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Bisoi A, Sarkar S, Singh PC. Flanking Effect on the Structure and Stability of Human Telomeric G-Quadruplex in Varying Salt Concentrations. J Phys Chem B 2024; 128:7121-7128. [PMID: 39007177 DOI: 10.1021/acs.jpcb.4c02969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
The stability of the human telomere G-quadruplex (G4) is directly linked to cancer disease. The human telomere is mostly associated with the flanking nucleobases, which can affect the stability of G4. Hence, in this study, the effect of the flanking nucleobases in the context of their chemical nature, number, and position on the structure and stability of G4 has been investigated in varying concentrations of KCl mimicking the normal and cancer KCl microenvironments. The addition of flanking nucleobases does not alter the G4 topology. However, the presence of merely a single flanking nucleobase destabilizes the telomeric G4. This destabilizing effect is more prominent for thymine than adenine flanking nucleobase, probably due to the formation of the intermolecular G4 topology by thymine. Interestingly, the change in the stability of the telomeric G4 in the presence of thymine flanking nucleobase is sensitive to the concentration of KCl relevant to the normal and cancerous microenvironments, in contrast to adenine. Flanking nucleobases have a greater impact at the 5' end compared to the 3' end, particularly noticeable in KCl concentrations resembling the normal microenvironment rather than the cancerous one. These findings indicate that the effect of the flanking nucleobases on telomeric G4 is different in the KCl salt relevant to normal and cancerous microenvironments. This study may be helpful in attaining molecular-level insight into the role of G4 in telomeric length regulation under normal and cancerous KCl salt conditions.
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Affiliation(s)
- Asim Bisoi
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 India
| | - Sunipa Sarkar
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 India
| | - Prashant Chandra Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032 India
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2
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Ji J, Sharma A, Pokhrel P, Karna D, Pandey S, Zheng YR, Mao H. Dynamic Structures and Fast Transition Kinetics of Oxidized G-Quadruplexes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2400485. [PMID: 38678502 DOI: 10.1002/smll.202400485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/04/2024] [Indexed: 05/01/2024]
Abstract
8-oxoguanines (8-oxoG) in cells form compromised G-quadruplexes (GQs), which may vary GQ mediated gene regulations. By mimicking molecularly crowded cellular environment using 40% DMSO or sucrose, here it is found that oxidized human telomeric GQs have stabilities close to the wild-type (WT) GQs. Surprisingly, while WT GQs show negative formation cooperativity between a Pt(II) binder and molecularly crowded environment, positive cooperativity is observed for oxidized GQ formation. Single-molecule mechanical unfolding reveals that 8-oxoG sequence formed more diverse and flexible structures with faster folding/unfolding transition kinetics, which facilitates the Pt(II) ligand to bind the best-fit structures with positive cooperativity. These findings offer new understanding on structures and properties of oxidized G-rich species in crowded environments. They also provide insights into the design of better ligands to target oxidized G-rich structures formed under oxidative cell stress.
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Affiliation(s)
- Jiahao Ji
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Arpit Sharma
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Pravin Pokhrel
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Deepak Karna
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Shankar Pandey
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Yao-Rong Zheng
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
| | - Hanbin Mao
- Department of Chemistry & Biochemistry, Kent State University, Kent, OH, 44242, USA
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3
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Libera V, Ripanti F, Petrillo C, Sacchetti F, Ramos-Soriano J, Galan MC, Schirò G, Paciaroni A, Comez L. Stability of Human Telomeric G-Quadruplexes Complexed with Photosensitive Ligands and Irradiated with Visible Light. Int J Mol Sci 2023; 24:ijms24109090. [PMID: 37240437 DOI: 10.3390/ijms24109090] [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: 04/26/2023] [Revised: 05/16/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Guanine-rich DNA sequences can fold into non-canonical nucleic acid structures called G-quadruplexes (G4s). These nanostructures have strong implications in many fields, from medical science to bottom-up nanotechnologies. As a result, ligands interacting with G4s have attracted great attention as candidates in medical therapies, molecular probe applications, and biosensing. In recent years, the use of G4-ligand complexes as photopharmacological targets has shown significant promise for developing novel therapeutic strategies and nanodevices. Here, we studied the possibility of manipulating the secondary structure of a human telomeric G4 sequence through the interaction with two photosensitive ligands, DTE and TMPyP4, whose response to visible light is different. The effect of these two ligands on G4 thermal unfolding was also considered, revealing the occurrence of peculiar multi-step melting pathways and the different attitudes of the two molecules on the quadruplex stabilization.
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Affiliation(s)
- Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesco Sacchetti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Javier Ramos-Soriano
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Maria Carmen Galan
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Giorgio Schirò
- CNRS, CEA, IBS, c/o University Grenoble Alpes, 38400 Grenoble, France
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- Istituto Officina dei Materiali-IOM, National Research Council-CNR, Via Alessandro Pascoli, 06123 Perugia, Italy
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4
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Sudhakar S, Barkau CL, Chilamkurthy R, Barber HM, Pater AA, Moran SD, Damha MJ, Pradeepkumar PI, Gagnon KT. Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly. J Biol Chem 2023; 299:104700. [PMID: 37059184 PMCID: PMC10200996 DOI: 10.1016/j.jbc.2023.104700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023] Open
Abstract
Ribonucleoproteins (RNPs) comprise one or more RNA and protein molecules that interact to form a stable complex, which commonly involves conformational changes in the more flexible RNA components. Here, we propose that Cas12a RNP assembly with its cognate CRISPR RNA (crRNA) guide instead proceeds primarily through Cas12a conformational changes during binding to more stable, prefolded crRNA 5' pseudoknot handles. Phylogenetic reconstructions and sequence and structure alignments revealed that the Cas12a proteins are divergent in sequence and structure while the crRNA 5' repeat region, which folds into a pseudoknot and anchors binding to Cas12a, is highly conserved. Molecular dynamics simulations of three Cas12a proteins and their cognate guides revealed substantial flexibility for unbound apo-Cas12a. In contrast, crRNA 5' pseudoknots were predicted to be stable and independently folded. Limited trypsin hydrolysis, differential scanning fluorimetry, thermal denaturation, and CD analyses supported conformational changes of Cas12a during RNP assembly and an independently folded crRNA 5' pseudoknot. This RNP assembly mechanism may be rationalized by evolutionary pressure to conserve CRISPR loci repeat sequence, and therefore guide RNA structure, to maintain function across all phases of the CRISPR defense mechanism.
