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Michael Sabo T, Trent JO, Chaires JB, Monsen RC. Strategy for modeling higher-order G-quadruplex structures recalcitrant to NMR determination. Methods 2024; 230:9-20. [PMID: 39032720 DOI: 10.1016/j.ymeth.2024.07.004] [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: 04/05/2024] [Revised: 06/22/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024] Open
Abstract
Guanine-rich nucleic acids can form intramolecularly folded four-stranded structures known as G-quadruplexes (G4s). Traditionally, G4 research has focused on short, highly modified DNA or RNA sequences that form well-defined homogeneous compact structures. However, the existence of longer sequences with multiple G4 repeats, from proto-oncogene promoters to telomeres, suggests the potential for more complex higher-order structures with multiple G4 units that might offer selective drug-targeting sites for therapeutic development. These larger structures present significant challenges for structural characterization by traditional high-resolution methods like multi-dimensional NMR and X-ray crystallography due to their molecular complexity. To address this current challenge, we have developed an integrated structural biology (ISB) platform, combining experimental and computational methods to determine self-consistent molecular models of higher-order G4s (xG4s). Here we outline our ISB method using two recent examples from our lab, an extended c-Myc promoter and long human telomere G4 repeats, that highlights the utility and generality of our approach to characterizing biologically relevant xG4s.
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Affiliation(s)
- T Michael Sabo
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - John O Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Jonathan B Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States
| | - Robert C Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, KY, United States.
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2
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Singh A, Jain N, Shankar U, Sharma TK, Kumar A. Characterization of G-quadruplex structures in genes involved in survival and pathogenesis of Acinetobacter baumannii as a potential drug target. Int J Biol Macromol 2024; 269:131806. [PMID: 38670179 DOI: 10.1016/j.ijbiomac.2024.131806] [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: 12/13/2023] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024]
Abstract
Acinetobacter baumannii is a notorious pathogen that commonly thrives in hospital environments and is responsible for numerous nosocomial infections in humans. The burgeoning multi-drug resistance leaves relatively minimal options for treating the bacterial infection, posing a significant problem and prompting the identification of new approaches for tackling the same. This motivated us to focus on non-canonical nucleic acid structures, mainly G-quadruplexes, as drug targets. G-quadruplexes have recently been gaining attention due to their involvement in multiple bacterial and viral pathogenesis. Herein, we sought to explore conserved putative G-quadruplex motifs in A. baumannii. In silico analysis revealed the presence of eight conserved motifs in genes involved in bacterial survival and pathogenesis. The biophysical and biomolecular analysis confirmed stable G-quadruplex formation by the motifs and showed a high binding affinity with the well-reported G-quadruplex binding ligand, BRACO-19. BRACO-19 exposure also decreased the growth of bacteria and downregulated the expression of G-quadruplex-harboring genes. The biofilm-forming ability of the bacteria was also affected by BRACO-19 addition. Taking all these observations into account, we have shown here for the first time the potential of G-quadruplex structures as a promising drug target in Acinetobacter baumannii, for addressing the challenges posed by this infamous pathogen.
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Affiliation(s)
- Aakriti Singh
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Neha Jain
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Uma Shankar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Tarun Kumar Sharma
- Department of Medical Biotechnology, Gujarat Biotechnology University, Gandhinagar 382355, India
| | - Amit Kumar
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India.
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3
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Roy S, Majee P, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes. Chem Sci 2024; 15:7982-7991. [PMID: 38817587 PMCID: PMC11134374 DOI: 10.1039/d4sc01755b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Understanding the structure and recognition of highly conserved regulatory segments of the integrated viral DNA genome that forms unique topologies can greatly aid in devising novel therapeutic strategies to counter chronic infections. In this study, we configured a probe system using highly environment-sensitive nucleoside analogs, 5-fluoro-2'-deoxyuridine (FdU) and 5-fluorobenzofuran-2'-deoxyuridine (FBFdU), to investigate the structural polymorphism of HIV-1 long terminal repeat (LTR) G-quadruplexes (GQs) by fluorescence and 19F NMR. FdU and FBFdU, serving as hairpin and GQ sensors, produced distinct spectral signatures for different GQ topologies adopted by LTR G-rich oligonucleotides. Importantly, systematic 19F NMR analysis in Xenopus laevis oocytes gave unprecedented information on the structure adopted by the LTR G-rich region in the cellular environment. The results indicate that it forms a unique GQ-hairpin hybrid architecture, a potent hotspot for selective targeting. Furthermore, structural models generated using MD simulations provided insights on how the probe system senses different GQs. Using the responsiveness of the probes and Taq DNA polymerase stop assay, we monitored GQ- and hairpin-specific ligand interactions and their synergistic inhibitory effect on the replication process. Our findings suggest that targeting GQ and hairpin motifs simultaneously using bimodal ligands could be a new strategy to selectively block the viral replication.
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Affiliation(s)
- Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
| | - Priyasha Majee
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Satyajit Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - Jeet Kalia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
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4
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Zhao Z, Wang J, Yu H, Wang X. Guide for phenotype-specific profiling of DNA G-quadruplex-regulated genes. STAR Protoc 2024; 5:102820. [PMID: 38198280 PMCID: PMC10820308 DOI: 10.1016/j.xpro.2023.102820] [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: 09/01/2023] [Revised: 11/06/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
DNA G-quadruplex (G4) is a non-canonical four-stranded secondary structure that has been shown to play a role in epigenetic modulation of gene expression. Here, we present a primer on phenotype-specific profiling of DNA G-quadruplex-regulated genes. We provide guidance on in silico exploration of G4-related genes and phenotypes, and in vitro and in vivo validation of the relationship between G4 and phenotype. We describe commonly utilized techniques and detail critical steps involved in determining the phenotype-specific G4-regulated genes for subsequent investigations.
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Affiliation(s)
- Zhuoyang Zhao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China
| | - Jianru Wang
- Department of Spine Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Key Laboratory of Orthopedics and Traumatology, Guangzhou 510080, China
| | - Huichuan Yu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China.
| | - Xiaolin Wang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Guangdong Institute of Gastroenterology, Guangzhou, Guangdong 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510655, China; Key Laboratory of Human Microbiome and Chronic Diseases (Sun Yat-sen University), Ministry of Education, Guangzhou, Guangdong 510655, China.
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5
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Bose D, Banerjee N, Roy A, Sengupta P, Chatterjee S. Switchable tetraplex elements in the heterogeneous nuclear ribonucleoprotein K promoter: micro-environment dictated structural transitions of G/C rich elements. J Biomol Struct Dyn 2024:1-18. [PMID: 38235706 DOI: 10.1080/07391102.2024.2303378] [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: 07/25/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
We have elucidated the hnRNP K promoter as a hotspot for tetraplex-based molecular switches receptive to micro-environmental stimuli. We have characterised the structural features of four tetraplex-forming loci and identified them as binding sites of transcription factors. These segments form either G-quadruplex or i-motif structures, the structural dynamicity of which has been studied in depth via several biophysical techniques. The tetraplexes display high dynamicity and are influenced by both pH and KCl concentrations in vitro. The loci complementary to these sequences form additional non-canonical secondary structures. In the cellular context, the most eminent observation of this study is the binding of hnRNP K to the i-motif forming sequences in its own promoter. We are the first to report a probable transcriptional autoregulatory function of hnRNP K in coordination with higher-order DNA structures. Herein, we also report the positive interaction of the endogenous tetraplexes with Sp1, a well-known transcriptional regulator. Treatment with tetraplex-specific small molecule ligands further uncovered G-quadruplexes' functioning as repressors and i-motifs as activators in this context. Together, our findings strongly indicate the critical regulatory role of the identified tetraplex elements in the hnRNP K promoter.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Debopriya Bose
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Nilanjan Banerjee
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Ananya Roy
- Department of Biological Sciences, Bose Institute, Kolkata, West Bengal, India
| | - Pallabi Sengupta
- Department of Medical Biochemistry and Biophysics, Kemihuset (K), Campus, Umeå, Umeå universitet, Umeå, Sweden
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Zareie AR, Dabral P, Verma SC. G-Quadruplexes in the Regulation of Viral Gene Expressions and Their Impacts on Controlling Infection. Pathogens 2024; 13:60. [PMID: 38251367 PMCID: PMC10819198 DOI: 10.3390/pathogens13010060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/23/2024] Open
Abstract
G-quadruplexes (G4s) are noncanonical nucleic acid structures that play significant roles in regulating various biological processes, including replication, transcription, translation, and recombination. Recent studies have identified G4s in the genomes of several viruses, such as herpes viruses, hepatitis viruses, and human coronaviruses. These structures are implicated in regulating viral transcription, replication, and virion production, influencing viral infectivity and pathogenesis. G4-stabilizing ligands, like TMPyP4, PhenDC3, and BRACO19, show potential antiviral properties by targeting and stabilizing G4 structures, inhibiting essential viral life-cycle processes. This review delves into the existing literature on G4's involvement in viral regulation, emphasizing specific G4-stabilizing ligands. While progress has been made in understanding how these ligands regulate viruses, further research is needed to elucidate the mechanisms through which G4s impact viral processes. More research is necessary to develop G4-stabilizing ligands as novel antiviral agents. The increasing body of literature underscores the importance of G4s in viral biology and the development of innovative therapeutic strategies against viral infections. Despite some ligands' known regulatory effects on viruses, a deeper comprehension of the multifaceted impact of G4s on viral processes is essential. This review advocates for intensified research to unravel the intricate relationship between G4s and viral processes, paving the way for novel antiviral treatments.
