51
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Miskiewicz J, Sarzynska J, Szachniuk M. How bioinformatics resources work with G4 RNAs. Brief Bioinform 2020; 22:5902714. [PMID: 32898859 PMCID: PMC8138894 DOI: 10.1093/bib/bbaa201] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Quadruplexes (G4s) are of interest, which increases with the number of identified G4 structures and knowledge about their biomedical potential. These unique motifs form in many organisms, including humans, where their appearance correlates with various diseases. Scientists store and analyze quadruplexes using recently developed bioinformatic tools—many of them focused on DNA structures. With an expanding collection of G4 RNAs, we check how existing tools deal with them. We review all available bioinformatics resources dedicated to quadruplexes and examine their usefulness in G4 RNA analysis. We distinguish the following subsets of resources: databases, tools to predict putative quadruplex sequences, tools to predict secondary structure with quadruplexes and tools to analyze and visualize quadruplex structures. We share the results obtained from processing specially created RNA datasets with these tools. Contact: mszachniuk@cs.put.poznan.pl Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.
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Affiliation(s)
- Joanna Miskiewicz
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
| | - Joanna Sarzynska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Marta Szachniuk
- Institute of Computing Science and European Centre for Bioinformatics and Genomics, Poznan University of Technology, Piotrowo 2, 60-965 Poznan, Poland
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52
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Bednářová K, Vorlíčková M, Renčiuk D. Diversity of Parallel Guanine Quadruplexes Induced by Guanine Substitutions. Int J Mol Sci 2020; 21:E6123. [PMID: 32854410 PMCID: PMC7503932 DOI: 10.3390/ijms21176123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/21/2020] [Accepted: 08/22/2020] [Indexed: 01/17/2023] Open
Abstract
Recently, we reported an inhibitory effect of guanine substitutions on the conformational switch from antiparallel to parallel quadruplexes (G4) induced by dehydrating agents. As a possible cause, we proposed a difference in the sensitivity of parallel and antiparallel quadruplexes to the guanine substitutions in the resulting thermodynamic stability. Reports on the influence of guanine substitutions on the biophysical properties of intramolecular parallel quadruplexes are rare. Moreover, such reports are often complicated by the multimerisation tendencies of parallel quadruplexes. To address this incomplete knowledge, we employed circular dichroism spectroscopy (CD), both as stopped-flow-assisted fast kinetics measurements and end-point measurements, accompanied by thermodynamic analyses, based on UV absorption melting profiles, and electrophoretic methods. We showed that parallel quadruplexes are significantly more sensitive towards guanine substitutions than antiparallel ones. Furthermore, guanine-substituted variants, which in principle might correspond to native genomic sequences, distinctly differ in their biophysical properties, indicating that the four guanines in each tetrad of parallel quadruplexes are not equal. In addition, we were able to distinguish by CD an intramolecular G4 from intermolecular ones resulting from multimerisation mediated by terminal tetrad association, but not from intermolecular G4s formed due to inter-strand Hoogsteen hydrogen bond formation. In conclusion, our study indicates significant variability in parallel quadruplex structures, otherwise disregarded without detailed experimental analysis.
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Affiliation(s)
| | | | - Daniel Renčiuk
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; (K.B.); (M.V.)
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53
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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54
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Bartas M, Brázda V, Bohálová N, Cantara A, Volná A, Stachurová T, Malachová K, Jagelská EB, Porubiaková O, Červeň J, Pečinka P. In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles. Front Microbiol 2020; 11:1583. [PMID: 32719673 PMCID: PMC7347907 DOI: 10.3389/fmicb.2020.01583] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Non-canonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain non-canonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5'UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3'UTR, inside 5'UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Non-canonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Alessio Cantara
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Tereza Stachurová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Kateřina Malachová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Eva B. Jagelská
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Otília Porubiaková
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
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55
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Price DA, Kartje ZJ, Hughes JA, Hill TD, Loth TM, Watts JK, Gagnon KT, Moran SD. Infrared Spectroscopy Reveals the Preferred Motif Size and Local Disorder in Parallel Stranded DNA G-Quadruplexes. Chembiochem 2020; 21:2792-2804. [PMID: 32372560 DOI: 10.1002/cbic.202000136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Infrared spectroscopy detects the formation of G-quadruplexes in guanine-rich nucleic acid sequences through shifts in the guanine C=O stretch mode. Here, we use ultrafast 2D infrared (IR) spectroscopy and isotope substitution to show that these shifts arise from vibrational delocalization among stacked G-quartets. This provides a direct measure of the sizes of locally ordered motifs in heterogeneous samples with substantial disordered regions. We find that parallel-stranded, potassium-bound DNA G-quadruplexes are limited to five consecutive G-quartets and 3-4 consecutive layers are preferred for longer polyguanine tracts. The resulting potassium-dependent G-quadruplex assembly landscape reflects the polyguanine tract lengths found in genomes, the ionic conditions prevalent in healthy mammalian cells, and the onset of structural disorder in disease states. Our study describes spectral markers that can be used to probe other G-quadruplex structures and provides insight into the fundamental limits of their formation in biological and artificial systems.