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Affiliation(s)
- Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Christopher L Barkau
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Ramadevi Chilamkurthy
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Halle M Barber
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA.
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5
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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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6
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To probe the binding of TMPyP4 to c-MYC G-quadruplex with in water and in imidazolium-based ionic liquids using spectroscopy coupled with molecular dynamics simulations. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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7
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Oblak D, Hadži S, Podlipnik Č, Lah J. Binding-Induced Diversity of a Human Telomeric G-Quadruplex Stability Phase Space. Pharmaceuticals (Basel) 2022; 15:ph15091150. [PMID: 36145371 PMCID: PMC9501445 DOI: 10.3390/ph15091150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 11/25/2022] Open
Abstract
The structural polymorphism of G-quadruplex nucleic acids is an important factor in their recognition by proteins and small-molecule ligands. However, it is not clear why the binding of several ligands alters G-quadruplex topology. We addressed this question by following the (un)folding and binding of the human telomeric fragment 5′-(GGGTTA)3GGGT-3′ (22GT) by calorimetry (DSC, ITC) and spectroscopy (CD). A thermodynamic analysis of the obtained data led to a detailed description of the topological phase space of stability (phase diagram) of 22GT and shows how it changes in the presence of a specific bisquinolinium ligand (360A). Various 1:1 and 2:1 ligand–quadruplex complexes were observed. With increasing temperature, the 1:1 complexes transformed into 2:1 complexes, which is attributed to the preferential binding of the ligand to the folding intermediates. Overall, the dissection of the thermodynamic parameters in combination with molecular modelling clarified the driving forces of the topological quadruplex transformations in a wide range of ligand concentrations and temperatures.
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8
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Libera V, Bianchi F, Rossi B, D’Amico F, Masciovecchio C, Petrillo C, Sacchetti F, Paciaroni A, Comez L. Solvent Vibrations as a Proxy of the Telomere G-Quadruplex Rearrangements across Thermal Unfolding. Int J Mol Sci 2022; 23:ijms23095123. [PMID: 35563512 PMCID: PMC9100830 DOI: 10.3390/ijms23095123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes (G4s) are noncanonical forms of DNA involved in many key genome functions. Here, we exploited UV Resonance Raman scattering to simultaneously explore the vibrational behavior of a human telomeric G4 (Tel22) and its aqueous solvent as the biomolecule underwent thermal melting. We found that the OH stretching band, related to the local hydrogen-bonded network of a water molecule, was in strict relation with the vibrational features of the G4 structure as a function of temperature. In particular, the modifications to the tetrahedral ordering of the water network were strongly coupled to the DNA rearrangements, showing changes in temperature that mirrored the multi-step melting process of Tel22. The comparison between circular dichroism and Raman results supported this view. The present findings provide novel insights into the impact of the molecular environment on G4 conformation. Improving current knowledge on the solvent structural properties will also contribute to a better understanding of the role played by water arrangement in the complexation of G4s with ligands.
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Affiliation(s)
- Valeria Libera
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Federico Bianchi
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Barbara Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Francesco D’Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Claudio Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy; (B.R.); (F.D.); (C.M.)
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, 06123 Perugia, Italy; (V.L.); (F.B.); (C.P.); (F.S.)
- Correspondence: (A.P.); (L.C.)
| | - Lucia Comez
- IOM-CNR c/o Department of Physics and Geology, Università degli Studi di Perugia, 06123 Perugia, Italy
- Correspondence: (A.P.); (L.C.)
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9
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Liu YC, Yang DY, Sheu SY. Insights into the free energy landscape and salt-controlled mechanism of the conformational conversions between human telomeric G-quadruplex structures. Int J Biol Macromol 2021; 191:230-242. [PMID: 34536474 DOI: 10.1016/j.ijbiomac.2021.09.057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/23/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022]
Abstract
G-quadruplexes have become attractive drug targets in cancer therapy. However, due to the polymorphism of G-quadruplex structures, it is difficult to experimentally verify the relevant structures of multiple intermediates and transition states in dynamic equilibrium. Hence, understanding the mechanism by which structural conversions of G-quadruplexes occur is still challenging. We conducted targeted molecular dynamics simulation with umbrella sampling to investigate how salt affects the conformational conversion of human telomeric G-quadruplex. Our results explore a unique view into the structures and energy barrier of the intermediates and transition states in the interconversion process. The pathway of G-quadruplex conformational interconversion was mapped out by a free energy landscape, consisting of branched parallel pathways with multiple energy basins. We propose a salt-controlled mechanism that as the salt concentration increases, the conformational conversion mechanism switches from multi-pathway folding to sequential folding pathways. The hybrid-I and hybrid-II structures are intermediates in the basket-propeller transformation. In high-salt solutions, the conformational conversion upon K+ binding is more feasible than upon Na+ binding. The free energy barrier for conformational conversions ranges from 1.6 to 4.6 kcal/mol. Our work will be beneficial in developing anticancer agents.
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Affiliation(s)
- Yu-Cheng Liu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 106, Taiwan.
| | - Sheh-Yi Sheu
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan.
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10
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Jana J, Weisz K. Thermodynamic Stability of G-Quadruplexes: Impact of Sequence and Environment. Chembiochem 2021; 22:2848-2856. [PMID: 33844423 PMCID: PMC8518667 DOI: 10.1002/cbic.202100127] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Indexed: 12/19/2022]
Abstract
G-quadruplexes have attracted growing interest in recent years due to their occurrence in vivo and their possible biological functions. In addition to being promising targets for drug design, these four-stranded nucleic acid structures have also been recognized as versatile tools for various technological applications. Whereas a large number of studies have yielded insight into their remarkable structural diversity, our current knowledge on G-quadruplex stabilities as a function of sequence and environmental factors only gradually emerges with an expanding collection of thermodynamic data. This minireview provides an overview of general rules that may be used to better evaluate quadruplex thermodynamic stabilities but also discusses present challenges in predicting most stable folds for a given sequence and environment.
