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Xu Y, Komiyama M. G-Quadruplexes in Human Telomere: Structures, Properties, and Applications. Molecules 2023; 29:174. [PMID: 38202757 PMCID: PMC10780218 DOI: 10.3390/molecules29010174] [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: 11/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024] Open
Abstract
G-quadruplexes, intricate four-stranded structures composed of G-tetrads formed by four guanine bases, are prevalent in both DNA and RNA. Notably, these structures play pivotal roles in human telomeres, contributing to essential cellular functions. Additionally, the existence of DNA:RNA hybrid G-quadruplexes adds a layer of complexity to their structural diversity. This review provides a comprehensive overview of recent advancements in unraveling the intricacies of DNA and RNA G-quadruplexes within human telomeres. Detailed insights into their structural features are presented, encompassing the latest developments in chemical approaches designed to probe these G-quadruplex structures. Furthermore, this review explores the applications of G-quadruplex structures in targeting human telomeres. Finally, the manuscript outlines the imminent challenges in this evolving field, setting the stage for future investigations.
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Affiliation(s)
- Yan Xu
- Division of Chemistry, Department of Medical Sciences, Faculty of Medicine, University of Miyazaki, 5200 Kihara, Kiyotake, Miyazaki 889-1692, Japan
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan
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2
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Malina J, Kostrhunova H, Scott P, Brabec V. Metallohelices stabilize DNA three-way junctions and induce DNA damage in cancer cells. Nucleic Acids Res 2023; 51:7174-7183. [PMID: 37351627 PMCID: PMC10415117 DOI: 10.1093/nar/gkad536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/24/2023] Open
Abstract
DNA three-way junctions (3WJ) represent one of the simplest supramolecular DNA structures arising as intermediates in homologous recombination in the absence of replication. They are also formed transiently during DNA replication. Here we examine the ability of Fe(II)-based metallohelices to act as DNA 3WJ binders and induce DNA damage in cells. We investigated the interaction of eight pairs of enantiomerically pure Fe(II) metallohelices with four different DNA junctions using biophysical and molecular biology methods. The results show that the metallohelices stabilize all types of tested DNA junctions, with the highest selectivity for the Y-shaped 3WJ and minimal selectivity for the 4WJ. The potential of the best stabilizer of DNA junctions and, at the same time, the most selective 3WJ binder investigated in this work to induce DNA damage was determined in human colon cancer HCT116 cells. These metallohelices proved to be efficient in killing cancer cells and triggering DNA damage that could yield therapeutic benefits.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
| | - Hana Kostrhunova
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, Brno, CZ-61200, Czech Republic
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Lin H, Zheng W, Li S, Wang Y, Wei D, Xie L, Lu W, Tian Z, Wang S, Qu J, Liu J. Internet of medical things-enabled CRISPR diagnostics for rapid detection of SARS-CoV-2 variants of concern. Front Microbiol 2022; 13:1070940. [PMID: 36466682 PMCID: PMC9715597 DOI: 10.3389/fmicb.2022.1070940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 10/31/2022] [Indexed: 02/12/2024] Open
Abstract
Previous studies have highlighted CRISPR-based nucleic acid detection as rapid and sensitive diagnostic methods for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here, we reported an optimized CRISPR-Cas12a diagnostic platform for the safe and rapid detection of SARS-CoV-2 variants of concern (VOCs). This platform, which was referred to as CALIBURN-v2, could complete the diagnosis on extracted RNA samples within 25 min in a closed-lid reaction mode and had 100-fold increase in detection sensitivity in comparison with previous platforms. Most importantly, by integrating a portable device and smartphone user interface, CALIBURN-v2 allowed for cloud server-based data collection and management, thus transforming the point-of-care testing (POCT) platform to internet of medical things (IoMT) applications. It was found that IoMT-enabled CALIBURN-v2 could achieve 95.56% (172 out of 180) sensitivity for SARS-CoV-2 wild type and 94.38% (84 out of 89) overall sensitivity for SARS-CoV-2 variants including Delta and Omicron strains. Therefore, our study provides a feasible approach for IoMT-enabled CRISPR diagnostics for the detection of SARS-CoV-2 VOCs.