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Affiliation(s)
| | | | - Subhash C. Verma
- Department of Microbiology and Immunology, University of Nevada, Reno School of Medicine, 1664 N Virginia Street, Reno, NV 89557, USA; (A.R.Z.); (P.D.)
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Luo Y, Granzhan A, Marquevielle J, Cucchiarini A, Lacroix L, Amrane S, Verga D, Mergny JL. Guidelines for G-quadruplexes: I. In vitro characterization. Biochimie 2023; 214:5-23. [PMID: 36596406 DOI: 10.1016/j.biochi.2022.12.019] [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: 10/29/2022] [Revised: 12/19/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Besides the well-known DNA double-helix, non-canonical nucleic acid structures regulate crucial biological activities. Among these oddities, guanine-rich DNA sequences can form unusual four-stranded secondary structures called G-quadruplexes (G4s). G4-prone sequences have been found in the genomes of most species, and G4s play important roles in essential processes such as transcription, replication, genome integrity and epigenetic regulation. Here, we present a short overview of G-quadruplexes followed by a detailed description of the biophysical and biochemical methods used to characterize G4s in vitro. The principles, experimental details and possible shortcomings of each method are discussed to provide a comprehensive view of the techniques used to study these structures. We aim to provide a set of guidelines for standardizing research on G-quadruplexes; these guidelines are not meant to be a dogmatic set of rules, but should rather provide useful information on the methods currently used to study these fascinating motifs.
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Affiliation(s)
- Yu Luo
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France
| | - Julien Marquevielle
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Anne Cucchiarini
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France
| | - Laurent Lacroix
- Institut de Biologie de L'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Samir Amrane
- Université de Bordeaux, ARNA Laboratory, INSERM U1212, CNRS UMR 5320, IECB, 33076, Bordeaux, France
| | - Daniela Verga
- CNRS UMR9187, INSERM U1196, Université Paris-Saclay, F-91405, Orsay, France; CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, F-91405, Orsay, France.
| | - Jean-Louis Mergny
- Laboratoire D'Optique et Biosciences, Ecole Polytechnique, CNRS, Inserm, Institut Polytechnique de Paris, 91120, Palaiseau, France; Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.
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8
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Roy A, Basu D, Bose D, Dutta A, Dastidar SG, Chatterjee S. Identification and characterization of a flexile G-quadruplex in the distal promoter region of stemness gene REX1. Int J Biol Macromol 2023; 231:123263. [PMID: 36649868 DOI: 10.1016/j.ijbiomac.2023.123263] [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: 10/25/2022] [Revised: 01/06/2023] [Accepted: 01/08/2023] [Indexed: 01/15/2023]
Abstract
We have identified a parallel G-quadruplex (R1WT) in the distal promoter region (-821 base-pairs upstream of the TSS) of the pluripotent gene REX1. Through biophysical and biochemical approach, we have characterized the G-quadruplex (GQ) as a potential molecular switch that may control REX1 promoter activity to determine the transcriptional fate. Small- molecule interactive study of the monomeric form of R1WT (characterized as R1mut2) with TMPyP4 and BRACO-19 revealed GQ destabilization upon interaction with TMPyP4 and stabilization upon interaction with BRACO-19. This distinctive drug interactivity suggests the in cellulo R1WT to be a promising drug target. The endogenous existence of R1WT was confirmed by BG4 antibody derived chromatin immunoprecipitation experiment. Here in, we also report the endogenous interaction of GQ specific transcription factors (TFs) with R1WT region in the human chromatin of cancer cell. The wild-type G-quadruplex was found to interact with four important transcription factors, (i) specificity protein (Sp1) (ii) non-metastatic cell 2 (NM23-H2): a diphosphatase (iii) cellular nucleic acid binding protein (CNBP) and (iv) heterogenous nuclear ribonucleoprotein K (hnRNPK) in the REX1 promoter. In contrast, nucleolin protein (NCL) binding was found to be low to the said G-quadruplex. The flexibility of R1WT between folded and unfolded states, obtained from experimental and computational analysis strongly suggests R1WT to be an important gene regulatory element in the genome. It controls promoter DNA relaxation with the coordinated interaction of transcription factors, the deregulation of which seeds stemness characteristic in cancer cells for further metastatic progression.
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Affiliation(s)
- Ananya Roy
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Debadrita Basu
- Department of Bioinformatics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Debopriya Bose
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Anindya Dutta
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Shubhra Ghosh Dastidar
- Department of Bioinformatics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, EN-80 Sector V, Salt Lake, Unified Campus, Kolkata 700091, India.
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Fang J, Xie C, Tao Y, Wei D. An overview of single-molecule techniques and applications in the study of nucleic acid structure and function. Biochimie 2023; 206:1-11. [PMID: 36179939 DOI: 10.1016/j.biochi.2022.09.014] [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: 03/08/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 11/02/2022]
Abstract
Nucleic acids are an indispensable component in all known life forms. The biological processes are regulated by Nucleic acids, which associate to form special high-order structures. since the high-level structures of nucleic acids are related to gene expression in cancer cells or viruses, it is very likely to become a potential drug target. Traditional biochemical methods are limited to distinguish the conformational distribution and dynamic transition process of single nucleic acid structure. The ligands based on the intermediate and transition states between different conformations are not designed by traditional biochemical methods. The single-molecule techniques enable real-time observation of the individual nucleic acid behavior due to its high resolution. Here, we introduce the application of single-molecule techniques in the study of small molecules to recognize nucleic acid structures, such as single-molecule FRET, magnetic tweezers, optical tweezers and atomic force microscopy. At the same time, we also introduce the specific advantages of single-molecule technology compared with traditional biochemical methods and some problems arisen in current research.
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Affiliation(s)
- Junkang Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Congbao Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yanfei Tao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China; Interdisciplinary Sciences Institute, Huazhong Agricultural University, Wuhan 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Shenzhen 518000, China; Shenzhen Branch, Huazhong Agricultural University, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
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10
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Pavlova AV, Dolinnaya NG, Zvereva MI, Kubareva EA, Monakhova MV. New DNA Plasmid Model for Studying DNA Mismatch Repair Response to the G4 Structure. Int J Mol Sci 2023; 24:ijms24021061. [PMID: 36674575 PMCID: PMC9863064 DOI: 10.3390/ijms24021061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 12/27/2022] [Accepted: 12/31/2022] [Indexed: 01/08/2023] Open
Abstract
G-quadruplexes (G4s), the most widely studied alternative DNA structures, are implicated in the regulation of the key cellular processes. In recent years, their involvement in DNA repair machinery has become the subject of intense research. Here, we evaluated the effect of G4 on the prokaryotic DNA mismatch repair (MMR) pathway from two bacterial sources with different mismatch repair mechanisms. The G4 folding, which competes with the maintenance of double-stranded DNA, is known to be controlled by numerous opposing factors. To overcome the kinetic barrier of G4 formation, we stabilized a parallel G4 formed by the d(GGGT)4 sequence in a DNA plasmid lacking a fragment complementary to the G4 motif. Unlike commonly used isolated G4 structures, our plasmid with an embedded stable G4 structure contained elements, such as a MutH cleavage site, required to initiate the repair process. G4 formation in the designed construct was confirmed by Taq polymerase stop assay and dimethyl sulfate probing. The G4-carrying plasmid, together with control ones (lacking a looped area or containing unstructured d(GT)8 insert instead of the G4 motif), were used as new type models to answer the question of whether G4 formation interferes with DNA cleavage as a basic function of MMR.
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Affiliation(s)
- Anzhela V. Pavlova
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, Moscow 119991, Russia
| | - Nina G. Dolinnaya
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, Moscow 119991, Russia
| | - Maria I. Zvereva
- Department of Chemistry, Lomonosov Moscow State University, Leninskye Gory 1, Moscow 119991, Russia
| | - Elena A. Kubareva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, Moscow 119991, Russia
- Correspondence: ; Tel.: +7-(495)-939-54-11
| | - Mayya V. Monakhova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Leninskye Gory 1, Moscow 119991, Russia
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11
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Yuan JH, Tu JL, Liu GC, Chen XC, Huang ZS, Chen SB, Tan JH. Visualization of ligand-induced c-MYC duplex-quadruplex transition and direct exploration of the altered c-MYC DNA-protein interactions in cells. Nucleic Acids Res 2022; 50:4246-4257. [PMID: 35412611 PMCID: PMC9071431 DOI: 10.1093/nar/gkac245] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 03/27/2022] [Accepted: 03/29/2022] [Indexed: 01/03/2023] Open
Abstract
Ligand-Induced duplex-quadruplex transition within the c-MYC promoter region is one of the most studied and advanced ideas for c-MYC regulation. Despite its importance, there is a lack of methods for monitoring such process in cells, hindering a better understanding of the essence of c-MYC G-quadruplex as a drug target. Here we developed a new fluorescent probe ISCH-MYC for specific c-MYC G-quadruplex recognition based on GTFH (G-quadruplex-Triggered Fluorogenic Hybridization) strategy. We validated that ISCH-MYC displayed distinct fluorescence enhancement upon binding to c-MYC G-quadruplex, which allowed the duplex-quadruplex transition detection of c-MYC G-rich DNA in cells. Using ISCH-MYC, we successfully characterized the induction of duplex to G-quadruplex transition in the presence of G-quadruplex stabilizing ligand PDS and further monitored and evaluated the altered interactions of relevant transcription factors Sp1 and CNBP with c-MYC G-rich DNA. Thus, our study provides a visualization strategy to explore the mechanism of G-quadruplex stabilizing ligand action on c-MYC G-rich DNA and relevant proteins, thereby empowering future drug discovery efforts targeting G-quadruplexes.