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Affiliation(s)
- Jagannath Jana
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
| | - Klaus Weisz
- Institute of BiochemistryUniversität GreifswaldFelix-Hausdorff Str. 417489GreifswaldGermany
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11
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Verma S, Ravichandiran V, Ranjan N. Beyond amyloid proteins: Thioflavin T in nucleic acid recognition. Biochimie 2021; 190:111-123. [PMID: 34118329 DOI: 10.1016/j.biochi.2021.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 05/25/2021] [Accepted: 06/04/2021] [Indexed: 01/01/2023]
Abstract
Thioflavin T (ThT) is a commercially available fluorescent dye that is commonly used in biomedical research for over five decades. It was first reported as an extrinsic fluorescent probe for the detection of amyloid fibrils and related processes and it has also been used extensively for assessing protein binding in fluorescence-based assays. Although the nucleic acid binding of ThT was reported half of a century ago in the 1970s, it was not widely explored until the start of this decade. In recent years, Thioflavin T has become a major tool in the recognition of many types of non-canonical nucleic acid conformations including duplexes, triplexes, and G-quadruplexes. The propensity of ThT binding is more towards base aberrations, bulges, and mismatches highlighting its importance in serving as a diagnostic tool in a variety of ailments/disease conditions. In this review, we cover major advancements in nucleic acid detection/binding by ThT to a variety of nucleic acid structures.
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Affiliation(s)
- Smita Verma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India; Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Velayutham Ravichandiran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Kolkata, Maniktala Main Road, Kolkata, 700054, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, New Transit Campus, Lucknow, Uttar Pradesh, 226002, India.
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12
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Label-Free Fluorescence Molecular Beacon Probes Based on G-Triplex DNA and Thioflavin T for Protein Detection. Molecules 2021; 26:molecules26102962. [PMID: 34067563 PMCID: PMC8156537 DOI: 10.3390/molecules26102962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/07/2021] [Accepted: 05/11/2021] [Indexed: 11/16/2022] Open
Abstract
Protein detection plays an important role in biological and biomedical sciences. The immunoassay based on fluorescence labeling has good specificity but a high labeling cost. Herein, on the basis of G-triplex molecular beacon (G3MB) and thioflavin T (ThT), we developed a simple and label-free biosensor for protein detection. The biotin and streptavidin were used as model enzymes. In the presence of target streptavidin (SA), the streptavidin hybridized with G3MB-b (biotin-linked-G-triplex molecular beacon) perfectly and formed larger steric hindrance, which hindered the hydrolysis of probes by exonuclease III (Exo III). In the absence of target streptavidin, the exonuclease III successively cleaved the stem of G3MB-b and released the G-rich sequences which self-assembled into a G-triplex and subsequently activated the fluorescence signal of thioflavin T. Compared with the traditional G-quadruplex molecular beacon (G4MB), the G3MB only needed a lower dosage of exonuclease III and a shorter reaction time to reach the optimal detection performance, because the concise sequence of G-triplex was good for the molecular beacon design. Moreover, fluorescence experiment results exhibited that the G3MB-b had good sensitivity and specificity for streptavidin detection. The developed label-free biosensor provides a valuable and general platform for protein detection.
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13
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Gao J, Liu Q, Liu W, Jin Y, Li B. Comparative evaluation and design of a G-triplex/thioflavin T-based molecular beacon. Analyst 2021; 146:2567-2573. [PMID: 33899063 DOI: 10.1039/d1an00252j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Both G-quadruplex (G4) and G-triplex (G3) can bind thioflavin T (ThT) to light up the fluorescence of ThT. G4/ThT and G3/ThT can be used as fluorescent indicators to construct a label-free molecular beacon (MB). In this work, we present a comparative perspective of G3/ThT-based MB and G4/ThT-based MB. The results showed that the G3/ThT-based MB had higher sensitivity and faster response speed than the G4/ThT-based MB. Furthermore, we systematically studied the effect of stem length and varying pairs on the response of the G3/ThT-based MB, and then proposed one rational design of the G3/ThT-based MB. This work demonstrates that the shorter G3 is more suitable for constructing the MB stem. This present work opens a promising way to develop a sensitive, simple and homogeneous biosensing method.
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Affiliation(s)
- Jingru Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Qiang Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Baoxin Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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14
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Harkness RW, Hennecker C, Grün JT, Blümler A, Heckel A, Schwalbe H, Mittermaier AK. Parallel reaction pathways accelerate folding of a guanine quadruplex. Nucleic Acids Res 2021; 49:1247-1262. [PMID: 33469659 PMCID: PMC7897495 DOI: 10.1093/nar/gkaa1286] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 12/21/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023] Open
Abstract
G-quadruplexes (G4s) are four-stranded, guanine-rich nucleic acid structures that can influence a variety of biological processes such as the transcription and translation of genes and DNA replication. In many cases, a single G4-forming nucleic acid sequence can adopt multiple different folded conformations that interconvert on biologically relevant timescales, entropically stabilizing the folded state. The coexistence of different folded conformations also suggests that there are multiple pathways leading from the unfolded to the folded state ensembles, potentially modulating the folding rate and biological activity. We have developed an experimental method for quantifying the contributions of individual pathways to the folding of conformationally heterogeneous G4s that is based on mutagenesis, thermal hysteresis kinetic experiments and global analysis, and validated our results using photocaged kinetic NMR experiments. We studied the regulatory Pu22 G4 from the c-myc oncogene promoter, which adopts at least four distinct folded isomers. We found that the presence of four parallel pathways leads to a 2.5-fold acceleration in folding; that is, the effective folding rate from the unfolded to folded ensembles is 2.5 times as large as the rate constant for the fastest individual pathway. Since many G4 sequences can adopt many more than four isomers, folding accelerations of more than an order of magnitude are possible via this mechanism.