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Affiliation(s)
- Huihuang Lin
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Weibo Zheng
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Yu Wang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Dong Wei
- Department of Infectious Diseases, Research Laboratory of Clinical Virology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leiying Xie
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wei Lu
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, China
| | - Shaowei Wang
- State Key Laboratory of Infrared Physics, Shanghai Institute of Technical Physics, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Clinical Research and Trial Center, Shanghai, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, Guangdong, China
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Rossi F, Paiardini A. A Machine Learning Perspective on DNA and RNA G-quadruplexes. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220224105702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Abstract:
G-quadruplexes (G4s) are particular structures found in guanine-rich DNA and RNA sequences that exhibit a wide diversity of three-dimensional conformations and exert key functions in the control of gene expression. G4s are able to interact with numerous small molecules and endogenous proteins, and their dysregulation can lead to a variety of disorders and diseases. Characterization and prediction of G4-forming sequences could elucidate their mechanism of action and could thus represent an important step in the discovery of potential therapeutic drugs. In this perspective, we propose an overview of G4s, discussing the state of the art of methodologies and tools developed to characterize and predict the presence of these structures in genomic sequences. In particular, we report on machine learning (ML) approaches and artificial neural networks (ANNs) that could open new avenues for the accurate analysis of quadruplexes, given their potential to derive informative features by learning from large, high-density datasets.
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Affiliation(s)
- Fabiana Rossi
- Department of Biochemical Sciences \'A. Rossi Fanelli\', University of Rome La Sapienza, Rome, Italy
| | - Alessandro Paiardini
- Department of Biochemical Sciences \'A. Rossi Fanelli\', University of Rome La Sapienza, Rome, Italy
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Malina J, Kostrhunova H, Scott P, Brabec V. Fe II Metallohelices Stabilize DNA G-Quadruplexes and Downregulate the Expression of G-Quadruplex-Regulated Oncogenes. Chemistry 2021; 27:11682-11692. [PMID: 34048082 DOI: 10.1002/chem.202101388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Indexed: 12/15/2022]
Abstract
DNA G-quadruplexes (G4s) have been identified within the promoter regions of many proto-oncogenes. Thus, G4s represent attractive targets for cancer therapy, and the design and development of new drugs as G4 binders is a very active field of medicinal chemistry. Here, molecular biophysics and biology methods were employed to investigate the interaction of chiral metallohelices with a series of four DNA G4s (hTelo, c-myc, c-kit1, c-kit2) that are formed by the human telomeric sequence (hTelo) and in the promoter regions of c-MYC and c-KIT proto-oncogenes. We show that the investigated water-compatible, optically pure metallohelices, which are made by self-assembly of simple nonpeptidic organic components around FeII ions and exhibit bioactivity emulating the natural systems, bind with high affinity to G4 DNA and much lower affinity to duplex DNA. Notably, both enantiomers of a metallohelix containing a m-xylenyl bridge (5 b) were found to effectively inhibit primer elongation catalyzed by Taq DNA polymerase by stabilizing G4 structures formed in the template strands containing c-myc and c-kit2 G4-forming sequences. Moreover, both enantiomers of 5 b downregulated the expression of c-MYC and c-KIT oncogenes in human embryonic kidney cells at mRNA and protein levels. As metallohelices also bind alternative nucleic acid structures, they hold promise as potential multitargeted drugs.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Hana Kostrhunova
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, 61265, Brno, Czech Republic
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Roy S, Ali A, Bhattacharya S. Theoretical Insight into the Library Screening Approach for Binding of Intermolecular G-Quadruplex RNA and Small Molecules through Docking and Molecular Dynamics Simulation Studies. J Phys Chem B 2021; 125:5489-5501. [PMID: 34029082 DOI: 10.1021/acs.jpcb.0c10991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The interactions of intermolecular G-quadruplex RNA and small molecules have been investigated by computational studies. Various anthraquinone, bisbenzimidazole, and carbazole-benzimidazole based ligands have shown a distinct preference to G-quadruplex structures as opposed to the corresponding duplex forms of DNA that were docked with telomeric G-quadruplex RNA. The comparative binding study of such ligands with G-quadruplex (G4) RNA showed higher binding affinities toward carbazole-benzimidazole ligands than those of the anthraquinone and bisbenzimidazole based ligands. A molecular dynamics simulation study was used to examine quadruplex-ligand interactions. Analysis of the binding free energy indicated the formation of the thermodynamically favorable RNA-ligand complex. The formation of several H-bonding interactions and the change of the solvent accessible surface area (SASA) also support the effective binding of the carbazole-benzimidazole ligands with G4 RNA structures. Thus, the library screening approach has assisted in getting a structure-activity relationship for the selected small molecules toward the G-quadruplex RNA binding, which can be applied in the targeting of G-quadruplex RNA medicated anticancer therapeutics.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Asfa Ali
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, Karnataka 560012, India.,School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata, West Bengal 700032, India
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