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Affiliation(s)
- David A Price
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Joanna A Hughes
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Tayler D Hill
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Taylor M Loth
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA.,Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
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56
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Reina C, Cavalieri V. Epigenetic Modulation of Chromatin States and Gene Expression by G-Quadruplex Structures. Int J Mol Sci 2020; 21:E4172. [PMID: 32545267 PMCID: PMC7312119 DOI: 10.3390/ijms21114172] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/07/2020] [Accepted: 06/10/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes are four-stranded helical nucleic acid structures formed by guanine-rich sequences. A considerable number of studies have revealed that these noncanonical structural motifs are widespread throughout the genome and transcriptome of numerous organisms, including humans. In particular, G-quadruplexes occupy strategic locations in genomic DNA and both coding and noncoding RNA molecules, being involved in many essential cellular and organismal functions. In this review, we first outline the fundamental structural features of G-quadruplexes and then focus on the concept that these DNA and RNA structures convey a distinctive layer of epigenetic information that is critical for the complex regulation, either positive or negative, of biological activities in different contexts. In this framework, we summarize and discuss the proposed mechanisms underlying the functions of G-quadruplexes and their interacting factors. Furthermore, we give special emphasis to the interplay between G-quadruplex formation/disruption and other epigenetic marks, including biochemical modifications of DNA bases and histones, nucleosome positioning, and three-dimensional organization of chromatin. Finally, epigenetic roles of RNA G-quadruplexes in post-transcriptional regulation of gene expression are also discussed. Undoubtedly, the issues addressed in this review take on particular importance in the field of comparative epigenetics, as well as in translational research.
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Affiliation(s)
- Chiara Reina
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, 90127 Palermo, Italy;
| | - Vincenzo Cavalieri
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, 90128 Palermo, Italy
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57
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Monsen RC, DeLeeuw L, Dean WL, Gray RD, Sabo T, Chakravarthy S, Chaires JB, Trent JO. The hTERT core promoter forms three parallel G-quadruplexes. Nucleic Acids Res 2020; 48:5720-5734. [PMID: 32083666 PMCID: PMC7261196 DOI: 10.1093/nar/gkaa107] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 12/13/2022] Open
Abstract
The structure of the 68 nt sequence with G-quadruplex forming potential within the hTERT promoter is disputed. One model features a structure with three stacked parallel G-quadruplex units, while another features an unusual duplex hairpin structure adjoined to two stacked parallel and antiparallel quadruplexes. We report here the results of an integrated structural biology study designed to distinguish between these possibilities. As part of our study, we designed a sequence with an optimized hairpin structure and show that its biophysical and biochemical properties are inconsistent with the structure formed by the hTERT wild-type sequence. By using circular dichroism, thermal denaturation, nuclear magnetic resonance spectroscopy, analytical ultracentrifugation, small-angle X-ray scattering, molecular dynamics simulations and a DNase I cleavage assay we found that the wild type hTERT core promoter folds into a stacked, three-parallel G-quadruplex structure. The hairpin structure is inconsistent with all of our experimental data obtained with the wild-type sequence. All-atom models for both structures were constructed using molecular dynamics simulations. These models accurately predicted the experimental hydrodynamic properties measured for each structure. We found with certainty that the wild-type hTERT promoter sequence does not form a hairpin structure in solution, but rather folds into a compact stacked three-G-quadruplex conformation.
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Affiliation(s)
- Robert C Monsen
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
| | - Lynn DeLeeuw
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
| | - T Michael Sabo
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team (BioCAT), Department of Biological Chemical and Physical Sciences, Illinois Institute of Technology, Chicago, IL 60616, USA
| | - Jonathan B Chaires
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
| | - John O Trent
- Department of Biochemistry & Molecular Genetics, University of Louisville, Louisville, KY 40202, USA
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA
- Department of Medicine, University of Louisville, Louisville, KY 40202, USA
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58
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Ma TZ, Zhang MJ, Liao TC, Li JH, Zou M, Wang ZM, Zhou CQ. Dimers formed with the mixed-type G-quadruplex binder pyridostatin specifically recognize human telomere G-quadruplex dimers. Org Biomol Chem 2020; 18:920-930. [DOI: 10.1039/c9ob02470k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
By adjusting the length of the polyether linkers, pyridostatin (PDS) dimers displayed higher binding selectivities and thermal stabilization towards human telomere antiparallel and mixed-type G-quadruplex dimers (G2T1).
