looping has remained elusive. Here we show that mature microRNA 9 (miR-9) is enriched at promoters and SE of genes that are inducible by transforming growth factor beta 1 (TGFB1) signaling. Moreover, we find that miR-9 is required for formation of G4s, promoter-super-enhancer looping and broad domains of the euchromatin histone mark H3K4me3 at TGFB1-responsive genes. Our study places miR-9 in the same functional context with G4s and promoter-enhancer interactions during 3D genome organization and transcriptional activation induced by TGFB1 signaling, a critical signaling pathway in cancer and fibrosis.
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Affiliation(s)
- Julio Cordero
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany.
- German Centre for Cardiovascular Research (DZHK), 68167, Mannheim, Germany.
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.
| | | | - Diana G Rogel-Ayala
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000, Nancy, France
| | - Karla Rubio
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000, Nancy, France
- Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, 02129, USA
- International Laboratory EPIGEN, Consejo de Ciencia y Tecnología del Estado de Puebla (CONCYTEP), Instituto de Ciencias, EcoCampus, Benemérita Universidad Autónoma de Puebla, 72570, Puebla, Mexico
| | - Adel Elsherbiny
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), 68167, Mannheim, Germany
| | - Samina Mahmood
- ECCPS Bioinformatics and Deep Sequencing Platform, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Witold Szymanski
- Department of Medicine, Institute of Translational Proteomics & Core Facility Translational Proteomics, Philipps-University Marburg, 35043, Marburg, Germany
| | - Johannes Graumann
- Department of Medicine, Institute of Translational Proteomics & Core Facility Translational Proteomics, Philipps-University Marburg, 35043, Marburg, Germany
| | - Thomas Braun
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Stefan Günther
- ECCPS Bioinformatics and Deep Sequencing Platform, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
- Department of Cardiac Development, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany
| | - Gergana Dobreva
- Department of Cardiovascular Genomics and Epigenomics, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, 68167, Mannheim, Germany
- German Centre for Cardiovascular Research (DZHK), 68167, Mannheim, Germany
- Helmholtz-Institute for Translational AngioCardioScience (HI-TAC) of the Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) at Heidelberg University, 69117, Heidelberg, Germany
| | - Guillermo Barreto
- Lung Cancer Epigenetics, Max-Planck-Institute for Heart and Lung Research, 61231, Bad Nauheim, Germany.
- Université de Lorraine, CNRS, Laboratoire IMoPA, UMR 7365, F-54000, Nancy, France.
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11
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Karna D, Liang L, Sharma G, Mandal S, Asamitsu S, Kawamoto Y, Hashiya K, Bando T, Sugiyama H, Mao H. Modulation of dynamic DNA G-quadruplex structures in the hTERT promoter region by ligands. Nucleic Acids Res 2024; 52:10775-10787. [PMID: 39217470 PMCID: PMC11472034 DOI: 10.1093/nar/gkae754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/09/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Small molecules can inhibit cellular processes such as replication and transcription by binding to the promoter regions that are prone to form G-quadruplexes. However, since G-quadruplexes exist throughout the human genome, the G-quadruplex binders suffer from specificity issues. To tackle this problem, a G-quadruplex binder (Pyridostatin, or PDS) is conjugated with a ligand (Polyamide, or PA) that can specifically recognize DNA sequences flanking the G-quadruplex forming region. The binding mechanism of this hybrid ligand to the hTERT promoter region (hTERT 5-12) is then elucidated using optical tweezers. During mechanical unfolding processes, different intermediate structures of hTERT 5-12 in presence of PDS, PA, or PA-PDS conjugate are observed. These intermediate structures are consistent with two folding patterns of G-quadruplexes in the hTERT 5-12 fragment. While the duplex DNA binder PA facilitates the folding of a hairpin-G-quadruplex structure, the PDS assists the formation of two tandem G-quadruplexes. Both replication stop assay in vitro and dual luciferase assay in vivo established the effectiveness of the PA-PDS conjugate for hTERT 5-12 targeting. We expect such a ligand dependent folding dynamics will provide guidelines to the development of drugs that not only target hTERT expressions, but also other oncogenes via interactions with specific G-quadruplex structures formed in their promotor regions.
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Affiliation(s)
- Deepak Karna
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Lin Liang
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Grinsun Sharma
- School of Biomedical Science, Kent State University, Kent, OH 44242, USA
| | - Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Sefan Asamitsu
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell–Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
- School of Biomedical Science, Kent State University, Kent, OH 44242, USA
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12
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Douglas ME. How to write an ending: Telomere replication as a multistep process. DNA Repair (Amst) 2024; 144:103774. [PMID: 39426311 DOI: 10.1016/j.dnarep.2024.103774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 10/01/2024] [Accepted: 10/04/2024] [Indexed: 10/21/2024]
Abstract
Telomeres are protective nucleoprotein caps found at the natural ends of eukaryotic chromosomes and are crucial for the preservation of stable chromosomal structure. In cycling cells, telomeres are maintained by a multi-step process called telomere replication, which involves the eukaryotic replisome navigating a complex repetitive template tightly bound by specific proteins, before terminating at the chromosome end prior to a 5' resection step that generates a protective 3' overhang. In this review, we examine mechanistic aspects of the telomere replication process and consider how individual parts of this multistep event are integrated and coordinated with one-another.
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Affiliation(s)
- Max E Douglas
- Telomere Biology Laboratory, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK.
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13
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Banjan B, Koshy AJ, Kalath H, John L, Soman S, Raju R, Revikumar A. Potential protein kinase inhibitors that target G-quadruplex DNA structures in the human telomeric regions. Mol Divers 2024; 28:3377-3391. [PMID: 38509417 DOI: 10.1007/s11030-023-10768-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 11/10/2023] [Indexed: 03/22/2024]
Abstract
Telomeric regions contain Guanine-rich sequences arranged in a planar manner and connected by Hoogsteen hydrogen bonds that can fold into G-quadruplex (G4) DNA structures, and can be stabilized by monovalent metal cations. The presence of G4 DNA holds significance in cancer-related processes, especially due to their regulatory potential at transcriptional and translational levels of oncogene and tumor suppressor genes. The objective of this current research is to explore the evolving realm of FDA-approved protein kinase inhibitors, with a specific emphasis on their capacity to stabilize the G4 DNA structures formed at the human telomeric regions. This involves investigating the possibility of repurposing FDA-approved protein kinase inhibitors as a novel approach for targeting multiple cancer types. In this context, we have selected 16 telomeric G4 DNA structures as targets and 71 FDA-approved small-molecule protein kinase inhibitors as ligands. To investigate their binding affinities, molecular docking of human telomeric G4 DNA with nuclear protein kinase inhibitors and their corresponding co-crystalized ligands were performed. We found that Ponatinib and Lapatinib interact with all the selected G4 targets, the binding free energy calculations, and molecular dynamic simulations confirm their binding efficacy and stability. Thus, it is hypothesized that Ponatinib and Lapatinib may stabilize human telomeric G4 DNA in addition to their ability to inhibit BCR-ABL and the other members of the EGFR family. As a result, we also hypothesize that the stabilization of G4 DNA might represent an additional underlying mechanism contributing to their efficacy in exerting anti-cancer effects.
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Affiliation(s)
- Bhavya Banjan
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Abel John Koshy
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Haritha Kalath
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Sowmya Soman
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India
| | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
| | - Amjesh Revikumar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed to Be University), Mangalore, Karnataka, 575018, India.
- Kerala Genome Data Centre, Kerala Development and Innovation Strategic Council, Vazhuthacaud, Thiruvananthapuram, Kerala, 695014, India.