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Affiliation(s)
- Robert W Harkness
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, McGill University, Montreal, QC H3A 0B8, Canada
| | | | - J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main 60438, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University, Frankfurt am Main 60438, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University, Frankfurt am Main 60438, Germany
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15
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Comez L, Bianchi F, Libera V, Longo M, Petrillo C, Sacchetti F, Sebastiani F, D'Amico F, Rossi B, Gessini A, Masciovecchio C, Amenitsch H, Sissi C, Paciaroni A. Polymorphism of human telomeric quadruplexes with drugs: a multi-technique biophysical study. Phys Chem Chem Phys 2020; 22:11583-11592. [PMID: 32400802 DOI: 10.1039/d0cp01483d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The human telomeric G-quadruplex structural motif of DNA has come to be known as a new and stimulating target for anticancer drug discovery. Small molecules that interact with G-quadruplex structures in a selective way have gained impressive interest in recent years as they may serve as potential therapeutic agents. Here, we show how circular dichroism, UV resonance Raman and small angle X-ray scattering spectroscopies can be effectively combined to provide insights into structural and molecular aspects of the interaction between human telomeric quadruplexes and ligands. This study focuses on the ability of berberine and palmatine to bind with human telomeric quadruplexes and provides analysis of the conformational landscape visited by the relevant complexes upon thermal unfolding. With increasing temperature, both free and bound G-quadruplexes undergo melting through a multi-state process, populating different intermediate states. Despite the structural similarity of the two ligands, valuable distinctive features characterising their interaction with the G-quadruplex emerged from our multi-technique approach.
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Affiliation(s)
- L Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - V Libera
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - M Longo
- JCNS Forschungszentrum Jülich GmbH at Heinz Maier-Leibnitz Zentrum (MLZ), 85748 Garching, Germany
| | - C Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
| | - F Sebastiani
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, 50019 Sesto Fiorentino, FI, Italy
| | - F D'Amico
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - B Rossi
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - A Gessini
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - C Masciovecchio
- Elettra Sincrotrone Trieste, S.S. 14 Km 163.5, 34012 Trieste, Italy
| | - H Amenitsch
- Institute of Inorganic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - C Sissi
- Dipartimento di Scienze del Farmaco, Via Marzolo 5, 35131 Padova, Italy and Interdepartmental Research Center for Innovative Biotechnologies (CRIBI), University of Padova, University of Padova, Italy
| | - A Paciaroni
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy.
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16
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Chaires JB, Gray RD, Dean WL, Monsen R, DeLeeuw LW, Stribinskis V, Trent JO. Human POT1 unfolds G-quadruplexes by conformational selection. Nucleic Acids Res 2020; 48:4976-4991. [PMID: 32232414 PMCID: PMC7229828 DOI: 10.1093/nar/gkaa202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
The reaction mechanism by which the shelterin protein POT1 (Protection of Telomeres 1) unfolds human telomeric G-quadruplex structures is not fully understood. We report here kinetic, thermodynamic, hydrodynamic and computational studies that show that a conformational selection mechanism, in which POT1 binding is coupled to an obligatory unfolding reaction, is the most plausible mechanism. Stopped-flow kinetic and spectroscopic titration studies, along with isothermal calorimetry, were used to show that binding of the single-strand oligonucleotide d[TTAGGGTTAG] to POT1 is both fast (80 ms) and strong (-10.1 ± 0.3 kcal mol-1). In sharp contrast, kinetic studies showed the binding of POT1 to an initially folded 24 nt G-quadruplex structure is four orders of magnitude slower. Fluorescence, circular dichroism and analytical ultracentrifugation studies showed that POT1 binding is coupled to quadruplex unfolding, with a final complex with a stoichiometry of 2 POT1 per 24 nt DNA. The binding isotherm for the POT1-quadruplex interaction was sigmoidal, indicative of a complex reaction. A conformational selection model that includes equilibrium constants for both G-quadruplex unfolding and POT1 binding to the resultant single-strand provided an excellent quantitative fit to the experimental binding data. POT1 unfolded and bound to any conformational form of human telomeric G-quadruplex (antiparallel, hybrid, parallel monomers or a 48 nt sequence with two contiguous quadruplexes), but did not avidly interact with duplex DNA or with other G-quadruplex structures. Finally, molecular dynamics simulations provided a detailed structural model of a 2:1 POT1:DNA complex that is fully consistent with experimental biophysical results.
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Affiliation(s)
- Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Robert Monsen
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Lynn W DeLeeuw
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Vilius Stribinskis
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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17
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Musumeci D, Mokhir A, Roviello GN. Synthesis and nucleic acid binding evaluation of a thyminyl l-diaminobutanoic acid-based nucleopeptide. Bioorg Chem 2020; 100:103862. [PMID: 32428744 DOI: 10.1016/j.bioorg.2020.103862] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/01/2020] [Accepted: 04/16/2020] [Indexed: 01/09/2023]
Abstract
Herein we present the synthesis of a l-diaminobutanoic acid (DABA)-based nucleopeptide (3), with an oligocationic backbone, realized by solid phase peptide synthesis using thymine-bearing DABA moieties alternating in the sequence with free ones. CD studies evidenced the ability of this oligothymine nucleopeptide, well soluble in aqueous solution, to alter the secondary structure particularly of complementary RNA (poly rA vs poly rU) and inosine-rich RNAs, like poly rI and poly rIC, and showed its preference in binding double vs single-stranded DNAs. Furthermore, ESI mass spectrometry revealed that 3 bound also G-quadruplex (G4) DNAs, with either parallel or antiparallel topologies (adopted in our experimental conditions by c-myc and tel22, respectively). However, it caused detectable changes only in the CD of c-myc (whose parallel G4 structure was also thermally stabilized by ~3 °C), while leaving unaltered the antiparallel structure of tel22. Interestingly, CD and UV analyses suggested that 3 induced a hybrid mixed parallel/antiparallel G4 DNA structure in a random-coil tel22 DNA obtained under salt-free buffer conditions. Titration of the random-coil telomeric DNA with 3 gave quantitative information on the stoichiometry of the obtained complex. Overall, the findings of this work suggest that DABA-based nucleopeptides are synthetic nucleic acid analogues potentially useful in antigene and antisense strategies. Nevertheless, the hexathymine DABA-nucleopeptide shows an interesting behaviour as molecular tool per se thanks to its efficacy in provoking G4 induction in random coil G-rich DNA, as well as for the possibility to bind and stabilize c-myc oncogene in a G4 structure.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, Federico II University, Via Cintia 21, 80126 Naples, Italy; Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - Andriy Mokhir
- Department of Chemistry and Pharmacy, Friedrich Alexander University, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini IBB - CNR, Via Mezzocannone 16, 80134 Naples, Italy.