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Affiliation(s)
- Tian-Zhu Ma
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Meng-Jia Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ting-Cong Liao
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jun-Hui Li
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Min Zou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Zhou-Mo Wang
- Medical School
- Science and Technology College of Hubei University for Nationalities
- Enshi 445000
- P. R. China
| | - Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
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59
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Marzano M, Falanga AP, Dardano P, D'Errico S, Rea I, Terracciano M, De Stefano L, Piccialli G, Borbone N, Oliviero G. π–π stacked DNA G-wire nanostructures formed by a short G-rich oligonucleotide containing a 3′–3′ inversion of polarity site. Org Chem Front 2020. [DOI: 10.1039/d0qo00561d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Rod-shaped G-wire assemblies potentially useful to obtain new hybrid and conducting materials were obtained by annealing short G-rich oligonucleotides incorporating a 3′–3′ inversion of polarity site in the presence of potassium or ammonium ions.
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Affiliation(s)
- Maria Marzano
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Andrea P. Falanga
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Principia Dardano
- Institute of Applied Sciences and Intelligent Systems
- National Council Research of Italy
- 80131 – Naples
- Italy
| | | | - Ilaria Rea
- Institute of Applied Sciences and Intelligent Systems
- National Council Research of Italy
- 80131 – Naples
- Italy
| | - Monica Terracciano
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Luca De Stefano
- Institute of Applied Sciences and Intelligent Systems
- National Council Research of Italy
- 80131 – Naples
- Italy
| | - Gennaro Piccialli
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Nicola Borbone
- Department of Pharmacy
- University of Naples Federico II
- 80131 – Naples
- Italy
| | - Giorgia Oliviero
- Department of Molecular Medicine and Medical Biotechnologies
- University of Naples Federico II
- 80131 – Naples
- Italy
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60
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Heddi B, Cheong VV, Schmitt E, Mechulam Y, Phan AT. Recognition of different base tetrads by RHAU (DHX36): X-ray crystal structure of the G4 recognition motif bound to the 3′-end tetrad of a DNA G-quadruplex. J Struct Biol 2020; 209:107399. [DOI: 10.1016/j.jsb.2019.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022]
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61
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Hu MH, Lin XT, Liu B, Tan JH. Dimeric aryl-substituted imidazoles may inhibit ALT cancer by targeting the multimeric G-quadruplex in telomere. Eur J Med Chem 2019; 186:111891. [PMID: 31759730 DOI: 10.1016/j.ejmech.2019.111891] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/10/2019] [Accepted: 11/14/2019] [Indexed: 11/17/2022]
Abstract
In 10-15% of cancers, telomere maintenance is provided by a telomerase-independent mechanism known as alternative lengthening of telomere (ALT), making telomerase inhibitors ineffective on these cancers. Ligands that stabilize telomeric G-quadruplex (G4) are considered to be able to inhibit either the ALT process or disrupt the T-loop structure, which would be promising therapeutic agents for ALT cancers. Notably, the 3'-terminal overhang of telomeric DNA might fold into multimeric G4 containing consecutive G4 subunits, which offers an attractive target for selective ligands considering large numbers of G4s widespread in the genome. In this study, a dimeric aryl-substituted imidazole (DIZ-3) was developed as a selective multimeric G4 ligand based on a G4-ligand-dimerizing strategy. Biophysical experiments revealed that DIZ-3 intercalated into the G4-G4 interface, stabilizing the higher-order structure. Furthermore, this ligand was demonstrated to induce cell cycle arrest and apoptosis, and thus inhibited cell proliferation in an ALT cancer cell line. Cancer cells were more sensitive to DIZ-3, relative to normal cells. Notably, DIZ-3 had little effect on the transcription of several G4-dependent oncogenes. This study provides a nice example for discovering dimeric agents to potentially treat ALT cancers via targeting telomeric multimeric G4.
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Affiliation(s)
- Ming-Hao Hu
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China.
| | - Xiao-Tong Lin
- School of Pharmaceutical Sciences, Shenzhen University Health Science Center, Shenzhen, 518060, China
| | - Bin Liu
- Shenzhen Key Laboratory of Polymer Science and Technology, College of Materials Science and Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
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62
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Lansdorp P, van Wietmarschen N. Helicases FANCJ, RTEL1 and BLM Act on Guanine Quadruplex DNA in Vivo. Genes (Basel) 2019; 10:genes10110870. [PMID: 31683575 PMCID: PMC6896191 DOI: 10.3390/genes10110870] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 02/03/2023] Open
Abstract
Guanine quadruplex (G4) structures are among the most stable secondary DNA structures that can form in vitro, and evidence for their existence in vivo has been steadily accumulating. Originally described mainly for their deleterious effects on genome stability, more recent research has focused on (potential) functions of G4 structures in telomere maintenance, gene expression, and other cellular processes. The combined research on G4 structures has revealed that properly regulating G4 DNA structures in cells is important to prevent genome instability and disruption of normal cell function. In this short review we provide some background and historical context of our work resulting in the identification of FANCJ, RTEL1 and BLM as helicases that act on G4 structures in vivo. Taken together these studies highlight important roles of different G4 DNA structures and specific G4 helicases at selected genomic locations and telomeres in regulating gene expression and maintaining genome stability.
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Affiliation(s)
- Peter Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
- European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV Groningen, The Netherlands.
| | - Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV Groningen, The Netherlands.
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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