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14
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Todkari IA, Chaudhary P, Kulkarni MJ, Ganesh KN. Supramolecular polyplexes from Janus peptide nucleic acids (bm-PNA-G5): self-assembled bm-PNA G-quadruplex and its tetraduplex with DNA. Org Biomol Chem 2024; 22:6810-6821. [PMID: 39113548 DOI: 10.1039/d4ob00968a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Nucleic acids (DNA and RNA) can form diverse secondary structures ranging from hairpins to duplex, triplex, G4-tetraplex and C4-i-motifs. Many of the DNA analogues designed as antisense oligonucleotides (ASO) are also adept at embracing such folded structures, although to different extents with altered stabilities. One such analogue, peptide nucleic acid (PNA), which is uncharged and achiral, forms hybrids with complementary DNA/RNA with greater stability and specificity than DNA:DNA/RNA hybrids. Like DNAs, these single-stranded PNAs can form PNA:DNA/RNA duplexes, PNA:DNA:PNA triplexes, PNA-G4 tetraplexes and PNA-C4-i-motifs. We have recently designed Janus-like bimodal PNAs endowed with two different nucleobase sequences on either side of a single aminoethylglycyl (aeg) PNA backbone and shown that these can simultaneously bind to two complementary DNA sequences from both faces of PNA. This leads to the formation of supramolecular polyplexes such as double duplexes, triple duplexes and triplexes of double duplexes with appropriate complementary DNA/RNA. Herein, we demonstrate that Janus/bimodal PNA with a poly G-sequence on the triazole side of the PNA backbone and mixed bases on the t-amide side, templates the initial formation of a (PNA-G5)4 tetraplex (triazole side), followed by the formation of a PNA:DNA duplex (t-amide side). Such a polyplex shows synergistic overall stabilisation compared to the isolated duplexes/quadruplex. The assembly of polyplexes with a shared backbone for duplexes and tetraplexes is programmable and may have potential applications in the self-assembly of nucleic acid nano- and origami structures. It is also shown that Janus PNAs enter the cells better than the standard aeg-PNA oligomers, and hence have implications for in vivo applications as well.
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Affiliation(s)
- Iranna Annappa Todkari
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
| | - Preeti Chaudhary
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.
| | - Mahesh J Kulkarni
- Division of Biochemistry, CSIR-National Chemical Laboratory, Pashan Road, Pune 411008, India
| | - Krishna N Ganesh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune 411008, India.
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Karkambadi Road, Tirupati 517507, India
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bengaluru 560064, India
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15
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Cueny RR, Voter AF, McKenzie AM, Morgenstern M, Myers KS, Place MM, Peters JM, Coon JJ, Keck JL. Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.12.607615. [PMID: 39185182 PMCID: PMC11343134 DOI: 10.1101/2024.08.12.607615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, reducing expression of certain translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation are less abundant in G4-stabilizing conditions. Our integrated systems approach allowed us to propose a model for how RNA G4s can present barriers to E. coli growth and that reducing the rate of translation can compensate for G4-related stress.
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Affiliation(s)
- Rachel R Cueny
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Andrew F Voter
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Aidan M McKenzie
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marcel Morgenstern
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, Madison Wisconsin, USA
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael M Place
- Great Lakes Bioenergy Research Center and the Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jason M Peters
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joshua J Coon
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- National Center for Quantitative Biology of Complex Systems, Madison Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | - James L Keck
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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16
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Joo SY, Sung K, Lee H. Balancing act: BRCA2's elaborate management of telomere replication through control of G-quadruplex dynamicity. Bioessays 2024; 46:e2300229. [PMID: 38922965 DOI: 10.1002/bies.202300229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024]
Abstract
In billion years of evolution, eukaryotes preserved the chromosome ends with arrays of guanine repeats surrounded by thymines and adenines, which can form stacks of four-stranded planar structure known as G-quadruplex (G4). The rationale behind the evolutionary conservation of the G4 structure at the telomere remained elusive. Our recent study has shed light on this matter by revealing that telomere G4 undergoes oscillation between at least two distinct folded conformations. Additionally, tumor suppressor BRCA2 exhibits a unique mode of interaction with telomere G4. To elaborate, BRCA2 directly interacts with G-triplex (G3)-derived intermediates that form during the interconversion of the two different G4 states. In doing so, BRCA2 remodels the G4, facilitating the restart of stalled replication forks. In this review, we succinctly summarize the findings regarding the dynamicity of telomeric G4, emphasize its importance in maintaining telomere replication homeostasis, and the physiological consequences of losing G4 dynamicity at the telomere.
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Affiliation(s)
- So Young Joo
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
| | - Keewon Sung
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul, South Korea
| | - Hyunsook Lee
- Department of Biological Sciences & Institute of Molecular Biology and Genetics (IMBG), Seoul National University, Seoul, South Korea
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17
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024; 26:1025-1036. [PMID: 38914786 DOI: 10.1038/s41556-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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18
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Zhuk AS, Stepchenkova EI, Zotova IV, Belopolskaya OB, Pavlov YI, Kostroma II, Gritsaev SV, Aksenova AY. G-Quadruplex Forming DNA Sequence Context Is Enriched around Points of Somatic Mutations in a Subset of Multiple Myeloma Patients. Int J Mol Sci 2024; 25:5269. [PMID: 38791307 PMCID: PMC11121618 DOI: 10.3390/ijms25105269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Multiple myeloma (MM) is the second most common hematological malignancy, which remains incurable despite recent advances in treatment strategies. Like other forms of cancer, MM is characterized by genomic instability, caused by defects in DNA repair. Along with mutations in DNA repair genes and genotoxic drugs used to treat MM, non-canonical secondary DNA structures (four-stranded G-quadruplex structures) can affect accumulation of somatic mutations and chromosomal abnormalities in the tumor cells of MM patients. Here, we tested the hypothesis that G-quadruplex structures may influence the distribution of somatic mutations in the tumor cells of MM patients. We sequenced exomes of normal and tumor cells of 11 MM patients and analyzed the data for the presence of G4 context around points of somatic mutations. To identify molecular mechanisms that could affect mutational profile of tumors, we also analyzed mutational signatures in tumor cells as well as germline mutations for the presence of specific SNPs in DNA repair genes or in genes regulating G-quadruplex unwinding. In several patients, we found that sites of somatic mutations are frequently located in regions with G4 context. This pattern correlated with specific germline variants found in these patients. We discuss the possible implications of these variants for mutation accumulation and specificity in MM and propose that the extent of G4 context enrichment around somatic mutation sites may be a novel metric characterizing mutational processes in tumors.
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Affiliation(s)
- Anna S. Zhuk
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Institute of Applied Computer Science, ITMO University, 197101 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Irina V. Zotova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia;
| | - Olesya B. Belopolskaya
- Resource Center “Bio-Bank Center”, Research Park of St. Petersburg State University, 198504 St. Petersburg, Russia;
- The Laboratory of Genogeography, Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Microbiology and Pathology, Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ivan I. Kostroma
- City Hospital No. 15, 198205 St. Petersburg, Russia; (I.I.K.); (S.V.G.)
| | | | - Anna Y. Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.S.Z.); (I.V.Z.)
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19
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Marshall PR, Davies J, Zhao Q, Liau WS, Lee Y, Basic D, Periyakaruppiah A, Zajaczkowski EL, Leighton LJ, Madugalle SU, Musgrove M, Kielar M, Brueckner AM, Gong H, Ren H, Walsh A, Kaczmarczyk L, Jackson WS, Chen A, Spitale RC, Bredy TW. DNA G-Quadruplex Is a Transcriptional Control Device That Regulates Memory. J Neurosci 2024; 44:e0093232024. [PMID: 38418220 PMCID: PMC11007313 DOI: 10.1523/jneurosci.0093-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/14/2024] [Accepted: 02/20/2024] [Indexed: 03/01/2024] Open
Abstract
The conformational state of DNA fine-tunes the transcriptional rate and abundance of RNA. Here, we report that G-quadruplex DNA (G4-DNA) accumulates in neurons, in an experience-dependent manner, and that this is required for the transient silencing and activation of genes that are critically involved in learning and memory in male C57/BL6 mice. In addition, site-specific resolution of G4-DNA by dCas9-mediated deposition of the helicase DHX36 impairs fear extinction memory. Dynamic DNA structure states therefore represent a key molecular mechanism underlying memory consolidation.One-Sentence Summary: G4-DNA is a molecular switch that enables the temporal regulation of the gene expression underlying the formation of fear extinction memory.