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Affiliation(s)
- Jia-Hao Yuan
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jia-Li Tu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Guo-Cai Liu
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiu-Cai Chen
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhi-Shu Huang
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Shuo-Bin Chen
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Jia-Heng Tan
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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12
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Feng Y, Tao S, Zhang P, Sperti FR, Liu G, Cheng X, Zhang T, Yu H, Wang XE, Chen C, Monchaud D, Zhang W. Epigenomic features of DNA G-quadruplexes and their roles in regulating rice gene transcription. PLANT PHYSIOLOGY 2022; 188:1632-1648. [PMID: 34893906 PMCID: PMC8896617 DOI: 10.1093/plphys/kiab566] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/04/2021] [Indexed: 06/01/2023]
Abstract
A DNA G-quadruplex (G4) is a non-canonical four-stranded nucleic acid structure involved in many biological processes in mammals. The current knowledge on plant DNA G4s, however, is limited; whether and how DNA G4s impact gene expression in plants is still largely unknown. Here, we applied a protocol referred to as BG4-DNA-IP-seq followed by a comprehensive characterization of DNA G4s in rice (Oryza sativa L.); we next integrated dG4s (experimentally detectable G4s) with existing omics data and found that dG4s exhibited differential DNA methylation between transposable element (TE) and non-TE genes. dG4 regions displayed genic-dependent enrichment of epigenomic signatures; finally, we showed that these sites displayed a positive association with expression of DNA G4-containing genes when located at promoters, and a negative association when located in the gene body, suggesting localization-dependent promotional/repressive roles of DNA G4s in regulating gene transcription. This study reveals interrelations between DNA G4s and epigenomic signatures, as well as implicates DNA G4s in modulating gene transcription in rice. Our study provides valuable resources for the functional characterization or bioengineering of some of key DNA G4s in rice.
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Affiliation(s)
- Yilong Feng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Shentong Tao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Pengyue Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Francesco Rota Sperti
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Guanqing Liu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuejiao Cheng
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Tao Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology and Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Hengxiu Yu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | - Xiu-e Wang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
| | - Caiyan Chen
- Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, Hunan 410125, China
| | - David Monchaud
- Institut de Chimie Moleculaire, ICMUB, CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, JCIC-MCP, CIC-MCP, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu 210095, China
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13
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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: 1.5] [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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14
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I. V. Ramos C, A. S. Almodôvar V, Candeias N, Santos T, Cruz C, Graça P. M. S. Neves M, Tomé AC. Diketopyrrolo[3,4–c]pyrrole derivative as a promising ligand for the stabilization of G-quadruplex DNA structures. Bioorg Chem 2022; 122:105703. [DOI: 10.1016/j.bioorg.2022.105703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/11/2022]
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15
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Shokri E, Hosseini M, Boldaji MN, Shahsavar K, amiri-Sadeghan A, Nasiri N, Bahmani A, Ganjali MR, Saboury AA. A novel DNA/hemin complex with enzyme-like activity selected from a hairpin DNAs library at zero H2O2 concentration. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Detecting G4 unwinding. Methods Enzymol 2022; 672:261-281. [DOI: 10.1016/bs.mie.2022.03.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Teng FY, Jiang ZZ, Guo M, Tan XZ, Chen F, Xi XG, Xu Y. G-quadruplex DNA: a novel target for drug design. Cell Mol Life Sci 2021; 78:6557-6583. [PMID: 34459951 PMCID: PMC11072987 DOI: 10.1007/s00018-021-03921-8] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/13/2021] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
G-quadruplex (G4) DNA is a type of quadruple helix structure formed by a continuous guanine-rich DNA sequence. Emerging evidence in recent years authenticated that G4 DNA structures exist both in cell-free and cellular systems, and function in different diseases, especially in various cancers, aging, neurological diseases, and have been considered novel promising targets for drug design. In this review, we summarize the detection method and the structure of G4, highlighting some non-canonical G4 DNA structures, such as G4 with a bulge, a vacancy, or a hairpin. Subsequently, the functions of G4 DNA in physiological processes are discussed, especially their regulation of DNA replication, transcription of disease-related genes (c-MYC, BCL-2, KRAS, c-KIT et al.), telomere maintenance, and epigenetic regulation. Typical G4 ligands that target promoters and telomeres for drug design are also reviewed, including ellipticine derivatives, quinoxaline analogs, telomestatin analogs, berberine derivatives, and CX-5461, which is currently in advanced phase I/II clinical trials for patients with hematologic cancer and BRCA1/2-deficient tumors. Furthermore, since the long-term stable existence of G4 DNA structures could result in genomic instability, we summarized the G4 unfolding mechanisms emerged recently by multiple G4-specific DNA helicases, such as Pif1, RecQ family helicases, FANCJ, and DHX36. This review aims to present a general overview of the field of G-quadruplex DNA that has progressed in recent years and provides potential strategies for drug design and disease treatment.
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Affiliation(s)
- Fang-Yuan Teng
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zong-Zhe Jiang
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Man Guo
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiao-Zhen Tan
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Feng Chen
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xu-Guang Xi
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, 712100, Shaanxi, China.
- LBPA, Ecole Normale Supérieure Paris-Saclay, CNRS, Université Paris Saclay, 61, Avenue du Président Wilson, 94235, Cachan, France.
| | - Yong Xu
- Experimental Medicine Center, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Department of Endocrinology and Metabolism, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
- Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, and Sichuan Clinical Research Center for Nephropathy, and Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
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18
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Yang M, Carter S, Parmar S, Bume DD, Calabrese DR, Liang X, Yazdani K, Xu M, Liu Z, Thiele CJ, Schneekloth JS. Targeting a noncanonical, hairpin-containing G-quadruplex structure from the MYCN gene. Nucleic Acids Res 2021; 49:7856-7869. [PMID: 34289065 DOI: 10.1093/nar/gkab594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/10/2021] [Accepted: 07/20/2021] [Indexed: 11/12/2022] Open
Abstract
The MYCN gene encodes the transcription factor N-Myc, a driver of neuroblastoma (NB). Targeting G-quadruplexes (G4s) with small molecules is attractive strategy to control the expression of undruggable proteins such as N-Myc. However, selective binders to G4s are challenging to identify due to the structural similarity of many G4s. Here, we report the discovery of a small molecule ligand (4) that targets the noncanonical, hairpin containing G4 structure found in the MYCN gene using small molecule microarrays (SMMs). Unlike many G4 binders, the compound was found to bind to a pocket at the base of the hairpin region of the MYCN G4. This compound stabilizes the G4 and has affinity of 3.5 ± 1.6 μM. Moreover, an improved analog, MY-8, suppressed levels of both MYCN and MYCNOS (a lncRNA embedded within the MYCN gene) in NBEB neuroblastoma cells. This work indicates that the approach of targeting complex, hybrid G4 structures that exist throughout the human genome may be an applicable strategy to achieve selectivity for targeting disease-relevant genes including protein coding (MYCN) as well as non-coding (MYCNOS) gene products.
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Affiliation(s)
- Mo Yang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Sakereh Carter
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Shaifaly Parmar
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Desta D Bume
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - David R Calabrese
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Xiao Liang
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Kamyar Yazdani
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
| | - Man Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-1928, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA
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19
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Kharel P, Becker G, Tsvetkov V, Ivanov P. Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res 2020; 48:12534-12555. [PMID: 33264409 PMCID: PMC7736831 DOI: 10.1093/nar/gkaa1126] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/23/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine-quadruplexes (G4s) are non-canonical four-stranded structures that can be formed in guanine (G) rich nucleic acid sequences. A great number of G-rich sequences capable of forming G4 structures have been described based on in vitro analysis, and evidence supporting their formation in live cells continues to accumulate. While formation of DNA G4s (dG4s) within chromatin in vivo has been supported by different chemical, imaging and genomic approaches, formation of RNA G4s (rG4s) in vivo remains a matter of discussion. Recent data support the dynamic nature of G4 formation in the transcriptome. Such dynamic fluctuation of rG4 folding-unfolding underpins the biological significance of these structures in the regulation of RNA metabolism. Moreover, rG4-mediated functions may ultimately be connected to mechanisms underlying disease pathologies and, potentially, provide novel options for therapeutics. In this framework, we will review the landscape of rG4s within the transcriptome, focus on their potential impact on biological processes, and consider an emerging connection of these functions in human health and disease.