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18
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Tian Y, Lu Q, Guo X, Wang S, Gao Y, Wang L. Au nanoparticles deposited on ultrathin two-dimensional covalent organic framework nanosheets for in vitro and intracellular sensing. NANOSCALE 2020; 12:7776-7781. [PMID: 32215408 DOI: 10.1039/c9nr08220d] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A novel composite nanomaterial is prepared by growing small Au nanoparticles on two-dimensional covalent organic framework nanosheets (Au NPs/COF NSs). The synthesized hybrid nanosheets are used as a new platform for multiplexed detection of hepatitis A virus DNA (HAV) and hepatitis B virus DNA (HBV). Additionally, this sensing platform based on Au NPs/COF NSs can be used as a candidate for monitoring the distribution of potassium ions (K+) and the intracellular K+ level in living cells. Accordingly, the sensing systems based on hybrid Au NPs/COF NSs have shown great potential for the investigation of biomolecules and related biological applications.
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Affiliation(s)
- Yuanyuan Tian
- Key Laboratory for Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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19
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Stadlbauer P, Kührová P, Vicherek L, Banáš P, Otyepka M, Trantírek L, Šponer J. Parallel G-triplexes and G-hairpins as potential transitory ensembles in the folding of parallel-stranded DNA G-Quadruplexes. Nucleic Acids Res 2019; 47:7276-7293. [PMID: 31318975 PMCID: PMC6698752 DOI: 10.1093/nar/gkz610] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 06/26/2019] [Accepted: 07/03/2019] [Indexed: 12/29/2022] Open
Abstract
Guanine quadruplexes (G4s) are non-canonical nucleic acids structures common in important genomic regions. Parallel-stranded G4 folds are the most abundant, but their folding mechanism is not fully understood. Recent research highlighted that G4 DNA molecules fold via kinetic partitioning mechanism dominated by competition amongst diverse long-living G4 folds. The role of other intermediate species such as parallel G-triplexes and G-hairpins in the folding process has been a matter of debate. Here, we use standard and enhanced-sampling molecular dynamics simulations (total length of ∼0.9 ms) to study these potential folding intermediates. We suggest that parallel G-triplex per se is rather an unstable species that is in local equilibrium with a broad ensemble of triplex-like structures. The equilibrium is shifted to well-structured G-triplex by stacked aromatic ligand and to a lesser extent by flanking duplexes or nucleotides. Next, we study propeller loop formation in GGGAGGGAGGG, GGGAGGG and GGGTTAGGG sequences. We identify multiple folding pathways from different unfolded and misfolded structures leading towards an ensemble of intermediates called cross-like structures (cross-hairpins), thus providing atomistic level of description of the single-molecule folding events. In summary, the parallel G-triplex is a possible, but not mandatory short-living (transitory) intermediate in the folding of parallel-stranded G4.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic
| | - Petra Kührová
- Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lukáš Vicherek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacky University, 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lukáš Trantírek
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Šlechtitelů 27, 771 46 Olomouc, Czech Republic.,Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic
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20
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Bonnat L, Dautriche M, Saidi T, Revol-Cavalier J, Dejeu J, Defrancq E, Lavergne T. Scaffold stabilization of a G-triplex and study of its interactions with G-quadruplex targeting ligands. Org Biomol Chem 2019; 17:8726-8736. [PMID: 31549116 DOI: 10.1039/c9ob01537j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-triplex nucleic acid structures (G3) have been conjectured to form in vivo but little is known about their physiological functions. The identification of ligands capable of specific binding to G3 structures is therefore highly appealing but remains elusive. Here we report on the assembly of a DNA conjugate which folds into a stable G3 structure. The structural mimic was used to probe the interactions between a G3 ligand and first-in-class G4 ligands, revealing signification binding promiscuity.
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Affiliation(s)
- Laureen Bonnat
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Maelle Dautriche
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Taous Saidi
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Johana Revol-Cavalier
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Jérôme Dejeu
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Eric Defrancq
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
| | - Thomas Lavergne
- Univ. Grenoble Alpes, Département de Chimie Moléculaire, CNRS, 570 rue de la chimie, CS 40700, Grenoble 38000, France.
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21
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Extreme mechanical diversity of human telomeric DNA revealed by fluorescence-force spectroscopy. Proc Natl Acad Sci U S A 2019; 116:8350-8359. [PMID: 30944218 DOI: 10.1073/pnas.1815162116] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
G-quadruplexes (GQs) can adopt diverse structures and are functionally implicated in transcription, replication, translation, and maintenance of telomere. Their conformational diversity under physiological levels of mechanical stress, however, is poorly understood. We used single-molecule fluorescence-force spectroscopy that combines fluorescence resonance energy transfer with optical tweezers to measure human telomeric sequences under tension. Abrupt GQ unfolding with K+ in solution occurred at as many as four discrete levels of force. Added to an ultrastable state and a gradually unfolding state, there were six mechanically distinct structures. Extreme mechanical diversity was also observed with Na+, although GQs were mechanically weaker. Our ability to detect small conformational changes at low forces enabled the determination of refolding forces of about 2 pN. Refolding was rapid and stochastically redistributed molecules to mechanically distinct states. A single guanine-to-thymine substitution mutant required much higher ion concentrations to display GQ-like unfolding and refolded via intermediates, contrary to the wild type. Contradicting an earlier proposal, truncation to three hexanucleotide repeats resulted in a single-stranded DNA-like mechanical behavior under all conditions, indicating that at least four repeats are required to form mechanically stable structures.
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22
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Abstract
Circular dichroism and stopped-flow UV spectroscopies were used to investigate the thermodynamic stability and the folding pathway of d[TGAG3TG3TAG3TG3TA2] at 25 °C in solutions containing 25 mM KCl. Under these conditions the oligonucleotide adopts a thermally stable, all-parallel G-quadruplex topography containing three stacked quartets. K+-induced folding shows three resolved relaxation times, each with distinctive spectral changes. Folding is complete within 200 s. These data indicate a folding pathway that involves at least two populated intermediates, one of which seems to be an antiparallel structure that rearranges to the final all-parallel conformation. Molecular dynamics reveals a stereochemically plausible folding pathway that does not involve complete unfolding of the intermediate. The rate of unfolding was determined using complementary DNA to trap transiently unfolded states to form a stable duplex. As assessed by 1D-1H NMR and fluorescence spectroscopy, unfolding is extremely slow with only one observable rate-limiting relaxation time.