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Affiliation(s)
- Paul R Marshall
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
- Genome Sciences and Cancer Division & Eccles Institute of Neuroscience, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Joshua Davies
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Qiongyi Zhao
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Wei-Siang Liau
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Yujin Lee
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Dean Basic
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Ambika Periyakaruppiah
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Esmi L Zajaczkowski
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Laura J Leighton
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Sachithrani U Madugalle
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Mason Musgrove
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Marcin Kielar
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Arie Maeve Brueckner
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Hao Gong
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alexander Walsh
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
| | - Lech Kaczmarczyk
- Department of Biomedical and Clinical Sciences (BKV), Division of Neurobiology (NEURO), Linköping University, Linköping 581 83, Sweden
| | - Walker S Jackson
- Department of Biomedical and Clinical Sciences (BKV), Division of Neurobiology (NEURO), Linköping University, Linköping 581 83, Sweden
| | - Alon Chen
- Neurobiology of Stress Laboratory, Department Brain Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, California 92697
| | - Timothy W Bredy
- Cognitive Neuroepigenetics Laboratory, The Queensland Brain Institute, University of Queensland, Brisbane, QLD 4072, Australia
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20
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Rivosecchi J, Jurikova K, Cusanelli E. Telomere-specific regulation of TERRA and its impact on telomere stability. Semin Cell Dev Biol 2024; 157:3-23. [PMID: 38088000 DOI: 10.1016/j.semcdb.2023.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/02/2023] [Indexed: 01/08/2024]
Abstract
TERRA is a class of telomeric repeat-containing RNAs that are expressed from telomeres in multiple organisms. TERRA transcripts play key roles in telomere maintenance and their physiological levels are essential to maintain the integrity of telomeric DNA. Indeed, deregulated TERRA expression or its altered localization can impact telomere stability by multiple mechanisms including fueling transcription-replication conflicts, promoting resection of chromosome ends, altering the telomeric chromatin, and supporting homologous recombination. Therefore, a fine-tuned control of TERRA is important to maintain the integrity of the genome. Several studies have reported that different cell lines express substantially different levels of TERRA. Most importantly, TERRA levels markedly vary among telomeres of a given cell type, indicating the existence of telomere-specific regulatory mechanisms which may help coordinate TERRA functions. TERRA molecules contain distinct subtelomeric sequences, depending on their telomere of origin, which may instruct specific post-transcriptional modifications or mediate distinct functions. In addition, all TERRA transcripts share a repetitive G-rich sequence at their 3' end which can form DNA:RNA hybrids and fold into G-quadruplex structures. Both structures are involved in TERRA functions and can critically affect telomere stability. In this review, we examine the mechanisms controlling TERRA levels and the impact of their telomere-specific regulation on telomere stability. We compare evidence obtained in different model organisms, discussing recent advances as well as controversies in the field. Furthermore, we discuss the importance of DNA:RNA hybrids and G-quadruplex structures in the context of TERRA biology and telomere maintenance.
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Affiliation(s)
- Julieta Rivosecchi
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Katarina Jurikova
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy; Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Mlynská dolina, 84215 Bratislava, Slovakia
| | - Emilio Cusanelli
- Laboratory of Cell Biology and Molecular Genetics, Department CIBIO, University of Trento, via Sommarive 9, 38123 Trento, Italy.
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21
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Bisoi A, Sarkar S, Singh PC. Loop nucleobases-dependent folding of G-quadruplex in normal and cancer cell-mimicking KCl microenvironments. Int J Biol Macromol 2024; 265:131050. [PMID: 38522708 DOI: 10.1016/j.ijbiomac.2024.131050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/05/2024] [Accepted: 03/11/2024] [Indexed: 03/26/2024]
Abstract
In this study, the folding of G-quadruplex (G4) from the telomeric DNA sequences having loop nucleobases of different chemical natures, numbers, and arrangements in 10 mM and 100 mM KCl salt conditions mimicking the cancerous and normal KCl salt microenvironments have been investigated. The data suggest that the structure and stability of the G4 are highly dependent on the KCl salt concentration. In general, the conformational flexibility of the folded G4 is higher in KCl salt relevant to cancer than in the normal case for any loop arrangements with the same number of nucleobases. The stability of the G4 decreases with the increase in the number of loop nucleobases for both salt conditions. However, the decrease in the stability of G4 having adenine in the loop region is significantly higher than the case of thymine, particularly more prominent in the KCl salt relevant to the cancer. The topology of the folded G4 and its stability also depend delicately on the permutation of the nucleobases in the loop and the salt concentrations for a particular sequence. The findings indicate that the structure and stability of G4 are noticeably different in KCl salt relevant to physiological and cancer conditions.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India.
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22
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Gajarsky M, Stadlbauer P, Sponer J, Cucchiarini A, Dobrovolna M, Brazda V, Mergny JL, Trantirek L, Lenarcic Zivkovic M. DNA Quadruplex Structure with a Unique Cation Dependency. Angew Chem Int Ed Engl 2024; 63:e202313226. [PMID: 38143239 DOI: 10.1002/anie.202313226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/11/2023] [Accepted: 12/22/2023] [Indexed: 12/26/2023]
Abstract
DNA quadruplex structures provide an additional layer of regulatory control in genome maintenance and gene expression and are widely used in nanotechnology. We report the discovery of an unprecedented tetrastranded structure formed from a native G-rich DNA sequence originating from the telomeric region of Caenorhabditis elegans. The structure is defined by multiple properties that distinguish it from all other known DNA quadruplexes. Most notably, the formation of a stable so-called KNa-quadruplex (KNaQ) requires concurrent coordination of K+ and Na+ ions at two distinct binding sites. This structure provides novel insight into G-rich DNA folding under ionic conditions relevant to eukaryotic cell physiology and the structural evolution of telomeric DNA. It highlights the differences between the structural organization of human and nematode telomeric DNA, which should be considered when using C. elegans as a model in telomere biology, particularly in drug screening applications. Additionally, the absence/presence of KNaQ motifs in the host/parasite introduces an intriguing possibility of exploiting the KNaQ fold as a plausible antiparasitic drug target. The structure's unique shape and ion dependency and the possibility of controlling its folding by using low-molecular-weight ligands can be used for the design or discovery of novel recognition DNA elements and sensors.
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Affiliation(s)
- Martin Gajarsky
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Current address: Center for Molecular Medicine Cologne, University of Cologne, 50931, Cologne, Germany
| | - Petr Stadlbauer
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Jiri Sponer
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Anne Cucchiarini
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Michaela Dobrovolna
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkynova 464, 61200, Brno, Czech Republic
| | - Vaclav Brazda
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Faculty of Chemistry, Brno University of Technology, Purkynova 464, 61200, Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
- Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Lukas Trantirek
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
| | - Martina Lenarcic Zivkovic
- Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 753/5, 62500, Brno, Czech Republic
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000, Ljubljana, Slovenia
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23
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Khan S, Singh A, Nain N, Kukreti S. Alkali cation-mediated topology displayed by an exonic G-rich sequence of TRPA1 gene. J Biomol Struct Dyn 2023; 41:9997-10008. [PMID: 36458452 DOI: 10.1080/07391102.2022.2150686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
G-rich sequences are intrinsic parts of the genome, widespread in promoters, telomeres, or other regulatory regions. The in vivo existence and biological significance have established the functional aspect of G-quadruplex structures and thus have developed immense interest in exploring their therapeutic aspects. Herein, using biophysical methods, we examined the structural status and comprehensive cation-dependence of a 17-bp G-rich genomic sequence (SKGT17) located in the coding region of the human TRPA1 gene, known to be associated with various neurovascular, cardiovascular, and respiratory conditions. TRPA1 is primarily seen as a therapeutic target for the development of novel analgesics. Bioinformatics analysis has suggested that 17-bp quadruplex motif is a binding site for transcription factor 'Sp1'. The formation and recognition of SKGT17 G-quadruplex might impact its regulatory functioning. Biophysical studies confirmed that the presence of alkali metal ions facilitated the formation of G-quadruplex in parallel topology. Native gel further substantiated the formation of a biomolecular species. Circular dichroism (CD), UV-thermal melting (Tm), and CD melting confirmed the formation of parallel G-quadruplex with metal ion-dependent stability. The stability of the G-quadruplex formed is found to be significantly high in the presence of K+ ions than that of other ions. Intriguingly, we have also established that this segment of the TRAP1 gene favors G-quadruplex formation over its participation in the corresponding duplex formation under K+ ions conditions. This study attempts to explain the rationale for the stabilization of G-quadruplex in the presence of alkali metal ions and may add to a better understanding and insights into DNA-metal ions interactions.
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi, Delhi, India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi, Delhi, India
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24
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Yan MP, Wee CE, Yen KP, Stevens A, Wai LK. G-quadruplex ligands as therapeutic agents against cancer, neurological disorders and viral infections. Future Med Chem 2023; 15:1987-2009. [PMID: 37933551 DOI: 10.4155/fmc-2023-0202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023] Open
Abstract
G-quadruplexes (G4s) within the human genome have undergone extensive molecular investigation, with a strong focus on telomeres, gene promoters and repetitive regulatory sequences. G4s play central roles in regulating essential biological processes, including telomere maintenance, replication, transcription and translation. Targeting these molecular processes with G4-binding ligands holds substantial therapeutic potential in anticancer treatments and has also shown promise in treating neurological, skeletal and muscular disorders. The presence of G4s in bacterial and viral genomes also suggests that G4-binding ligands could be a critical tool in fighting infections. This review provides an overview of the progress and applications of G4-binding ligands, their proposed mechanisms of action, challenges faced and prospects for their utilization in anticancer treatments, neurological disorders and antiviral activities.