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Affiliation(s)
- Prakash Kharel
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Gertraud Becker
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Tsvetkov
- Computational Oncology Group, I. M. Sechenov First Moscow State Medical University, Moscow 119146, Russia
- Federal Research and Clinical Center for Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow 119435, Russia
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow 117912, Russia
| | - Pavel Ivanov
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Harvard Initiative for RNA Medicine, Boston, MA 02115, USA
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20
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Wang F, Wang C, Liu Y, Lan W, Wang R, Huang S, Cao C. NMR
Studies on the Interaction between Oncogene
RET
G‐Quadruplex
and Berberine
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Fei Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
| | - Chunxi Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
| | - Yaping Liu
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
| | - Wenxian Lan
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
| | - Renxiao Wang
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
| | - Shaohua Huang
- Institute of Drug Discovery Technology, Ningbo University No 818 Fenghua Road, Ningbo Zhejiang 315211 China
| | - Chunyang Cao
- State Key Laboratory of Bioorganic and Natural Product Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China
- University of Chinese Academy of Science No. 19A, Yuquan Road, Shijingshan District Beijing 100049 China
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21
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Responses of DNA Mismatch Repair Proteins to a Stable G-Quadruplex Embedded into a DNA Duplex Structure. Int J Mol Sci 2020; 21:ijms21228773. [PMID: 33233554 PMCID: PMC7699706 DOI: 10.3390/ijms21228773] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 12/26/2022] Open
Abstract
DNA mismatch repair (MMR) plays a crucial role in the maintenance of genomic stability. The main MMR protein, MutS, was recently shown to recognize the G-quadruplex (G4) DNA structures, which, along with regulatory functions, have a negative impact on genome integrity. Here, we studied the effect of G4 on the DNA-binding activity of MutS from Rhodobacter sphaeroides (methyl-independent MMR) in comparison with MutS from Escherichia coli (methyl-directed MMR) and evaluated the influence of a G4 on the functioning of other proteins involved in the initial steps of MMR. For this purpose, a new DNA construct was designed containing a biologically relevant intramolecular stable G4 structure flanked by double-stranded regions with the set of DNA sites required for MMR initiation. The secondary structure of this model was examined using NMR spectroscopy, chemical probing, fluorescent indicators, circular dichroism, and UV spectroscopy. The results unambiguously showed that the d(GGGT)4 motif, when embedded in a double-stranded context, adopts a G4 structure of a parallel topology. Despite strong binding affinities of MutS and MutL for a G4, the latter is not recognized by E. coli MMR as a signal for repair, but does not prevent MMR processing when a G4 and G/T mismatch are in close proximity.
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22
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Majee P, Shankar U, Pasadi S, Muniyappa K, Nayak D, Kumar A. Genome-wide analysis reveals a regulatory role for G-quadruplexes during Adenovirus multiplication. Virus Res 2020; 283:197960. [DOI: 10.1016/j.virusres.2020.197960] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
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23
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Jara-Espejo M, Fleming AM, Burrows CJ. Potential G-Quadruplex Forming Sequences and N6-Methyladenosine Colocalize at Human Pre-mRNA Intron Splice Sites. ACS Chem Biol 2020; 15:1292-1300. [PMID: 32396327 PMCID: PMC7309266 DOI: 10.1021/acschembio.0c00260] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Maturation of mRNA in humans involves modifying the 5' and 3' ends, splicing introns, and installing epitranscriptomic modifications that are essential for mRNA biogenesis. With respect to epitranscriptomic modifications, they are usually installed in specific consensus motifs, although not all sequences are modified suggesting a secondary structural component to site selection. Using bioinformatic analysis of published data, we identify in human mature-mRNA that potential RNA G-quadruplex (rG4) sequences colocalize with the epitranscriptomic modifications N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). Using the only available pre-mRNA data sets from the literature, we demonstrate colocalization of potential rG4s and m6A was greatest overall and occurred in introns near 5' and 3' splice sites. The loop lengths and sequence context of the m6A-bearing potential rG4s exhibited short loops most commonly comprised of single A nucleotides. This observation is consistent with a literature report of intronic m6A found in SAG (S = C or G) consensus motifs that are also recognized by splicing factors. The localization of m6A and potential rG4s in pre-mRNA at intron splice junctions suggests that these features could function together in alternative splicing. A similar analysis for potential rG4s around sites of Ψ installation or A-to-I editing in mRNA also found a colocalization; however, the frequency was less than that observed with m6A. These bioinformatic analyses guide a discussion of future experiments to understand how noncanonical rG4 structures may collaborate with epitranscriptomic modifications in the human cellular context to impact cellular phenotype.
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Affiliation(s)
- Manuel Jara-Espejo
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
- Department of Morphology, Piracicaba Dental School, University of Campinas-UNICAMP, Av. Limeira 901, Piracicaba, CEP 13414-018 Sao Paulo, Brazil
| | - Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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24
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Williams JD, Houserova D, Johnson BR, Dyniewski B, Berroyer A, French H, Barchie AA, Bilbrey DD, Demeis JD, Ghee KR, Hughes AG, Kreitz NW, McInnis CH, Pudner SC, Reeves MN, Stahly AN, Turcu A, Watters BC, Daly GT, Langley RJ, Gillespie MN, Prakash A, Larson ED, Kasukurthi MV, Huang J, Jinks-Robertson S, Borchert GM. Characterization of long G4-rich enhancer-associated genomic regions engaging in a novel loop:loop 'G4 Kissing' interaction. Nucleic Acids Res 2020; 48:5907-5925. [PMID: 32383760 PMCID: PMC7293029 DOI: 10.1093/nar/gkaa357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 12/27/2022] Open
Abstract
Mammalian antibody switch regions (∼1500 bp) are composed of a series of closely neighboring G4-capable sequences. Whereas numerous structural and genome-wide analyses of roles for minimal G4s in transcriptional regulation have been reported, Long G4-capable regions (LG4s)-like those at antibody switch regions-remain virtually unexplored. Using a novel computational approach we have identified 301 LG4s in the human genome and find LG4s prone to mutation and significantly associated with chromosomal rearrangements in malignancy. Strikingly, 217 LG4s overlap annotated enhancers, and we find the promoters regulated by these enhancers markedly enriched in G4-capable sequences suggesting G4s facilitate promoter-enhancer interactions. Finally, and much to our surprise, we also find single-stranded loops of minimal G4s within individual LG4 loci are frequently highly complementary to one another with 178 LG4 loci averaging >35 internal loop:loop complements of >8 bp. As such, we hypothesized (then experimentally confirmed) that G4 loops within individual LG4 loci directly basepair with one another (similar to characterized stem-loop kissing interactions) forming a hitherto undescribed, higher-order, G4-based secondary structure we term a 'G4 Kiss or G4K'. In conclusion, LG4s adopt novel, higher-order, composite G4 structures directly contributing to the inherent instability, regulatory capacity, and maintenance of these conspicuous genomic regions.
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Affiliation(s)
- Jonathan D Williams
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Bradley R Johnson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Brad Dyniewski
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Alexandra Berroyer
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Hannah French
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Addison A Barchie
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Dakota D Bilbrey
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Jeffrey D Demeis
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Kanesha R Ghee
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Alexandra G Hughes
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Naden W Kreitz
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Cameron H McInnis
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Susanna C Pudner
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Monica N Reeves
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ashlyn N Stahly
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Ana Turcu
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Brianna C Watters
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
| | - Grant T Daly
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Raymond J Langley
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Mark N Gillespie
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Aishwarya Prakash
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
- Department of Biochemistry and Molecular Biology, University of South Alabama, Mitchell Cancer Institute, Mobile, AL 36688, USA
| | - Erik D Larson
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
- Department of Biomedical Sciences, Western Michigan University Homer Stryker MD School of Medicine, Kalamazoo, MI 49007, USA
| | | | - Jingshan Huang
- School of Computing, University of South Alabama, Mobile, AL 36688, USA
| | - Sue Jinks-Robertson
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Glen M Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
- Department of Biology, University of South Alabama, Mobile, AL 36688, USA
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25
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He YD, Zheng KW, Wen CJ, Li XM, Gong JY, Hao YH, Zhao Y, Tan Z. Selective Targeting of Guanine-Vacancy-Bearing G-Quadruplexes by G-Quartet Complementation and Stabilization with a Guanine-Peptide Conjugate. J Am Chem Soc 2020; 142:11394-11403. [PMID: 32491844 DOI: 10.1021/jacs.0c00774] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Stabilization of G-quadruplexes (G4s) formed in guanine-rich (G-rich) nucleic acids by small-molecule ligands has been extensively explored as a therapeutic approach for diseases such as cancer. Finding ligands with sufficient affinity and specificity toward G4s remains a challenge, and many ligands reported seemed to compromise between the two features. To cope with this challenge, we focused on targeting a particular type of G4s, i.e., the G-vacancy-bearing G-quadruplexes (GVBQs), by taking a structure complementation strategy to enhance both affinity and selectivity. In this approach, a G-quadruplex-binding peptide RHAU23 is guided toward a GVBQ by a guanine moiety covalently linked to the peptide. The filling-in of the vacancy in a GVBQ by the guanine ensures an exclusive recognition of GVBQ. Moreover, the synergy between the RHAU23 and the guanine dramatically improves both the affinity toward and stabilization of the GVBQ. Targeting a GVBQ in DNA by this bifunctional peptide strongly suppresses in vitro replication. This study demonstrates a novel and promising alternative targeting strategy to a distinctive panel of G4s that are as abundant as the canonical ones in the human genome.