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23
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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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24
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Masaki Y, Inde T, Maruyama A, Seio K. Tolerance of N 2-heteroaryl modifications on guanine bases in a DNA G-quadruplex. Org Biomol Chem 2019; 17:859-866. [DOI: 10.1039/c8ob03100b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To systematically determine the effect of N2-heteroaryl modification on the stability of G-quadruplex structures, six types of N2-heteroarylated deoxyguanosines were incorporated into oligonucleotides with intramolecular quadruplex-forming sequences obtained from the human telomere sequence.
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Affiliation(s)
- Yoshiaki Masaki
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Takeshi Inde
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Atsuya Maruyama
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohji Seio
- Department of Life Science and Technology
- Tokyo Institute of Technology
- Yokohama
- Japan
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25
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Abstract
Guanine-rich DNA oligonucleotides can adopt G-quadruplex (G4) structures in the presence of specific cations. Folding and unfolding of G4 can be characterized thermodynamically, providing the information on the stability of various G4 conformations. We show how the relevant thermodynamic and sometimes kinetic parameters are obtained by employing differential scanning calorimetry (DSC) and global fitting of an appropriate model to the DSC data. We demonstrate that best-fit values of the thermodynamic parameters can be interpreted in terms of the driving forces accompanying the G4 folding/interconversion and how they are translated into the phase diagrams, which provide an elegant description of the G4 phase space over a wide range of solution conditions.
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Affiliation(s)
- San Hadži
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
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26
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Prislan I, Sajko S, Ulrih NP, Fürst L. Proof of concept web application for understanding the energetic basis of oligonucleotide unfolding. RSC Adv 2019; 9:41453-41461. [PMID: 35541576 PMCID: PMC9076490 DOI: 10.1039/c9ra09800c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/27/2019] [Indexed: 11/21/2022] Open
Abstract
Measuring and quantifying thermodynamic parameters that determine both the stability of and interactions between biological macromolecules are an essential and necessary complement to structural studies. Although basic thermodynamic parameters for an observed process can be readily obtained, the data interpretation is often slow and analysis quality can be extremely variable. We have started to develop a web application that will help users to perform thermodynamic characterizations of oligonucleotide unfolding. The application can perform global fitting of calorimetric and spectroscopic data, and uses a three-state equilibrium model to obtain thermodynamic parameters for each transition step – namely, the Gibbs energy, the enthalpy, and the heat capacity. In addition, the application can define the number of K+ ions and the number of water molecules being released or taken up during unfolding. To test our application, we used UV spectroscopy, circular dichroism, and differential scanning calorimetry to monitor folding and unfolding of a model 22-nucleotide-long sequence of a human 3′-telomeric overhang, known as Tel22. The obtained data were uploaded to the web application and the global fit revealed that unfolding of Tel22 involves at least one intermediate state, and that K+ ions are released during the unfolding, whereas water molecules are taken up. A novel web application: performing global fitting of oligonucleotide unfolding experimental data in style.![]()
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Affiliation(s)
- Iztok Prislan
- Biotechnical Faculty
- University of Ljubljana
- Ljubljana
- Slovenia
| | - Sara Sajko
- Max Perutz Labs Vienna
- Medical University of Vienna
- 1030 Vienna
- Austria
| | | | - Luka Fürst
- Faculty of Computer and Information Science
- University of Ljubljana
- Ljubljana
- Slovenia
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27
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Bianchi F, Comez L, Biehl R, D’Amico F, Gessini A, Longo M, Masciovecchio C, Petrillo C, Radulescu A, Rossi B, Sacchetti F, Sebastiani F, Violini N, Paciaroni A. Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway. Nucleic Acids Res 2018; 46:11927-11938. [PMID: 30407585 PMCID: PMC6294516 DOI: 10.1093/nar/gky1092] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/28/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.
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Affiliation(s)
- Federico Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Ralf Biehl
- JCNS & ICS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
| | - Francesco D’Amico
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Marialucia Longo
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Aurel Radulescu
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Federico Sebastiani
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Nicolò Violini
- JCNS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
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28
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Lu XM, Li H, You J, Li W, Wang PY, Li M, Dou SX, Xi XG. Folding Dynamics of Parallel and Antiparallel G-Triplexes under the Influence of Proximal DNA. J Phys Chem B 2018; 122:9499-9506. [DOI: 10.1021/acs.jpcb.8b08110] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Xi-Ming Lu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing You
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - 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 100190, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
- LBPA, IDA, ENS Cachan, CNRS, Université Paris-Saclay, Cachan F-94235, France
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29
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Zhu J, Fleming AM, Burrows CJ. The RAD17 Promoter Sequence Contains a Potential Tail-Dependent G-Quadruplex That Downregulates Gene Expression upon Oxidative Modification. ACS Chem Biol 2018; 13:2577-2584. [PMID: 30063821 DOI: 10.1021/acschembio.8b00522] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our laboratory has recently proposed that the oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in G-rich promoter regions of DNA repair genes can serve as a regulatory mechanism of gene transcription. These regions also have the potential to fold into G-quadruplexes (G4). The human RAD17 promoter sequence has such a region in the template strand of the gene. In this work, the potential G-quadruplex sequence (PQS) of the RAD17 gene promoter was analyzed in different sequence contexts. With two extra nucleotides of the native sequence on either side of the G4, the structure was found to fold into a hybrid-like G4, similar to the hybrid-1 fold that the human telomere sequence can adopt. With only one nucleotide on either side of the PQS, the topology of the structure was observed to be mixed, and without extra nucleotides on the ends, the sequence adopted a parallel fold. Next, the sequence was studied with synthetic incorporation of the oxidative modification OG into specific sites and installed into the promoter of plasmids with a luciferase gene. These plasmids were transfected into a human cell line to observe the effect of the G4s on transcription. The RAD17 PQS was found to decrease luciferase expression with the presence of OG that is consistent with RAD17 expression under oxidative stress. This serves as an example of how oxidative modification could affect transcription in the context of a G4.