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Affiliation(s)
- Mock Phooi Yan
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Chua Eng Wee
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
| | - Khor Poh Yen
- Faculty Pharmacy & Health Sciences, Universiti Kuala Lumpur, Royal College of Medicine Perak, 3, Jalan Greentown, Ipoh, Perak, 30450, Malaysia
| | - Aaron Stevens
- Department of Pathology & Molecular Medicine, University of Otago, Wellington, 6021, New Zealand
| | - Lam Kok Wai
- Centre for Drug & Herbal Development, Faculty of Pharmacy, Universiti Kebangsaan Malaysia, Jalan Raja Muda Abdul Aziz, Kuala Lumpur, 50300, Malaysia
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25
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Bhowmick R, Hickson ID, Liu Y. Completing genome replication outside of S phase. Mol Cell 2023; 83:3596-3607. [PMID: 37716351 DOI: 10.1016/j.molcel.2023.08.023] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 09/18/2023]
Abstract
Mitotic DNA synthesis (MiDAS) is an unusual form of DNA replication that occurs during mitosis. Initially, MiDAS was characterized as a process associated with intrinsically unstable loci known as common fragile sites that occurs after cells experience DNA replication stress (RS). However, it is now believed to be a more widespread "salvage" mechanism that is called upon to complete the duplication of any under-replicated genomic region. Emerging data suggest that MiDAS is a DNA repair process potentially involving two or more pathways working in parallel or sequentially. In this review, we introduce the causes of RS, regions of the human genome known to be especially vulnerable to RS, and the strategies used to complete DNA replication outside of S phase. Additionally, because MiDAS is a prominent feature of aneuploid cancer cells, we will discuss how targeting MiDAS might potentially lead to improvements in cancer therapy.
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Affiliation(s)
- Rahul Bhowmick
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3B, 2200 Copenhagen N, Denmark; Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
| | - Ying Liu
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3B, 2200 Copenhagen N, Denmark.
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26
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Stitch M, Avagliano D, Graczyk D, Clark IP, González L, Towrie M, Quinn SJ. Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe. J Am Chem Soc 2023; 145:21344-21360. [PMID: 37736878 PMCID: PMC10557146 DOI: 10.1021/jacs.3c06099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 09/23/2023]
Abstract
The nitrile containing Ru(II)polypyridyl complex [Ru(phen)2(11,12-dCN-dppz)]2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV-visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG3(TTAG3)3]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm-1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D2O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.
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Affiliation(s)
- Mark Stitch
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Davide Avagliano
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Department
of Chemistry, Chemical Physics Theory Group, University of Toronto, 80 St. George St., Toronto, Ontario M5S 3H6, Canada
| | - Daniel Graczyk
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ian P. Clark
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Leticia González
- Institute
of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
- Vienna
Research Platform on Accelerating Photoreaction Discovery, University of Vienna, Währingerstr. 19, 1090 Vienna, Austria
| | - Michael Towrie
- Central
Laser Facility, STFC Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0QX, U.K.
| | - Susan J Quinn
- School
of Chemistry, University College Dublin, Dublin, D04 V1W8, Ireland
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27
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Han ZQ, Wen LN. Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol 2023; 15:1149-1173. [PMID: 37546556 PMCID: PMC10401460 DOI: 10.4251/wjgo.v15.i7.1149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/11/2023] [Accepted: 05/08/2023] [Indexed: 07/12/2023] Open
Abstract
Genomic instability and inflammation are considered to be two enabling characteristics that support cancer development and progression. G-quadruplex structure is a key element that contributes to genomic instability and inflammation. G-quadruplexes were once regarded as simply an obstacle that can block the transcription of oncogenes. A ligand targeting G-quadruplexes was found to have anticancer activity, making G-quadruplexes potential anticancer targets. However, further investigation has revealed that G-quadruplexes are widely distributed throughout the human genome and have many functions, such as regulating DNA replication, DNA repair, transcription, translation, epigenetics, and inflammatory response. G-quadruplexes play double regulatory roles in transcription and translation. In this review, we focus on G-quadruplexes as novel targets for the treatment of gastrointestinal cancers. We summarize the application basis of G-quadruplexes in gastrointestinal cancers, including their distribution sites, structural characteristics, and physiological functions. We describe the current status of applications for the treatment of esophageal cancer, pancreatic cancer, hepatocellular carcinoma, gastric cancer, colorectal cancer, and gastrointestinal stromal tumors, as well as the associated challenges. Finally, we review the prospective clinical applications of G-quadruplex targets, providing references for targeted treatment strategies in gastrointestinal cancers.
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Affiliation(s)
- Zong-Qiang Han
- Department of Laboratory Medicine, Beijing Xiaotangshan Hospital, Beijing 102211, China
| | - Li-Na Wen
- Department of Clinical Nutrition, Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, China
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28
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Gao Z, Yuan J, He X, Wang H, Wang Y. Phase Separation Modulates the Formation and Stabilities of DNA Guanine Quadruplex. JACS AU 2023; 3:1650-1657. [PMID: 37388701 PMCID: PMC10301798 DOI: 10.1021/jacsau.3c00106] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 07/01/2023]
Abstract
In the presence of monovalent alkali metal ions, G-rich DNA sequences containing four runs of contiguous guanines can fold into G-quadruplex (G4) structures. Recent studies showed that these structures are located in critical regions of the human genome and assume important functions in many essential DNA metabolic processes, including replication, transcription, and repair. However, not all potential G4-forming sequences are actually folded into G4 structures in cells, where G4 structures are known to be dynamic and modulated by G4-binding proteins as well as helicases. It remains unclear whether there are other factors influencing the formation and stability of G4 structures in cells. Herein, we showed that DNA G4s can undergo phase separation in vitro. In addition, immunofluorescence microscopy and ChIP-seq experiments with the use of BG4, a G4 structure-specific antibody, revealed that disruption of phase separation could result in global destabilization of G4 structures in cells. Together, our work revealed phase separation as a new determinant in modulating the formation and stability of G4 structures in human cells.
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Affiliation(s)
- Zi Gao
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Jun Yuan
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California, 92521-0403, United States
| | - Xiaomei He
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Handing Wang
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
| | - Yinsheng Wang
- Department
of Chemistry, University of California Riverside, Riverside, California, 92521-0403, United
States
- Environmental
Toxicology Graduate Program, University
of California Riverside, Riverside, California, 92521-0403, United States
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29
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Pandya N, Singh M, Rani R, Kumar V, Kumar A. G-quadruplex-mediated specific recognition, stabilization and transcriptional repression of bcl-2 by small molecule. Arch Biochem Biophys 2023; 734:109483. [PMID: 36513132 DOI: 10.1016/j.abb.2022.109483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/22/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022]
Abstract
The presence of the G-quadruplex (G4) structure in the promoter region of the human bcl-2 oncogenes makes it a promising target for developing anti-cancer therapeutics. Bcl-2 inhibits apoptosis, and its frequent overexpression in cancer cells contributes to tumor initiation, progression, and resistance to therapy. Small molecules that can specifically bind to bcl-2 G4 with high affinity and selectivity are remaining elusive. Here, we report that small molecule 1,3-bis-) furane-2yl-methylidene-amino) guanidine (BiGh) binds to bcl-2 G4 DNA structure with very high affinity and selectivity over other genomic G4 DNA structures and duplex DNA. BiGh stabilizes folded parallel conformation of bcl-2 G4 via non-covalent and electrostatic interactions and increases the thermal stabilization up to 15 °C. The ligand significantly suppresses the bcl-2 transcription in HeLa cells by a G4-dependent mechanism and induces cell cycle arrest which promotes apoptosis. The in silico ADME profiling confirms the potential 'drug-likeness' of BiGh. Our results showed that BiGh stabilizes the bcl-2 G-quadruplex motif, downregulates the bcl-2 gene transcription as well as translation process in cervical cancer cells, and exhibits potential anti-cancer activity. This work provides a potential platform for the development of lead compound(s) as G4 stabilizers with drug-like properties of BiGh for cancer therapeutics.
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Affiliation(s)
- Nirali Pandya
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India
| | - Mamta Singh
- Amity Institute of Biotechnology, Amity University Noida, Uttar Pradesh, 201303, India
| | - Reshma Rani
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Noida, Uttar Pradesh, 201303, India
| | - Vinit Kumar
- Amity Institute of Biotechnology, Amity University Noida, Uttar Pradesh, 201303, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore, Madhya Pradesh, 453552, India.