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Affiliation(s)
- Yi-de He
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Ke-Wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Cui-Jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Xin-Min Li
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Jia-Yuan Gong
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | - Yu-Hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
| | | | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China.,Center for Healthy Aging, Changzhi Medical College, Changzhi 046000, Shanxi, P. R. China
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26
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Wen CJ, Gong JY, Zheng KW, He YD, Zhang JY, Hao YH, Tan Z. Targeting nucleic acids with a G-triplex-to-G-quadruplex transformation and stabilization using a peptide-PNA G-tract conjugate. Chem Commun (Camb) 2020; 56:6567-6570. [PMID: 32396929 DOI: 10.1039/d0cc02102d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A dual-functional peptide-PNA (peptide nucleic acid) conjugate consisting of a PNA G3-tract and an RHAU23 peptide is devised to target nucleic acids bearing three tandem guanine tracts (G-tracts). The PNA G3-tract joins the three G-tracts to form a stable bimolecular G-quadruplex (G4) and the resulting G4 is then bound by the RHAU23 moiety to form an extra stable G4-peptide complex. Owing to this synergistic dual structural enforcement, the conjugate accomplished extremely high selectivity and nM to sub-nM affinities towards its targets that are up to 1000 times greater than the small molecule G4 ligands. As a result, the conjugate impacts the tracking activity of motor proteins on DNA with superior selectivity and potency that are rarely seen in other G4-targeting approaches.
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Affiliation(s)
- Cui-Jiao Wen
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China.
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27
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Zhang JY, Xia Y, Hao YH, Tan Z. DNA:RNA hybrid G-quadruplex formation upstream of transcription start site. Sci Rep 2020; 10:7429. [PMID: 32366914 PMCID: PMC7198591 DOI: 10.1038/s41598-020-64117-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 03/30/2020] [Indexed: 11/09/2022] Open
Abstract
Bioinformatic analysis reveals an enrichment of putative DNA:RNA hybrid G-quadruplex-forming sequences (PHQS) on both sides of the transcription start sites (TSSs) in the genome of warm-blooded animals, suggesting a positive selection of PHQSs in evolution and functional role of DNA:RNA hybrid G-quadruplexes (HQs) in transcription. The formation of HQs downstream of TSS in transcribed DNA has been documented under in vitro conditions; however, it is still not known if such HQs can form at the upstream side of TSSs. In this study, we report that such HQs can form in transcription in DNA with two to three guanine tracts if RNA carrying the required number of G-tracts is supplied. We also show that the formation of such HQs is dependent on the negative supercoiling generated by RNA polymerases. These results suggest that HQs may also form at the upstream side of TSSs in vivo and play a role in transcription since the two requirements are satisfied in cells.
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Affiliation(s)
- Jia-Yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China.,CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Multidisciplinary Research Division, Institute of High Energy Physics, Chinese Academy of Sciences (CAS), Beijing, 100049, P. R. China
| | - Ye Xia
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China
| | - Yu-Hua Hao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, P. R. China. .,Center for Healthy Aging, Changzhi Medical College, Changzhi, 046000, Shanxi, P. R. China.
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28
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Dey S, Sczepanski JT. In vitro selection of l-DNA aptamers that bind a structured d-RNA molecule. Nucleic Acids Res 2020; 48:1669-1680. [PMID: 31950158 PMCID: PMC7038948 DOI: 10.1093/nar/gkz1236] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/25/2019] [Accepted: 01/03/2020] [Indexed: 12/22/2022] Open
Abstract
The development of structure-specific RNA binding reagents remains a central challenge in RNA biochemistry and drug discovery. Previously, we showed in vitro selection techniques could be used to evolve l-RNA aptamers that bind tightly to structured d-RNAs. However, whether similar RNA-binding properties can be achieved using aptamers composed of l-DNA, which has several practical advantages compared to l-RNA, remains unknown. Here, we report the discovery and characterization of the first l-DNA aptamers against a structured RNA molecule, precursor microRNA-155, thereby establishing the capacity of DNA and RNA molecules of the opposite handedness to form tight and specific ‘cross-chiral’ interactions with each other. l-DNA aptamers bind pre-miR-155 with low nanomolar affinity and high selectivity despite the inability of l-DNA to interact with native d-RNA via Watson–Crick base pairing. Furthermore, l-DNA aptamers inhibit Dicer-mediated processing of pre-miRNA-155. The sequence and structure of l-DNA aptamers are distinct from previously reported l-RNA aptamers against pre-miR-155, indicating that l-DNA and l-RNA interact with the same RNA sequence through unique modes of recognition. Overall, this work demonstrates that l-DNA may be pursued as an alternative to l-RNA for the generation of RNA-binding aptamers, providing a robust and practical approach for targeting structured RNAs.
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Affiliation(s)
- Sougata Dey
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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29
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Peng S, Bie B, Jia H, Tang H, Zhang X, Sun Y, Wei Q, Wu F, Yuan Y, Deng H, Zhou X. Efficient Separation of Nucleic Acids with Different Secondary Structures by Metal-Organic Frameworks. J Am Chem Soc 2020; 142:5049-5059. [PMID: 32069054 DOI: 10.1021/jacs.9b10936] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the use of metal-organic frameworks (MOFs) for the selective separation of nucleic acids (DNA and RNA) with different secondary structures through size, shape, length, and capability of conformational transition. Three MOFs with precisely controlled pore environments, Co-IRMOF-74-II, -III, and -IV, composed of Co2+ and organic linkers (II, III, and IV), respectively, were used for the inclusion of nucleic acid into their pores from the solution. This was proven to be a spontaneous process from disordered free state to restricted ordered state via circular dichroism (CD) spectroscopy. Three critical factors were identified for their inclusion: (1) size selection induced by steric hindrance, (2) conformation transition energy selection induced by stability, and (3) molecular weight selection. These selection rules were used to extract nucleic acids with flexible and unstable secondary structures from complex mixtures of multiple nucleic acids, leaving those with rigid and stable secondary structures in the mother liquor. This provides the possibility to separate and enrich nucleic acids in bulk through their different structure feature, which is highly desirable in genome-wide structural measurement of nucleic acids. Unlike methods that rely on specific binding antibodies or ligand, this MOF method is capable of selecting all kinds of nucleic acids with similar secondary structure features; therefore, it is suitable for the handling of a large variety and quantity of nucleic acids at the same time. This method also has the potential to gather information about the folding stability of biomolecules with secondary structures.
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Affiliation(s)
- Shuang Peng
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Binglin Bie
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.,The Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Hongnan Jia
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.,The Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Heng Tang
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiong Zhang
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yuqing Sun
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Qi Wei
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Fan Wu
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yushu Yuan
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Hexiang Deng
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China.,The Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers-Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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30
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Kim N. The Interplay between G-quadruplex and Transcription. Curr Med Chem 2019; 26:2898-2917. [PMID: 29284393 PMCID: PMC6026074 DOI: 10.2174/0929867325666171229132619] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/22/2017] [Accepted: 12/21/2017] [Indexed: 12/25/2022]
Abstract
G4 DNA is a non-canonical DNA structure consisting of a stacked array of Gquartets held together by base pairing between guanine bases. The formation of G4 DNA requires a cluster of guanine-runs within a strand of DNA. Even though the chemistry of this remarkable DNA structure has been under investigation for decades, evidence supporting the biological relevance of G4 DNA has only begun to emerge and point to very important and conserved biological functions. This review will specifically focus on the interplay between transcription and G4 DNA and discuss two alternative but interconnected perspectives. The first part of the review will describe the evidence substantiating the intriguing idea that a shift in DNA structural conformation could be another layer of non-genetic or epigenetic regulator of gene expression and thereby an important determinant of cell fate. The second part will describe the recent genetic studies showing that those genomic loci containing G4 DNA-forming guanine-rich sequences are potential hotspots of genome instability and that the level and orientation of transcription is critical in the materialization of genome instability associated with these sequences.
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Affiliation(s)
- Nayun Kim
- Department of Microbiology and Molecular Genetics, The University of Texas Health Science Center at Houston; The University of Texas Graduate School of Biomedical Sciences, Houston, TX, United States
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31
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Identification of putative G-quadruplex DNA structures in S. pombe genome by quantitative PCR stop assay. DNA Repair (Amst) 2019; 82:102678. [DOI: 10.1016/j.dnarep.2019.102678] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/08/2019] [Accepted: 07/26/2019] [Indexed: 12/31/2022]
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32
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Weldon C, Dacanay JG, Gokhale V, Boddupally PVL, Behm-Ansmant I, Burley GA, Branlant C, Hurley LH, Dominguez C, Eperon IC. Specific G-quadruplex ligands modulate the alternative splicing of Bcl-X. Nucleic Acids Res 2019; 46:886-896. [PMID: 29156002 PMCID: PMC5778605 DOI: 10.1093/nar/gkx1122] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 10/26/2017] [Indexed: 12/23/2022] Open
Abstract
Sequences with the potential to form RNA G-quadruplexes (G4s) are common in mammalian introns, especially in the proximity of the 5′ splice site (5′SS). However, the difficulty of demonstrating that G4s form in pre-mRNA in functional conditions has meant that little is known about their effects or mechanisms of action. We have shown previously that two G4s form in Bcl-X pre-mRNA, one close to each of the two alternative 5′SS. If these G4s affect splicing but are in competition with other RNA structures or RNA binding proteins, then ligands that stabilize them would increase the proportion of Bcl-X pre-mRNA molecules in which either or both G4s had formed, shifting Bcl-X splicing. We show here that a restricted set of G4 ligands do affect splicing, that their activity and specificity are strongly dependent on their structures and that they act independently at the two splice sites. One of the ligands, the ellipticine GQC-05, antagonizes the major 5′SS that expresses the anti-apoptotic isoform of Bcl-X and activates the alternative 5′SS that expresses a pro-apoptotic isoform. We propose mechanisms that would account for these see-saw effects and suggest that these effects contribute to the ability of GQC-05 to induce apoptosis.