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Affiliation(s)
- Judy Zhu
- 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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30
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Marchand A, Rosu F, Zenobi R, Gabelica V. Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry. J Am Chem Soc 2018; 140:12553-12565. [PMID: 30183275 DOI: 10.1021/jacs.8b07302] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Designing ligands targeting G-quadruplex nucleic acid structures and affecting cellular processes is complicated because there are multiple target sequences and some are polymorphic. Further, structure alone does not reveal the driving forces for ligand binding. To know why a ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry enables one to detect and quantify each specific stoichiometry (number of strands, cations, and ligands) and thus to simultaneously determine the equilibrium constants for each complex. Using a temperature-controlled nanoelectrospray source, we determined the temperature dependence of the equilibrium constants, and thus the enthalpic and entropic contributions to the formation of each stoichiometry. Enthalpy drives the formation of each quartet-K+-quartet unit, whereas entropy drives the formation of quartet-K+-triplet units. Consequently, slip-stranded structures can become more abundant as the temperature increases. In the presence of ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy), we observed that, even when only a 1:1 (ligand/quadruplex) complex is observed at room temperature, new states are populated at intermediate temperatures, including 2:1 complexes. In most cases, ligand-G4-quadruplex binding is entropically driven, and we discuss that this may have resulted from biases when ranking ligand potency using melting experiments. Other thermodynamic profiles could be linked to topology changes in terms of number of G-quartets (reflected in the number of specific K+ ions in the complex). The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and topology changes in terms of number of G-quartets.
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Affiliation(s)
- Adrien Marchand
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Frédéric Rosu
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Valérie Gabelica
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
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Tian Y, Shuai Z, Shen J, Zhang L, Chen S, Song C, Zhao B, Fan Q, Wang L. Plasmonic Heterodimers with Binding Site-Dependent Hot Spot for Surface-Enhanced Raman Scattering. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800669. [PMID: 29736956 DOI: 10.1002/smll.201800669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/28/2018] [Indexed: 06/08/2023]
Abstract
A novel plasmonic heterodimer nanostructure with a controllable self-assembled hot spot is fabricated by the conjugation of individual Au@Ag core-shell nanocubes (Au@Ag NCs) and varisized gold nanospheres (GNSs) via the biotin-streptavidin interaction from the ensemble to the single-assembly level. Due to their featured configurations, three types of heterogeneous nanostructures referred to as Vertice, Vicinity, and Middle are proposed and a single hot spot forms between the nanocube and nanosphere, which exhibits distinct diversity in surface plasmon resonance effect. Herein, the calculated surface-enhanced Raman scattering enhancement factors of the three types of heterodimers show a narrow distribution and can be tuned in orders of magnitude by controlling the size of GNSs onto individual Au@Ag NCs. Particularly, the Vertice heterodimer with unique configuration can provide extraordinary enhancement of the electric field for the single hot spot region due to the collaborative interaction of lightning rod effect and interparticle plasmon coupling effect. This established relationship between the architecture and the corresponding optical properties of the heterodimers provides the basis for creating controllable platforms which can be exploited in the applications of plasmonic devices, electronics, and biodetection.
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Affiliation(s)
- Yuanyuan Tian
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Zhenhua Shuai
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Jingjing Shen
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lei Zhang
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Shufen Chen
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Chunyuan Song
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Baomin Zhao
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Quli Fan
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
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32
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Morgan RK, Molnar MM, Batra H, Summerford B, Wadkins RM, Brooks TA. Effects of 5-Hydroxymethylcytosine Epigenetic Modification on the Stability and Molecular Recognition of VEGF i-Motif and G-Quadruplex Structures. J Nucleic Acids 2018; 2018:9281286. [PMID: 29862069 PMCID: PMC5976936 DOI: 10.1155/2018/9281286] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/31/2018] [Accepted: 04/03/2018] [Indexed: 12/14/2022] Open
Abstract
Promoters often contain asymmetric G- and C-rich strands, in which the cytosines are prone to epigenetic modification via methylation (5-mC) and 5-hydroxymethylation (5-hmC). These sequences can also form four-stranded G-quadruplex (G4) or i-motif (iM) secondary structures. Although the requisite sequences for epigenetic modulation and iM/G4 formation are similar and can overlap, they are unlikely to coexist. Despite 5-hmC being an oxidization product of 5-mC, the two modified bases cluster at distinct loci. This study focuses on the intersection of G4/iM formation and 5-hmC modification using the vascular endothelial growth factor (VEGF) gene promoter's CpG sites and examines whether incorporation of 5-hmC into iM/G4 structures had any physicochemical effect on formation, stability, or recognition by nucleolin or the cationic porphyrin, TMPyP4. No marked changes were found in the formation or stability of iM and G4 structures; however, changes in recognition by nucleolin or TMPyP4 occurred with 5-hmC modification wherein protein and compound binding to 5-hmC modified G4s was notably reduced. G4/iM structures in the VEGF promoter are promising therapeutic targets for antiangiogenic therapy, and this work contributes to a comprehensive understanding of their governing principles related to potential transcriptional control and targeting.
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Affiliation(s)
- Rhianna K. Morgan
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Michael M. Molnar
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Harshul Batra
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
| | - Bethany Summerford
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Randy M. Wadkins
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677, USA
| | - Tracy A. Brooks
- School of Pharmacy, Department of BioMolecular Sciences, Division of Pharmacology, University of Mississippi, University, MS 38677, USA
- School of Pharmacy and Pharmaceutical Sciences, Department of Pharmaceutical Sciences, Binghamton University, Binghamton, NY 13902, USA
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33
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Zhou H, Wu ZF, Han QJ, Zhong HM, Peng JB, Li X, Fan XL. Stable and Label-Free Fluorescent Probe Based on G-triplex DNA and Thioflavin T. Anal Chem 2018; 90:3220-3226. [PMID: 29378390 DOI: 10.1021/acs.analchem.7b04666] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
G-triplexes have recently been identified as a new kind of DNA structures. They perhaps possess specific biological and chemical functions similar as identified G-quadruplex but can be formed by shorter G-rich sequences with only three G-tracts. However, until now, limited G-triplexes sequences have been reported, which might be due to the fact that their stability is one of the biggest concerns during their functional studies and application research. Herein, we found a G-rich sequence (5'-TGGGTAGGGCGGG-3') which can form a stable G-triplex (Tm ∼ 60 °C) at room temperature. The stable G-triplex can combine with thioflavin T and function as an efficient fluorescence light-up probe. Comparing with the traditional G-quadruplex based probe, this triplex based probe was easy to be controlled and excited. Finally, the probe was successfully applied into constructing a label-free molecular beacon for miRNA detection. Taking advantage of these abilities of the G-triplex based fluorescent probe, the challenges faced during designing G-rich sequences based fluorescent biosensors can be efficiently solved. These findings provide important information for the future application of G-triplex.