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30
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Chung WC, Ravichandran S, Park D, Lee GM, Kim YE, Choi Y, Song MJ, Kim KK, Ahn JH. G-quadruplexes formed by Varicella-Zoster virus reiteration sequences suppress expression of glycoprotein C and regulate viral cell-to-cell spread. PLoS Pathog 2023; 19:e1011095. [PMID: 36630443 PMCID: PMC9873165 DOI: 10.1371/journal.ppat.1011095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 01/24/2023] [Accepted: 01/02/2023] [Indexed: 01/12/2023] Open
Abstract
G-quadruplex (G4) formed by repetitive guanosine-rich sequences plays important roles in diverse cellular processes; however, its roles in viral infection are not fully understood. In this study, we investigated the genome-wide distribution of G4-forming sequences (G4 motifs) in Varicella-Zoster virus (VZV) and found that G4 motifs are enriched in the internal repeat short and the terminal repeat short regions flanking the unique short region and also in some reiteration (R) sequence regions. A high density of G4 motifs in the R2 region was found on the template strand of ORF14, which encodes glycoprotein C (gC), a virulent factor for viral growth in skin. Analyses such as circular dichroism spectroscopy, thermal difference spectra, and native polyacrylamide gel electrophoresis with oligodeoxynucleotides demonstrated that several G4 motifs in ORF14 form stable G4 structures. In transfection assays, gC expression from the G4-disrupted ORF14 gene was increased at the transcriptional level and became more resistant to suppression by G4-ligand treatment. The recombinant virus containing the G4-disrupted ORF14 gene expressed a higher level of gC mRNA, while it showed a slightly reduced growth. This G4-disrupted ORF14 virus produced smaller plaques than the wild-type virus. Our results demonstrate that G4 formation via reiteration sequences suppresses gC expression during VZV infection and regulates viral cell-to-cell spread.
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Affiliation(s)
- Woo-Chang Chung
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Subramaniyam Ravichandran
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Daegyu Park
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Gwang Myeong Lee
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Young-Eui Kim
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Youngju Choi
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
| | - Moon Jung Song
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Precision Medicine, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
- Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Jin-Hyun Ahn
- Department of Microbiology, Sungkyunkwan University School of Medicine, Suwon, Republic of Korea
- Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
- * E-mail:
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31
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Volná A, Bartas M, Nezval J, Pech R, Pečinka P, Špunda V, Červeň J. Beyond the Primary Structure of Nucleic Acids: Potential Roles of Epigenetics and Noncanonical Structures in the Regulations of Plant Growth and Stress Responses. Methods Mol Biol 2023; 2642:331-361. [PMID: 36944887 DOI: 10.1007/978-1-0716-3044-0_18] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Epigenetics deals with changes in gene expression that are not caused by modifications in the primary sequence of nucleic acids. These changes beyond primary structures of nucleic acids not only include DNA/RNA methylation, but also other reversible conversions, together with histone modifications or RNA interference. In addition, under particular conditions (such as specific ion concentrations or protein-induced stabilization), the right-handed double-stranded DNA helix (B-DNA) can form noncanonical structures commonly described as "non-B DNA" structures. These structures comprise, for example, cruciforms, i-motifs, triplexes, and G-quadruplexes. Their formation often leads to significant differences in replication and transcription rates. Noncanonical RNA structures have also been documented to play important roles in translation regulation and the biology of noncoding RNAs. In human and animal studies, the frequency and dynamics of noncanonical DNA and RNA structures are intensively investigated, especially in the field of cancer research and neurodegenerative diseases. In contrast, noncanonical DNA and RNA structures in plants have been on the fringes of interest for a long time and only a few studies deal with their formation, regulation, and physiological importance for plant stress responses. Herein, we present a review focused on the main fields of epigenetics in plants and their possible roles in stress responses and signaling, with special attention dedicated to noncanonical DNA and RNA structures.
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Affiliation(s)
- Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jakub Nezval
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Radomír Pech
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Global Change Research Institute, Czech Academy of Sciences, Brno, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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Vinayagamurthy S, Bagri S, Mergny JL, Chowdhury S. Telomeres expand sphere of influence: emerging molecular impact of telomeres in non-telomeric functions. Trends Genet 2023; 39:59-73. [PMID: 36404192 PMCID: PMC7614491 DOI: 10.1016/j.tig.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/18/2022]
Abstract
Although the impact of telomeres on physiology stands well established, a question remains: how do telomeres impact cellular functions at a molecular level? This is because current understanding limits the influence of telomeres to adjacent subtelomeric regions despite the wide-ranging impact of telomeres. Emerging work in two distinct aspects offers opportunities to bridge this gap. First, telomere-binding factors were found with non-telomeric functions. Second, locally induced DNA secondary structures called G-quadruplexes are notably abundant in telomeres, and gene regulatory regions genome wide. Many telomeric factors bind to G-quadruplexes for non-telomeric functions. Here we discuss a more general model of how telomeres impact the non-telomeric genome - through factors that associate at telomeres and genome wide - and influence cell-intrinsic functions, particularly aging, cancer, and pluripotency.
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Affiliation(s)
- Soujanya Vinayagamurthy
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sulochana Bagri
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jean-Louis Mergny
- Institute of Biophysics of the CAS, v.v.i. Královopolská 135, 612 65 Brno, Czech Republic; Laboratoire d'Optique et Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Shantanu Chowdhury
- Integrative and Functional Biology Unit, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; GNR Knowledge Centre for Genome and Informatics, CSIR Institute of Genomics and Integrative Biology, New Delhi 110025, India.
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Yang D, Xu F, Wang P. Reconfigurable Two-Dimensional DNA Molecular Arrays. Methods Mol Biol 2023; 2639:69-81. [PMID: 37166711 DOI: 10.1007/978-1-0716-3028-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
In biology, molecular cascade signaling is an essential tool to mediate various pathways and downstream behaviors. Mimicking these molecular cascades plays an important role in synthetic biology. The use of DNA self-assembly represents an elegant way to build sophisticated molecular cascades. For instance, a DNA molecular array connected by a number of dynamic anti-junction units was able to realize prescribed, multistep, long-range cascaded transformation. The dynamic DNA molecular array is able to execute transformations with programmable initiation, propagation, and regulation. The transformation of the array can be initiated at selected units and then propagated, without addition of extra triggers, to neighboring units and eventually the entire array.
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Affiliation(s)
- Donglei Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao, Tong University, Shanghai, China
| | - Fan Xu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao, Tong University, Shanghai, China
| | - Pengfei Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao, Tong University, Shanghai, China.
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Brush GS. Anomalies in dye-terminator DNA sequencing caused by a natural G-quadruplex. PLoS One 2022; 17:e0279423. [PMID: 36574393 PMCID: PMC9794070 DOI: 10.1371/journal.pone.0279423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 11/24/2022] [Indexed: 12/29/2022] Open
Abstract
A G-rich DNA sequence from yeast that can form a non-canonical G-quadruplex structure was cloned into a plasmid vector and subjected to Sanger sequencing using dye-labeled dideoxynucleotides. Two different effects were observed. In one, presence of the G4 sequence on the template strand led to incorrect incorporation of an A residue at an internal position in the G4 sequence. In the other, the nascent strand caused attenuation of the readout coincident with synthesis of the G-rich DNA. The two effects are novel examples of disruption in DNA synthesis caused by a G4 sequence. These results provide a new example of a DNA structure that could influence genomic stability in human cells.
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Affiliation(s)
- George S. Brush
- Department of Oncology, Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine,Detroit, MI, United States of America
- * E-mail:
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35
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Shiekh S, Jack A, Saurabh A, Mustafa G, Kodikara S, Gyawali P, Hoque M, Pressé S, Yildiz A, Balci H. Shelterin reduces the accessibility of telomeric overhangs. Nucleic Acids Res 2022; 50:12885-12895. [PMID: 36511858 PMCID: PMC9825182 DOI: 10.1093/nar/gkac1176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 10/25/2022] [Accepted: 11/25/2022] [Indexed: 12/15/2022] Open
Abstract
Telomeres terminate with a 50-300 bases long single-stranded G-rich overhang, which can be misrecognized as a DNA damage repair site. Shelterin plays critical roles in maintaining and protecting telomere ends by regulating access of various physiological agents to telomeric DNA, but the underlying mechanism is not well understood. Here, we measure how shelterin affects the accessibility of long telomeric overhangs by monitoring transient binding events of a short complementary peptide nucleic acid (PNA) probe using FRET-PAINT in vitro. We observed that the POT1 subunit of shelterin reduces the accessibility of the PNA probe by ∼2.5-fold, indicating that POT1 effectively binds to and protects otherwise exposed telomeric sequences. In comparison, a four-component shelterin stabilizes POT1 binding to the overhang by tethering POT1 to the double-stranded telomeric DNA and reduces the accessibility of telomeric overhangs by ∼5-fold. This enhanced protection suggests shelterin restructures the junction between single and double-stranded telomere, which is otherwise the most accessible part of the telomeric overhang.