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Affiliation(s)
- Carika Weldon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Justine G Dacanay
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Vijay Gokhale
- College of Pharmacy and College of Pharmacy and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA
| | - Peda Venkat L Boddupally
- Fluoroorganic Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, Telangana 500 007, India
| | - Isabelle Behm-Ansmant
- IMoPA (Ingénierie Moléculaire et Physiopathologie Articulaire), UMR 7365 CNRS-UL, Biopôle de l'Université de Lorraine, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK
| | - Christiane Branlant
- IMoPA (Ingénierie Moléculaire et Physiopathologie Articulaire), UMR 7365 CNRS-UL, Biopôle de l'Université de Lorraine, 9 Avenue de la Forêt de Haye, 54505 Vandoeuvre-lès-Nancy, France
| | - Laurence H Hurley
- College of Pharmacy and College of Pharmacy and BIO5 Institute, University of Arizona, Tucson, AZ 85721, USA.,Arizona Cancer Center, University of Arizona, Tucson, AZ 85724, USA
| | - Cyril Dominguez
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ian C Eperon
- Leicester Institute of Structural & Chemical Biology and Department of Molecular & Cell Biology, University of Leicester, Leicester LE1 7RH, UK
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33
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Bulged and Canonical G-Quadruplex Conformations Determine NDPK Binding Specificity. Molecules 2019; 24:molecules24101988. [PMID: 31126138 PMCID: PMC6572678 DOI: 10.3390/molecules24101988] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/20/2019] [Accepted: 05/22/2019] [Indexed: 11/17/2022] Open
Abstract
Guanine-rich DNA strands can adopt tertiary structures known as G-quadruplexes (G4s) that form when Hoogsteen base-paired guanines assemble as planar stacks, stabilized by a central cation like K+. In this study, we investigated the conformational heterogeneity of a G-rich sequence from the 5′ untranslated region of the Zea mayshexokinase4 gene. This sequence adopted an extensively polymorphic G-quadruplex, including non-canonical bulged G-quadruplex folds that co-existed in solution. The nature of this polymorphism depended, in part, on the incorporation of different sets of adjacent guanines into a quadruplex core, which permitted the formation of the different conformations. Additionally, we showed that the maize homolog of the human nucleoside diphosphate kinase (NDPK) NM23-H2 protein—ZmNDPK1—specifically recognizes and promotes formation of a subset of these conformations. Heteromorphic G-quadruplexes play a role in microorganisms’ ability to evade the host immune system, so we also discuss how the underlying properties that determine heterogeneity of this sequence could apply to microorganism G4s.
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34
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Mandal S, Kawamoto Y, Yue Z, Hashiya K, Cui Y, Bando T, Pandey S, Hoque ME, Hossain MA, Sugiyama H, Mao H. Submolecular dissection reveals strong and specific binding of polyamide-pyridostatin conjugates to human telomere interface. Nucleic Acids Res 2019; 47:3295-3305. [PMID: 30820532 PMCID: PMC6468309 DOI: 10.1093/nar/gkz135] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 02/13/2019] [Accepted: 02/26/2019] [Indexed: 01/20/2023] Open
Abstract
To modulate biological functions, G-quadruplexes in genome are often non-specifically targeted by small molecules. Here, specificity is increased by targeting both G-quadruplex and its flanking duplex DNA in a naturally occurring dsDNA-ssDNA telomere interface using polyamide (PA) and pyridostatin (PDS) conjugates (PA-PDS). We innovated a single-molecule assay in which dissociation constant (Kd) of the conjugate can be separately evaluated from the binding of either PA or PDS. We found Kd of 0.8 nM for PA-PDS, which is much lower than PDS (Kd ∼ 450 nM) or PA (Kd ∼ 35 nM). Functional assays further indicated that the PA-PDS conjugate stopped the replication of a DNA polymerase more efficiently than PA or PDS. Our results not only established a new method to dissect multivalent binding into actions of individual monovalent components, they also demonstrated a strong and specific G-quadruplex targeting strategy by conjugating highly specific duplex-binding molecules with potent quadruplex ligands.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Zhizhou Yue
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | - Kaori Hashiya
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Yunxi Cui
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 94 Weijin Road, Tianjin 300071, China
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH 44242, USA
| | | | | | - 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 & Biochemistry, Kent State University, Kent, OH 44242, USA
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35
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Redstone SCJ, Fleming AM, Burrows CJ. Oxidative Modification of the Potential G-Quadruplex Sequence in the PCNA Gene Promoter Can Turn on Transcription. Chem Res Toxicol 2019; 32:437-446. [PMID: 30604962 DOI: 10.1021/acs.chemrestox.8b00332] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Because of its low redox potential, guanine (G) is the most frequent site of oxidation in the genome. Metabolic processes generate reactive oxygen species (ROS) that can oxidize G to yield 8-oxo-7,8-dihydroguanine (OG) as a key two-electron oxidation product. In a genome, G-rich sites including many gene promoters are sensitive to oxidative modification, and some of these regions have the propensity to form G-quadruplexes (G4s). Recently, OG formation in G-rich gene promoters was demonstrated to regulate mRNA expression via the base excision repair (BER) pathway. The proliferating cell nuclear antigen ( PCNA) gene was previously found to be activated by metabolic ROS, and the gene has a five G-track potential G4 in the coding strand of its promoter. Herein, we demonstrated the ability for four G runs of the PCNA promoter sequence to adopt a parallel-stranded G4. Next, we identified G nucleotides in the PCNA G4 sequence sensitive to oxidative modification. The G oxidation product OG and its initial BER product, an abasic site, were synthetically incorporated into the four- and five-track PCNA sequences at the sensitive sites followed by interrogation of G4 folding by five methods. We found the modifications impacted the G4 folds with positional dependency. Additionally, the fifth G track maintained the stability of the modified G4s by extrusion of the oxidatively modified G run. Finally, we synthetically inserted a portion of the promoter into a reporter plasmid with OG at select oxidation-prone positions to monitor expression in human glioblastoma cells. Our results demonstrate that OG formation in the context of the PCNA G4 can lead to increased gene expression consistent with the previous studies identifying that metabolic ROS activates transcription of the gene. This study provides another example of a G4 with the potential to serve as a regulatory agent for gene expression upon G oxidation.
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Affiliation(s)
- Samuel C J Redstone
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Aaron M Fleming
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
| | - Cynthia J Burrows
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112-0850 , United States
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Abstract
The genome-wide occurrence of G-quadruplexes and their demonstrated biological activities call for detailed understanding on the stability and transition kinetics of the structures. Although the core structural element in a G-quadruplex is simple and requires only four tandem repeats of Guanine rich sequences, there is rather rich conformational diversity in this structure. Corresponding to this structural diversity, it displays involved transition kinetics within individual G-quadruplexes and complicated interconversion among different G-quadruplex species. Due to the inherently high signal-to-noise ratio in the measurement, single-molecule tools offer a unique capability to investigate the thermodynamic, kinetic, and mechanical properties of G-quadruplexes with dynamic conformations. In this chapter, we describe different single molecule methods such as atomic-force microscopy (AFM), single-molecule fluorescence resonance energy transfer (smFRET), optical, magnetic, and magneto-optical tweezers to investigate G-quadruplex structures as well as their interactions with small-molecule ligands.
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Affiliation(s)
- Shankar Mandal
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA
| | | | - Hanbin Mao
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, USA.
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37
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Onel B, Wu G, Sun D, Lin C, Yang D. Electrophoretic Mobility Shift Assay and Dimethyl Sulfate Footprinting for Characterization of G-Quadruplexes and G-Quadruplex-Protein Complexes. Methods Mol Biol 2019; 2035:201-222. [PMID: 31444751 DOI: 10.1007/978-1-4939-9666-7_11] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA G-quadruplexes are globular nucleic acid secondary structures which occur throughout the human genome under physiological conditions. There is accumulating evidence supporting G-quadruplex involvement in a number of important aspects of genome functions, including transcription, replication, and genomic stability, and that protein and enzyme recognition of G-quadruplexes may represent a key event to regulate physiological or pathological pathways. Two important techniques to study G-quadruplexes and their protein interactions are the electrophoretic mobility shift assay (EMSA) and dimethyl sulfate (DMS) footprinting assay. EMSA, one of the most sensitive and robust methods for studying the DNA-protein interactions, can be used to determine the binding parameters and relative affinities of a protein for the G-quadruplex. DMS footprinting is a powerful assay for the initial characterization of G-quadruplexes, which can be used to deduce the guanine bases involved in the formation of G-tetrads under physiological salt conditions. DMS footprinting can also reveal important information in G-quadruplex-protein complexes on protein contacts and regional changes in DNA G-quadruplex upon protein binding. In this paper, we will provide a detailed protocol for the EMSA and DMS footprinting assays for characterization of G-quadruplexes and G-quadruplex-protein complexes. Expected outcomes and references to extensions of the method will be further discussed.