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Affiliation(s)
- Sajad Shiekh
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Amanda Jack
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
| | - Ayush Saurabh
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Golam Mustafa
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | | | - Prabesh Gyawali
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Mohammed Enamul Hoque
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
| | - Ahmet Yildiz
- Biophysics Graduate Group, University of California, Berkeley, CA 94720, USA
- Physics Department, University of California, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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Bazzicalupi C, Bonardi A, Biver T, Ferraroni M, Papi F, Savastano M, Lombardi P, Gratteri P. Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis. Int J Mol Sci 2022; 23:ijms232214061. [PMID: 36430540 PMCID: PMC9693123 DOI: 10.3390/ijms232214061] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/09/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
The interaction between the series of berberine derivatives 1-5 (NAX071, NAX120, NAX075, NAX077 and NAX079) and human telomeric G-quadruplexes (G4), which are able to inhibit the Telomerase enzyme's activity in malignant cells, was investigated. The derivatives bear a pyridine moiety connected by a hydrocarbon linker of varying length (n = 1-5, with n number of aliphatic carbon atoms) to the C13 position of the parent berberine. As for the G4s, both bimolecular 5'-TAGGGTTAGGGT-3' (Tel12) and monomolecular 5'-TAGGGTTAGGGTTAGGGTTAGGG-3' (Tel23) DNA oligonucleotides were considered. Spectrophotometric titrations, melting tests, X-ray diffraction solid state analysis and in silico molecular dynamics (MD) simulations were used to describe the different systems. The results were compared in search of structure-activity relationships. The analysis pointed out the formation of 1:1 complexes between Tel12 and all ligands, whereas both 1:1 and 2:1 ligand/G4 stoichiometries were found for the adduct formed by NAX071 (n = 1). Tel12, with tetrads free from the hindrance by the loop, showed a higher affinity. The details of the different binding geometries were discussed, highlighting the importance of H-bonds given by the berberine benzodioxole group and a correlation between the strength of binding and the hydrocarbon linker length. Theoretical (MD) and experimental (X-ray) structural studies evidence the possibility for the berberine core to interact with one or both G4 strands, depending on the constraints given by the linker length, thus affecting the G4 stabilization effect.
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Affiliation(s)
- Carla Bazzicalupi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
- Correspondence: (C.B.); (P.G.)
| | - Alessandro Bonardi
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA—Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Firenze, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Marta Ferraroni
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Francesco Papi
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA—Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Firenze, Italy
| | - Matteo Savastano
- Department of Chemistry, University of Florence, Via della Lastruccia 3, 50019 Firenze, Italy
| | - Paolo Lombardi
- Naxospharma srl, Via G. Di Vittorio 70, Novate Milanese, 20026 Milano, Italy
| | - Paola Gratteri
- Laboratory of Molecular Modeling Cheminformatics & QSAR, Department NEUROFARBA—Pharmaceutical and Nutraceutical Section, University of Firenze, Via Ugo Schiff 6, 50019 Firenze, Italy
- Correspondence: (C.B.); (P.G.)
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Cueny RR, McMillan SD, Keck JL. G-quadruplexes in bacteria: insights into the regulatory roles and interacting proteins of non-canonical nucleic acid structures. Crit Rev Biochem Mol Biol 2022; 57:539-561. [PMID: 36999585 PMCID: PMC10336854 DOI: 10.1080/10409238.2023.2181310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 04/01/2023]
Abstract
G-quadruplexes (G4s) are highly stable, non-canonical DNA or RNA structures that can form in guanine-rich stretches of nucleic acids. G4-forming sequences have been found in all domains of life, and proteins that bind and/or resolve G4s have been discovered in both bacterial and eukaryotic organisms. G4s regulate a variety of cellular processes through inhibitory or stimulatory roles that depend upon their positions within genomes or transcripts. These include potential roles as impediments to genome replication, transcription, and translation or, in other contexts, as activators of genome stability, transcription, and recombination. This duality suggests that G4 sequences can aid cellular processes but that their presence can also be problematic. Despite their documented importance in bacterial species, G4s remain understudied in bacteria relative to eukaryotes. In this review, we highlight the roles of bacterial G4s by discussing their prevalence in bacterial genomes, the proteins that bind and unwind G4s in bacteria, and the processes regulated by bacterial G4s. We identify limitations in our current understanding of the functions of G4s in bacteria and describe new avenues for studying these remarkable nucleic acid structures.
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Affiliation(s)
- Rachel R. Cueny
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Sarah D. McMillan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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38
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Dynamic folding and accessibility of telomeric overhang. Proc Natl Acad Sci U S A 2022; 119:e2211219119. [PMID: 36070346 PMCID: PMC9499555 DOI: 10.1073/pnas.2211219119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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39
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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40
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Jiang XC, Tu FH, Wei LY, Wang BZ, Yuan H, Yuan JM, Rao Y, Huang SL, Li QJ, Ou TM, Wang HG, Tan JH, Chen SB, Huang ZS. Discovery of a Novel G-Quadruplex and Histone Deacetylase (HDAC) Dual-Targeting Agent for the Treatment of Triple-Negative Breast Cancer. J Med Chem 2022; 65:12346-12366. [PMID: 36053318 DOI: 10.1021/acs.jmedchem.2c01058] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of triple-negative breast cancer (TNBC) is highly associated with G-quadruplex (G4); thus, targeting G4 is a potential strategy for TNBC therapy. Because concomitant histone deacetylases (HDAC) inhibition could amplify the impact of G4-targeting compounds, we designed and synthesized two novel series of G4/HDAC dual-targeting compounds by connecting the zinc-binding pharmacophore of HDAC inhibitors to the G4-targeting isaindigotone scaffold (1). Among the new compounds, a6 with the potent HDAC inhibitory and G4 stabilizing activity could induce more DNA G4 formation than SAHA and 1 in TNBC cells. Remarkably, a6 caused more G4-related DNA damage and G4-related differentially expressed genes, consistent with its effect on disrupting the cell cycle, invasion, and glycolysis. Furthermore, a6 significantly suppresses the proliferation of various TNBC cells and the MDA-MB-231 xenograft model without evident toxicity. Our study suggests a novel strategy for TNBC therapeutics through dual-targeting HDAC and G4.
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Affiliation(s)
- Xin-Chen Jiang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Fang-Hai Tu
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Li-Yuan Wei
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Bo-Zheng Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hao Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing-Mei Yuan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Yong Rao
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shi-Liang Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Qing-Jiang Li
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Hong-Gen Wang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Sun Yat-sen University, Guangzhou 510006, China
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Dey A, Pandav K, Nath M, Barthwal R, Prasad R. Molecular rec§ognition of telomere DNA sequence by 2, 6 anthraquinone derivatives leads to thermal stabilization and induces apoptosis in cancer cells. Int J Biol Macromol 2022; 221:355-370. [PMID: 36041576 DOI: 10.1016/j.ijbiomac.2022.08.156] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/25/2022]
Abstract
According to current research, anti-cancer anthraquinones impact telomere disruption and may interact with G-quadruplex DNA that triggers signaling to apoptosis. The present study represents the biophysical investigation of oxidative stress, late apoptosis, and induced senescence among cancer cells after binding laboratory synthesized piperidine-based anthraquinone derivatives, 2, 6- Bis [(3-piperidino)acetamido)]anthracene-9,10-dione (N1P) and 2, 6-Bis [piperidino)propionamido]anthracene-9,10-dione (N2P), with G-quadruplex DNA. We employed biophysical approaches to explore the interaction of synthetic anthraquinone derivatives with quadruplex DNA sequences to influence biological activities in the presence of K+ and Na+ cations. The binding affinity for N2P and N1P are Kb = 5.8 × 106 M-1 and Kb = 1.0 × 106 M-1, respectively, leading to hypo-/hyper-chromism with 5-7 nm red shift and significant fluorescence quenching and changes in ellipticity resulting in external binding of both the ligands to G-quadruplex DNA. Ligand binding induced enhancement of thermostability of G4 DNA is greater in Na+ environment (ΔTm = 34 °C) as compared to that in K+ environment (ΔTm = 21 °C), thereby restricting telomerase binding access to telomeres. Microscopic images of treated cells indicated cellular shape, nuclear condensation, and fragmentation alterations. The findings pave the path for therapeutic research, given the great potential of modifying anthraquinone substituent groups towards improved efficacy, ROS generation, and G-quadruplex DNA selectivity.
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Affiliation(s)
- Arpita Dey
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Kumud Pandav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Mala Nath
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Ritu Barthwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
| | - Ramasare Prasad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
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Peng P, Wang S, Cai S, Cheng J, Tao D, Jaffrezic-Renault N, Guo Z. An ultrasensitive hairpin sensor based on g-C 3N 4 nanocomposite for the detection of miRNA-155 in breast cancer patient serum. Anal Bioanal Chem 2022; 414:7325-7334. [PMID: 35974199 DOI: 10.1007/s00216-022-04284-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022]
Abstract
Achieving the early diagnosis of breast cancer, through ultrasensitive detection of tumor marker miRNA-155, is a significant challenge. Therefore, an ultrasensitive hairpin electrochemical biosensor based on graphite-like phase carbon nitride composite was proposed. In this paper, poly(D-glucosamine) (PDG) was used as a stabilizer and reducing agent to prepare gold nanoparticles at room temperature, and then a graphite-like phase with a two-dimensional lamellar structure carbon nitride was further combined with it to obtain the poly(D-glucosamine)/gold nanoparticles/graphite-like phase carbon nitride nanocomposite (PDG/AuNPs/g-C3N4), in order to achieve the goal of signal amplification. The specific hairpin capture probe (HP) that recognized and bound miRNA-155 was then grafted. The hairpin biosensor showed a linear range of 0.1 fM-1 pM with a detection limit of 0.05 fM using differential pulse voltammetry (DPV) electrochemical analysis. Furthermore, the excellent performance hairpin electrochemical biosensor had been applied to the detection of miRNA-155 in human serum samples with good recovery.
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Affiliation(s)
- Pingping Peng
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, 430065, People's Republic of China.,School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, People's Republic of China
| | - Sheng Wang
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siyuan Cai
- Langfang Normal University, Langfang, 065000, China
| | - Jing Cheng
- School of Public Health, Medical College, Wuhan University of Science and Technology, Wuhan, 430065, People's Republic of China
| | - Dan Tao
- School of Public Health, The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Guizhou Medical University, Guiyang, 550025, China
| | - Nicole Jaffrezic-Renault
- Institute of Analytical Sciences, University of Lyon, UMR-CNRS 5280, 5, La Doua Street, 69100, Villeurbanne, France.
| | - Zhenzhong Guo
- Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Wuhan University of Science and Technology, Wuhan, 430065, People's Republic of China.
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Abstract
We present single-molecule experimental and computational modeling studies investigating the accessibility of human telomeric overhangs of physiologically relevant lengths. We studied 25 different overhangs that contain 4-28 repeats of GGGTTA (G-Tract) sequence and accommodate one to seven tandem G-quadruplex (GQ) structures. Using the FRET-PAINT method, we probed the distribution of accessible sites via a short imager strand, which is complementary to a G-Tract and transiently binds to available sites. We report accessibility patterns that periodically change with overhang length and interpret these patterns in terms of the underlying folding landscape and folding frustration. Overhangs that have [4n]G-Tracts, (12, 16, 20…) demonstrate the broadest accessibility patterns where the peptide nucleic acid probe accesses G-Tracts throughout the overhang. On the other hand, constructs with [4n+2]G-Tracts, (14, 18, 22…) have narrower patterns where the neighborhood of the junction between single- and double-stranded telomeres is most accessible. We interpret these results as the folding frustration being higher in [4n]G-Tract constructs compared to [4n+2]G-Tract constructs. We also developed a computational model that tests the consistency of different folding stabilities and cooperativities between neighboring GQs with the observed accessibility patterns. Our experimental and computational studies suggest the neighborhood of the junction between single- and double-stranded telomeres is least stable and most accessible, which is significant as this is a potential site where the connection between POT1/TPP1 (bound to single-stranded telomere) and other shelterin proteins (localized on double-stranded telomere) is established.
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44
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Cirri D, Bazzicalupi C, Ryde U, Bergmann J, Binacchi F, Nocentini A, Pratesi A, Gratteri P, Messori L. Computationally enhanced X-ray diffraction analysis of a gold(III) complex interacting with the human telomeric DNA G-quadruplex. Unravelling non-unique ligand positioning. Int J Biol Macromol 2022; 211:506-513. [PMID: 35561865 DOI: 10.1016/j.ijbiomac.2022.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/14/2022] [Accepted: 05/04/2022] [Indexed: 11/18/2022]
Abstract
The crystal structure of the human telomeric DNA Tel24 G-quadruplex (Tel24 = TAG3(T2AG3)3T) in complex with the novel [AuL] species (with L = 2,4,6-tris(2-pyrimidyl)-1,3,5-triazine - TPymT-α) was solved by a novel joint molecular mechanical (MM)/quantum mechanical (QM) innovative approach. The quantum-refinement crystallographic method (crystallographic refinement enhanced with quantum mechanical calculation) was adapted to treat the [AuL]/G-quadruplex structure, where each gold complex in the binding site was found spread over four equally occupied positions. The four positions were first determined by docking restrained to the crystallographically determined metal ions' coordinates. Then, the quantum refinement method was used to resolve the poorly defined density around the ligands and improve the crystallographic determination, revealing that the binding preferences of this metallodrug toward Tel24 G-quadruplex arise from a combined effect of pyrimidine stacking, metal-guanine interactions and charge-charge neutralizing action of the π-acid triazine. The occurrence of interaction in solution with the Tel24 G-quadruplex DNA was further proved through DNA melting experiments, which showed a slight destabilisation of the quadruplex upon adduct formation.
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Affiliation(s)
- Damiano Cirri
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Carla Bazzicalupi
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy.
| | - Ulf Ryde
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden.
| | - Justin Bergmann
- Division of Theoretical Chemistry, Lund University, Chemical Centre, P. O. Box 124, SE-221 00 Lund, Sweden
| | - Francesca Binacchi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Alessio Nocentini
- Department NEUROFARBA - Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Alessandro Pratesi
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Paola Gratteri
- Department NEUROFARBA - Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019, Sesto Fiorentino, Florence, Italy.
| | - Luigi Messori
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
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45
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Lee J, Sung K, Joo SY, Jeong JH, Kim SK, Lee H. Dynamic interaction of BRCA2 with telomeric G-quadruplexes underlies telomere replication homeostasis. Nat Commun 2022; 13:3396. [PMID: 35697743 PMCID: PMC9192595 DOI: 10.1038/s41467-022-31156-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 05/31/2022] [Indexed: 12/02/2022] Open
Abstract
BRCA2-deficient cells precipitate telomere shortening upon collapse of stalled replication forks. Here, we report that the dynamic interaction between BRCA2 and telomeric G-quadruplex (G4), the non-canonical four-stranded secondary structure, underlies telomere replication homeostasis. We find that the OB-folds of BRCA2 binds to telomeric G4, which can be an obstacle during replication. We further demonstrate that BRCA2 associates with G-triplex (G3)-derived intermediates, which are likely to form during direct interconversion between parallel and non-parallel G4. Intriguingly, BRCA2 binding to G3 intermediates promoted RAD51 recruitment to the telomere G4. Furthermore, MRE11 resected G4-telomere, which was inhibited by BRCA2. Pathogenic mutations at the OB-folds abrogated the binding with telomere G4, indicating that the way BRCA2 associates with telomere is innate to its tumor suppressor activity. Collectively, we propose that BRCA2 binding to telomeric G4 remodels it and allows RAD51-mediated restart of the G4-driven replication fork stalling, simultaneously preventing MRE11-mediated breakdown of telomere. G-quadruplex (G4) can be formed in telomeric DNA. Here the authors show that BRCA2 interacts with telomere G4 structure generated during telomere replication, protecting telomere from nuclease attack.
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Affiliation(s)
- Junyeop Lee
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea
| | - Keewon Sung
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea
| | - So Young Joo
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea
| | - Jun-Hyeon Jeong
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University, Seoul, 08826, South Korea.
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, Seoul, 08826, South Korea.