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Affiliation(s)
- Buket Onel
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Guanhui Wu
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Daekyu Sun
- University of Arizona, College of Pharmacy, Tucson, AZ, USA.,BIO5 Institute, Tucson, AZ, USA.,Arizona Cancer Center, Tucson, AZ, USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA
| | - Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN, USA. .,Purdue Center for Cancer Research, West Lafayette, IN, USA. .,Purdue Institute for Drug Discovery, West Lafayette, IN, USA.
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38
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Zheng KW, Zhang JY, Tan Z. Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA. Methods Mol Biol 2019; 2035:243-255. [PMID: 31444754 DOI: 10.1007/978-1-4939-9666-7_14] [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: 06/10/2023]
Abstract
In vitro transcription of double-stranded DNA (dsDNA) induces a formation of two types of G-quadruplexes, intramolecular DNA G-quadruplexes or DNA:RNA hybrid G-quadruplexes, in clusters of guanine tracts. The formation of G-quadruplexes can be characterized by native PEG polyacrylamide gel electrophoresis, DMS footprinting, and ligand-induced photocleavage footprinting. The type of G-quadruplexes can be distinguished by transcription with 7-deaza-GTP (dzGTP) or 4-thio-uridine-5'-triphosphate (4SU) to detect the participation of RNA transcript.
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Affiliation(s)
- Ke-Wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.
| | - Jia-Yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
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39
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Smith-Carpenter JE, Taylor JS. Photocrosslinking of G-Quadruplex-Forming Sequences found in Human Promoters. Photochem Photobiol 2018; 95:252-266. [PMID: 30084501 DOI: 10.1111/php.12991] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/05/2018] [Indexed: 01/28/2023]
Abstract
While is it well known that human telomeric DNA sequences can adopt G-quadruplex structures, some promoters sequences have also been found to form G-quadruplexes, and over 40% of promoters contain putative G-quadruplex-forming sequences. Because UV light has been shown to crosslink human telomeric G-quadruplexes by cyclobutane pyrimidine dimer (CPD) formation between T's on adjacent loops, UV light might also be able to photocrosslink G-quadruplexes in promoters. To investigate this possibility, 15 potentially UV-crosslinkable G-quadruplex-forming sequences found in a search of human DNA promoters were UVB irradiated in vitro, and three were confirmed to have formed nonadjacent CPDs by mass spectrometry. In addition to nonadjacent T=T CPDs found in human telomeric DNA, a nonadjacent T=U CPD was discovered that presumably arose from deamination of a nonadjacent T=C CPD. Analysis of the three sequences by circular dichroism, melting temperature analysis and chemical footprinting confirmed the presence of G-quadruplexes that could explain the formation of the nonadjacent CPDs. The formation of nonadjacent CPDs from the sequences in vitro suggests that they might be useful probes for the presence of non-B DNA structures, such as G-quadruplexes, in vivo, and if they were to form in vivo, might also have significant biological consequences.
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40
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Kumari B, Kumari R, Das P. Visual detection of G-quadruplex with mushroom derived highly fluorescent carbon quantum dots. J Pharm Biomed Anal 2018; 157:137-144. [DOI: 10.1016/j.jpba.2018.05.013] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 01/04/2023]
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41
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Zhao Y, Uhler JP. Identification of a G-quadruplex forming sequence in the promoter of UCP1. Acta Biochim Biophys Sin (Shanghai) 2018; 50:718-722. [PMID: 29796650 DOI: 10.1093/abbs/gmy059] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 05/04/2018] [Indexed: 11/14/2022] Open
Abstract
G-quadruplexes are higher-order nucleic acid structures formed in G-rich sequences in DNA or RNA. G-quadruplexes are distributed in many locations in the human genome, including promoter regions, and are viewed as promising therapeutic targets. Uncoupling protein-1 (UCP1) is a mitochondrial thermogenic gene critical for energy expenditure in the form of heat in the brown adipose tissue. UCP1 is only expressed during brown fat cell differentiation and is a candidate target for treating obesity. However, the regulation of UCP1 expression is not clear. We reported here that a G-quadruplex forming sequence exists in the promoter of UCP1. The 5,10,15,20-tetra(N-methyl-4-pyridyl) porphyrin (TMPyP4) enhanced cellular expression of UCP1 and destabilized the G-quadruplex formed by the sequence from the promoter of UCP1. Mutations in the G-quadruplex regulated the cellular activity of UCP1 promoter as evidenced by a UCP1-promoter luciferase assay. These results suggest that G-quadruplex structure is a potential target to regulate the expression of UCP1.
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Affiliation(s)
- Yuanbo Zhao
- Department of Chemical Biology, School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Jay P Uhler
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
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42
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Kaboudin B, Saghatchi F, Kazemi F, Akbari-Birgani S. A Novel Magnetic Carbon Nanotubes Functionalized with Pyridine Groups: Synthesis, Characterization and Their Application as an Efficient Carrier for Plasmid DNA and Aptamer. ChemistrySelect 2018. [DOI: 10.1002/slct.201800708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Babak Kaboudin
- Department of Chemistry; Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang; Zanjan 45137-66731 Iran
- Center for Research in Basic Sciences and Contemporary Technologies
| | - Fatemeh Saghatchi
- Department of Chemistry; Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang; Zanjan 45137-66731 Iran
| | - Foad Kazemi
- Department of Chemistry; Institute for Advanced Studies in Basic Sciences (IASBS), Gava Zang; Zanjan 45137-66731 Iran
| | - Shiva Akbari-Birgani
- Center for Research in Basic Sciences and Contemporary Technologies
- Faculty of Biological Sciences; Institute for Advanced Studies in Basic Sciences (IASBS), GavaZang; Zanjan 45137-66731 Iran
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43
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Biswas B, Kumari P, Vivekanandan P. Pac1 Signals of Human Herpesviruses Contain a Highly Conserved G-Quadruplex Motif. ACS Infect Dis 2018; 4:744-751. [PMID: 29493219 DOI: 10.1021/acsinfecdis.7b00279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Packaging signals ( pac1 and pac2) of human herpesviruses (HHVs) that contain GC-rich elements are essential for cleavage and packaging of the virus. Here, we report the presence of putative G-quadruplex sequences (PQSs) in the packaging signal ( pac1) of all HHVs. Importantly, the residues critical for the formation of G-quadruplex structures were highly conserved as compared to those not critical for the formation of this DNA secondary structure, indicating that G-quadruplexes are positively selected within pac1 in the evolution of herpesviruses. CD spectroscopy, NMR spectroscopy, native/denaturing gel, and DMS footprinting confirmed the formation of G-quadruplex structures in all pac1 PQS oligonucleotides analyzed; the majority of the PQS had the propensity to form intermolecular structures. The presence of highly conserved G-quadruplex motifs at genomic locations critical for virus packaging has not been previously recognized. Our findings provide a new perspective on the putative functions of G-quadruplexes in virus genomes.
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Affiliation(s)
- Banhi Biswas
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
| | - Pooja Kumari
- International Centre for Genetic Engineering and Biotechnology, New Delhi, Delhi 110067, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, Delhi 110016, India
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44
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Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications. J Nucleic Acids 2018; 2018:5307106. [PMID: 29666699 PMCID: PMC5831849 DOI: 10.1155/2018/5307106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/25/2017] [Accepted: 11/05/2017] [Indexed: 02/06/2023] Open
Abstract
Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.