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46
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Moe MM, Benny J, Liu J. Collision-induced dissociation of homodimeric and heterodimeric radical cations of 9-methylguanine and 9-methyl-8-oxoguanine: correlation between intra-base pair proton transfer originating from the N1-H at a Watson-Crick edge and non-statistical dissociation. Phys Chem Chem Phys 2022; 24:9263-9276. [PMID: 35403654 DOI: 10.1039/d2cp00312k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has been shown previously in protonated, deprotonated and ionized guanine-cytosine base pairs that intra-base pair proton transfer from the N1-H at the Watson-Crick edge of guanine to the complementary nucleobase prompts non-statistical dissociation of the base-pair system, and the dissociation of a proton-transferred base-pair structure is kinetically more favored than that of the starting, conventional base-pair structure. However, the fundamental chemistry underlying this anomalous and intriguing kinetics has not been completely revealed, which warrants the examination of more base-pair systems in different structural contexts in order to derive a generalized base-pair structure-kinetics correlation. The purpose of the present work is to expand the investigation to the non-canonical homodimeric and heterodimeric radical cations of 9-methylguanine (9MG) and 9-methyl-8-oxoguanine (9MOG), i.e., [9MG·9MG]˙+, [9MOG·9MG]˙+ and [9MOG·9MOG]˙+. Experimentally, collision-induced dissociation tandem mass spectrometry coupled with an electrospray ionization (ESI) source was used for the formation of base-pair radical cations, followed by detection of dissociation product ions and cross sections in the collisions with Xe gas under single ion-molecule collision conditions and as a function of the center-of-mass collision energy. Computationally, density functional theory and coupled cluster theory were used to calculate and identify probable base-pair structures and intra-base pair proton transfer and hydrogen transfer reactions, followed by kinetics modeling to explore the properties of dissociation transition states and kinetic factors. The significance of this work is twofold: it provides insight into base-pair opening kinetics in three biologically-important, non-canonical systems upon oxidative and ionization damage; and it links non-statistical dissociation to intra-base pair proton-transfer originating from the N1-H at the Watson-Crick edge of 8-oxoguanine, enhancing understanding towards the base-pair fragmentation assisted by proton transfer.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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47
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Frasson I, Pirota V, Richter SN, Doria F. Multimeric G-quadruplexes: A review on their biological roles and targeting. Int J Biol Macromol 2022; 204:89-102. [PMID: 35124022 DOI: 10.1016/j.ijbiomac.2022.01.197] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 01/20/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
Abstract
In human cells, nucleic acids adopt several non-canonical structures that regulate key cellular processes. Among them, G-quadruplexes (G4s) are stable structures that form in guanine-rich regions in vitro and in cells. G4 folded/unfolded state shapes numerous cellular processes, including genome replication, transcription, and translation. Moreover, G4 folding is involved in genomic instability. G4s have been described to multimerize, forming high-order structures in both DNA and/or RNA strands. Multimeric G4s can be formed by adjacent intramolecular G4s joined by stacking interactions or connected by short loops. Multimeric G4s can also originate from the assembly of guanines embedded on independent DNA or RNA strands. Notably, crucial regions of the human genome, such as the 3'-terminal overhang of the telomeric DNA as well as the open reading frame of genes involved in the preservation of neuron viability in the human central and peripheral nervous system are prone to form multimeric G4s. The biological importance of such structures has been recently described, with multimeric G4s playing potentially protective or deleterious effects in the pathogenic cascade of various diseases. Here, we portray the multifaceted scenario of multimeric G4s, in terms of structural properties, biological roles, and targeting strategies.
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Affiliation(s)
- Ilaria Frasson
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy
| | - Valentina Pirota
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy; G4-INTERACT, USERN, v. le Taramelli 10, 27100 Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padova, via A. Gabelli 63, 35121 Padova, Italy.
| | - Filippo Doria
- Department of Chemistry, University of Pavia, v. le Taramelli 10, 27100 Pavia, Italy.
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48
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Vannutelli A, Perreault JP, Ouangraoua A. G-quadruplex occurrence and conservation: more than just a question of guanine–cytosine content. NAR Genom Bioinform 2022; 4:lqac010. [PMID: 35261973 PMCID: PMC8896161 DOI: 10.1093/nargab/lqac010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 12/06/2021] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
G-quadruplexes are motifs found in DNA and RNA that can fold into tertiary structures. Until now, they have been studied experimentally mainly in humans and a few other species. Recently, predictions have been made with bacterial and archaeal genomes. Nevertheless, a global comparison of predicted G4s (pG4s) across and within the three living kingdoms has not been addressed. In this study, we aimed to predict G4s in genes and transcripts of all kingdoms of living organisms and investigated the differences in their distributions. The relation of the predictions with GC content was studied. It appears that GC content is not the only parameter impacting G4 predictions and abundance. The distribution of pG4 densities varies depending on the class of transcripts and the group of species. Indeed, we have observed that, in coding transcripts, there are more predicted G4s than expected for eukaryotes but not for archaea and bacteria, while in noncoding transcripts, there are as many or fewer predicted G4s in all species groups. We even noticed that some species with the same GC content presented different pG4 profiles. For instance, Leishmania major and Chlamydomonas reinhardtii both have 60% of GC content, but the former has a pG4 density of 0.07 and the latter 1.16.
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Affiliation(s)
- Anaïs Vannutelli
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
- Department of Biochemistry and Functional Genomics, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, QC J1E 4K8, Canada
| | - Jean-Pierre Perreault
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
| | - Aïda Ouangraoua
- Department of Computer Science, Faculté des sciences, Université de Sherbrooke, QC, J1K 2R1, Canada
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49
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Hoque ME, Mahendran T, Basu S. Reversal of G-Quadruplexes' Role in Translation Control When Present in the Context of an IRES. Biomolecules 2022; 12:314. [PMID: 35204814 PMCID: PMC8869680 DOI: 10.3390/biom12020314] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/08/2022] [Accepted: 02/14/2022] [Indexed: 02/01/2023] Open
Abstract
G-quadruplexes (GQs) are secondary nucleic acid structures that play regulatory roles in various cellular processes. G-quadruplex-forming sequences present within the 5' UTR of mRNAs can function not only as repressors of translation but also as elements required for optimum function. Based upon previous reports, the majority of the 5' UTR GQ structures inhibit translation, presumably by blocking the ribosome scanning process that is essential for detection of the initiation codon. However, there are certain mRNAs containing GQs that have been identified as positive regulators of translation, as they are needed for translation initiation. While most cellular mRNAs utilize the 5' cap structure to undergo cap-dependent translation initiation, many rely on cap-independent translation under certain conditions in which the cap-dependent initiation mechanism is not viable or slowed down, for example, during development, under stress and in many diseases. Cap-independent translation mainly occurs via Internal Ribosomal Entry Sites (IRESs) that are located in the 5' UTR of mRNAs and are equipped with structural features that can recruit the ribosome or other factors to initiate translation without the need for a 5' cap. In this review, we will focus only on the role of RNA GQs present in the 5' UTR of mRNAs, where they play a critical role in translation initiation, and discuss the potential mechanism of this phenomenon, which is yet to be fully delineated.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH 44242, USA; (M.E.H.); (T.M.)
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50
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Milovanović B, Petković M, Etinski M. Alkaline earth cations binding mode tailors excited-state charge transfer properties of guanine quadruplex: A TDDFT study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120584. [PMID: 34794899 DOI: 10.1016/j.saa.2021.120584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/25/2021] [Accepted: 11/02/2021] [Indexed: 06/13/2023]
Abstract
Quadruplexes formed by nucleic acids and their derivates tend to chelate different monovalent and bivalent cations, which simultaneously affect their excited electronic states properties. Cation binding to every and every other cavity of the central ion channel could be exploited for tuning exited-state charge transfer properties. In this work we utilize set of descriptors constructed on the basis of the one-electron transition density matrix obtained using linear-response TDDFT to study excited states properties of four crystallized tetramolecular quadruplexes that chelate alkaline earth cations (Ca2+, Sr2+ and Ba2+). Here, we show that alkaline earth cations situated at adjacent vacancies promote existence of the nucleobase-metal charge separation (CS) states, contrary to the structures with cations that occupy every second available vacancy. We argued that stabilization of these CS states is due to the strong electric field that stabilizes d orbitals of the cations which accept an excited-electron. Moreover, CS content is increased and redshifted below the first bright transition when number of the chelated cations is increased. Hydration effects stabilized CS states and increased their relative content. We also identified electron detachment states in the broad energy range for the Ca2+ containing system. These findings are valuable for understanding and development of the novel nanostructures based on the quadruplex scaffold with adjustable optical properties.
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Affiliation(s)
- Branislav Milovanović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Milena Petković
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia
| | - Mihajlo Etinski
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, Belgrade, Serbia.
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