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45
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Fleming AM, Zhu J, Ding Y, Visser JA, Zhu J, Burrows CJ. Human DNA Repair Genes Possess Potential G-Quadruplex Sequences in Their Promoters and 5'-Untranslated Regions. Biochemistry 2018; 57:991-1002. [PMID: 29320161 DOI: 10.1021/acs.biochem.7b01172] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The cellular response to oxidative stress includes transcriptional changes, particularly for genes involved in DNA repair. Recently, our laboratory demonstrated that oxidation of 2'-deoxyguanosine (G) to 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) in G-rich potential G-quadruplex sequences (PQSs) in gene promoters impacts the level of gene expression up or down depending on the position of the PQS in the promoter. In the present report, bioinformatic analysis found that the 390 human DNA repair genes in the genome ontology initiative harbor 2936 PQSs in their promoters and 5'-untranslated regions (5'-UTRs). The average density of PQSs in human DNA repair genes was found to be nearly 2-fold greater than the average density of PQSs in all coding and noncoding human genes (7.5 vs 4.3 per gene). The distribution of the PQSs in the DNA repair genes on the nontranscribed (coding) vs transcribed strands reflects that of PQSs in all human genes. Next, literature data were interrogated to select 30 PQSs to catalog their ability to adopt G-quadruplex (G4) folds in vitro using five different experimental tests. The G4 characterization experiments concluded that 26 of the 30 sequences could adopt G4 topologies in solution. Last, four PQSs were synthesized into the promoter of a luciferase plasmid and cotransfected with the G4-specific ligands pyridostatin, Phen-DC3, or BRACO-19 in human cells to determine whether the PQSs could adopt G4 folds. The cell studies identified changes in luciferase expression when the G4 ligands were present, and the magnitude of the expression changes dependent on the PQS and the coding vs template strand on which the sequence resided. Our studies demonstrate PQSs exist at a high density in human DNA repair gene promoters and a subset of the identified sequences may fold in vitro and in vivo.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Judy Zhu
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Yun Ding
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Joshua A Visser
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Julia Zhu
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah , Salt Lake City, Utah 84112-0850, United States
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46
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Onel B, Carver M, Agrawal P, Hurley LH, Yang D. The 3'-end region of the human PDGFR-β core promoter nuclease hypersensitive element forms a mixture of two unique end-insertion G-quadruplexes. Biochim Biophys Acta Gen Subj 2017; 1862:846-854. [PMID: 29288770 DOI: 10.1016/j.bbagen.2017.12.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/16/2017] [Accepted: 12/22/2017] [Indexed: 11/30/2022]
Abstract
BACKGROUND While the most stable G-quadruplex formed in the human PDGFR-β promoter nuclease hypersensitive element (NHE) is the 5'-mid G-quadruplex, the 3'-end sequence that contains a 3'-GGA run forms a less stable G-quadruplex. Recently, the 3'-end G-quadruplex was found to be a transcriptional repressor and can be selectively targeted by a small molecule for PDGFR-β downregulation. METHOD We use 1D and 2D high-field NMR, in combination with Dimethylsulfate Footprinting, Circular Dichroism Spectroscopy, and Electrophoretic Mobility Shift Assay. RESULTS We determine that the PDGFR-β extended 3'-end NHE sequence forms two novel end-insertion intramolecular G-quadruplexes that co-exist in equilibrium under physiological salt conditions. One G-quadruplex has a 3'-non-adjacent flanking guanine inserted into the 3'-external tetrad (3'-insertion-G4), and another has a 5'-non-adjacent flanking guanine inserted into the 5'-external tetrad (5'-insertion-G4). The two guanines in the GGA-run move up or down within the G-quadruplex to accommodate the inserted guanine. Each end-insertion G-quadruplex has a low thermal stability as compared to the 5'-mid G-quadruplex, but the selective stabilization of GSA1129 shifts the equilibrium toward the 3'-end G-quadruplex in the PDGFR-β NHE. CONCLUSION An equilibrium mixture of two unique end-insertion intramolecular G-quadruplexes forms in the PDGFR-β NHE 3'-end sequence that contains a GGA-run and non-adjacent guanines in both the 3'- and 5'- flanking segments; the novel end-insertion structures of the 3'-end G-quadruplex are selectively stabilized by GSA1129. GENERAL SIGNIFICANCE We show for the first time that an equilibrium mixture of two unusual end-insertion G-quadruplexes forms in a native promoter sequence and appears to be the molecular recognition for PDGFR-β downregulation.
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Affiliation(s)
- Buket Onel
- Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave, West Lafayette, IN 47907, USA
| | - Megan Carver
- University of Arizona, College of Pharmacy, 1703 East Mabel Street, Tucson, AZ 85721, USA
| | - Prashansa Agrawal
- Case Western Reserve University, Department of Chemistry, Cleveland, OH 44106, USA
| | - Laurence H Hurley
- University of Arizona, College of Pharmacy, 1703 East Mabel Street, Tucson, AZ 85721, USA; BIO5 Institute, 1657 East Helen Street, Tucson, AZ 85721, USA; Arizona Cancer Center, 1515 North Campbell Avenue, Tucson, AZ 85724, USA
| | - Danzhou Yang
- Purdue University, College of Pharmacy, Medicinal Chemistry and Molecular Pharmacology, 575 W Stadium Ave, West Lafayette, IN 47907, USA; Purdue University, Center for Cancer Research, 201 S University St, West Lafayette, IN 47906, USA; Purdue Institute for Drug Discovery, 720 Clinic Dr, West Lafayette, IN 47907, USA.
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47
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Greco ML, Kotar A, Rigo R, Cristofari C, Plavec J, Sissi C. Coexistence of two main folded G-quadruplexes within a single G-rich domain in the EGFR promoter. Nucleic Acids Res 2017; 45:10132-10142. [PMID: 28973461 PMCID: PMC5737278 DOI: 10.1093/nar/gkx678] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/22/2017] [Indexed: 12/15/2022] Open
Abstract
EGFR is an oncogene which codifies for a tyrosine kinase receptor that represents an important target for anticancer therapy. Indeed, several human cancers showed an upregulation of the activity of this protein. The promoter of this gene contains some G-rich domains, thus representing a yet unexplored point of intervention to potentially silence this gene. Here, we explore the conformational equilibria of a 30-nt long sequence located at position −272 (EGFR-272). By merging spectroscopic and electrophoretic analysis performed on the wild-type sequence as well as on a wide panel of related mutants, we were able to prove that in potassium ion containing solution this sequence folds into two main G-quadruplex structures, one parallel and one hybrid. They show comparable thermal stabilities and affinities for the metal ion and, indeed, they are always co-present in solution. The folding process is driven by a hairpin occurring in the domain corresponding to the terminal loop which works as an important stabilizing element for both the identified G-quadruplex arrangements.
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Affiliation(s)
- Maria L Greco
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
| | - Anita Kotar
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
| | - Camilla Cristofari
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
| | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,EN-FIST Center of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, v. Marzolo 5, Padova 35131, Italy
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48
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Teng FY, Hou XM, Fan SH, Rety S, Dou SX, Xi XG. Escherichia coli DNA polymerase I can disrupt G-quadruplex structures during DNA replication. FEBS J 2017; 284:4051-4065. [PMID: 28986969 DOI: 10.1111/febs.14290] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 08/24/2017] [Accepted: 10/03/2017] [Indexed: 12/14/2022]
Abstract
Non-canonical four-stranded G-quadruplex (G4) DNA structures can form in G-rich sequences that are widely distributed throughout the genome. The presence of G4 structures can impair DNA replication by hindering the progress of replicative polymerases (Pols), and failure to resolve these structures can lead to genetic instability. In the present study, we combined different approaches to address the question of whether and how Escherichia coli Pol I resolves G4 obstacles during DNA replication and/or repair. We found that E. coli Pol I-catalyzed DNA synthesis could be arrested by G4 structures at low protein concentrations and the degree of inhibition was strongly dependent on the stability of the G4 structures. Interestingly, at high protein concentrations, E. coli Pol I was able to overcome some kinds of G4 obstacles without the involvement of other molecules and could achieve complete replication of G4 DNA. Mechanistic studies suggested that multiple Pol I proteins might be implicated in G4 unfolding, and the disruption of G4 structures requires energy derived from dNTP hydrolysis. The present work not only reveals an unrealized function of E. coli Pol I, but also presents a possible mechanism by which G4 structures can be resolved during DNA replication and/or repair in E. coli.
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Affiliation(s)
- Fang-Yuan Teng
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - San-Hong Fan
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China
| | - Stephane Rety
- Univ Lyon, ENS de Lyon, Univ Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, Lyon, France
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, China.,LBPA, Ecole normale supérieure Paris-Saclay, CNRS, Université Paris Saclay, Cachan, France
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49
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Qiao Q, Wang L, Meng FL, Hwang JK, Alt FW, Wu H. AID Recognizes Structured DNA for Class Switch Recombination. Mol Cell 2017; 67:361-373.e4. [PMID: 28757211 PMCID: PMC5771415 DOI: 10.1016/j.molcel.2017.06.034] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/03/2017] [Accepted: 06/27/2017] [Indexed: 12/27/2022]
Abstract
Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro. By solving crystal structures of maltose binding protein (MBP)-fused AID alone and in complex with deoxycytidine monophosphate, we surprisingly identify a bifurcated substrate-binding surface that explains structured substrate recognition by capturing two adjacent single-stranded overhangs simultaneously. Moreover, G4 substrates induce cooperative AID oligomerization. Structure-based mutations that disrupt bifurcated substrate recognition or oligomerization both compromise CSR in splenic B cells. Collectively, our data implicate intrinsic preference of AID for structured substrates and uncover the importance of G4 recognition and oligomerization of AID in CSR.
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Affiliation(s)
- Qi Qiao
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Li Wang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Fei-Long Meng
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Joyce K Hwang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Frederick W Alt
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
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50
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Harkness RW, Mittermaier AK. G-quadruplex dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017. [PMID: 28642152 DOI: 10.1016/j.bbapap.2017.06.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations. The impact of these dynamics on biological function is currently not well understood. Recently, structural dynamics have been demonstrated to entropically stabilize GQ ensembles, potentially modulating gene expression. Transient, low-populated states in GQ ensembles may additionally regulate nucleic acid interactions and function. This review will underscore the interplay of GQ dynamics and biological function, focusing on several dynamic processes for biological GQs and the characterization of GQ dynamics by nuclear magnetic resonance (NMR) spectroscopy in conjunction with other biophysical techniques. This article is part of a Special Issue entitled: Biophysics in Canada, edited by Lewis Kay, John Baenziger, Albert Berghuis and Peter Tieleman.
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Affiliation(s)
- Robert W Harkness
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada
| | - Anthony K Mittermaier
- McGill University Department of Chemistry, 801 Sherbrooke St. W., Montreal, QC H3A 0B8, Canada.
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