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Affiliation(s)
- Hui Zhou
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Zhi-Fang Wu
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Qian-Jin Han
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Hong-Mei Zhong
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Jun-Bin Peng
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Xun Li
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
| | - Xiao-Lin Fan
- College of Chemistry and Chemical Engineering , Gannan Normal University , Ganzhou , 341000 , China
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34
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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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35
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Hou XM, Fu YB, Wu WQ, Wang L, Teng FY, Xie P, Wang PY, Xi XG. Involvement of G-triplex and G-hairpin in the multi-pathway folding of human telomeric G-quadruplex. Nucleic Acids Res 2017; 45:11401-11412. [PMID: 28977514 PMCID: PMC5737514 DOI: 10.1093/nar/gkx766] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 08/22/2017] [Indexed: 01/07/2023] Open
Abstract
G-quadruplex (G4) can be formed by G-rich DNA sequences that are widely distributed throughout the human genome. Although G-triplex and G-hairpin have been proposed as G4 folding intermediates, their formation still requires further investigation by experiments. Here, we employed single-molecule FRET to characterize the folding dynamics of G4 from human telomeric sequence. First, we observed four states during G4 folding initially assigned to be anti-parallel G4, G-triplex, G-hairpin and unfolded ssDNA. Then we constructed putative intra-strand G-triplex, G-hairpin structures and confirmed their existences in both NaCl and KCl. Further studies revealed those structures are going through dynamic transitions between different states and show relatively weak dependence on cations, unlike G4. Based on those results and molecular dynamics simulations, we proposed a multi-pathway folding mechanism for human telomeric G4. The present work may shed new light on our current understanding about the existence and stability of G4 intermediate states.
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Affiliation(s)
- Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yi-Ben Fu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Wen-Qiang Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Wang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fang-Yuan Teng
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ping Xie
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Peng-Ye Wang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China.,Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normale Supérieure de Cachan, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235 Cachan, France
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36
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Sagi J. In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids? J Nucleic Acids 2017; 2017:1641845. [PMID: 29181193 PMCID: PMC5664352 DOI: 10.1155/2017/1641845] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/15/2017] [Indexed: 01/03/2023] Open
Abstract
Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events.
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Affiliation(s)
- Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
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37
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Carr CE, Marky LA. Melting Behavior of a DNA Four-Way Junction Using Spectroscopic and Calorimetric Techniques. J Am Chem Soc 2017; 139:14443-14455. [DOI: 10.1021/jacs.7b06429] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carolyn E. Carr
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
| | - Luis A. Marky
- Department of Pharmaceutical
Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025, United States
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38
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Rigo R, Sissi C. Characterization of G4-G4 Crosstalk in the c-KIT Promoter Region. Biochemistry 2017; 56:4309-4312. [PMID: 28763217 DOI: 10.1021/acs.biochem.7b00660] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The proximal promoter of c-KIT contains a peculiar domain that consists of three short G-rich sequences that are close together and can fold into noncanonical DNA secondary structures called G-quadruplexes (G4). Here, we focused on a sequence containing two consecutive G4 (kit2 and kit*). By electrophoretic, surface plasmon resonance, and spectroscopic techniques, we demonstrated that they retain the ability to fold into G4 upon being inserted into the extended sequence. Here, we highlighted the occurrence of crosstalk between the two forming units. This previously unexplored G4-G4 interaction modulates both the conformation and the stability of the overall arrangement of the c-KIT promoter. It is not supported by stacking of single nucleotides but refers to a G4-G4 interaction surface surrounded by a two-nucleotides loop that might represent a reliable unprecedented target for anticancer therapy.
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Affiliation(s)
- Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , Via Marzolo 5, 35131 Padova, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , Via Marzolo 5, 35131 Padova, Italy
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39
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Aslanyan L, Ko J, Kim BG, Vardanyan I, Dalyan YB, Chalikian TV. Effect of Urea on G-Quadruplex Stability. J Phys Chem B 2017; 121:6511-6519. [DOI: 10.1021/acs.jpcb.7b03479] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lusine Aslanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Jordan Ko
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Byul G. Kim
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Ishkhan Vardanyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Yeva B. Dalyan
- Department
of Molecular Physics, Faculty of Physics, Yerevan State University, 1 Alex Manoogian Street, Yerevan 375025, Armenia
| | - Tigran V. Chalikian
- Department
of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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40
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Abstract
Based on the Shannon's information communication theory, information amount of the entire length of a polymeric macromolecule can be calculated in bits through adding the entropies of each building block. Proteins, DNA and RNA are such macromolecules. When only the building blocks' variation is considered as the source of entropy, there is seemingly lower information in case of the protein if this approach is applied directly on a protein of specific size and the coding sequence size of the mRNA corresponding to the particular length of the protein. This decrease in the information amount seems contradictory but this apparent conflict is resolved by considering the conformational variations in proteins as a new variable in the calculation and balancing the approximated entropy of the coding part of the mRNA and the protein. Probabilities can change therefore we also assigned hypothetical probabilities to the conformational states, which represent the uneven distribution as the time spent in one conformation, providing the probability of the presence in either or one of the possible conformations. Results that are obtained by using hypothetical probabilities are in line with the experimental values of variations in the conformational-state of protein populations. This equalization approach has further biological relevance that it compensates for the degeneracy in the codon usage during protein translation and it leads to the conclusion that the alphabet size for the protein is rather optimal for the proper protein functioning within the thermodynamic milieu of the cell. The findings were also discussed in relation to the codon bias and have implications in relation to the codon evolution concept. Eventually, this work brings the fields of protein structural studies and molecular protein translation processes together with a novel approach.
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Affiliation(s)
- Y Adiguzel
- Biophysics Department, School of Medicine, Istanbul Kemerburgaz University, Istanbul, Turkey.
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41
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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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42
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Endoh T, Sugimoto N. Conformational Dynamics of mRNA in Gene Expression as New Pharmaceutical Target. CHEM REC 2017; 17:817-832. [DOI: 10.1002/tcr.201700016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Tamaki Endoh
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
- Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST); Konan University; 7-1-20 Minatojima-minamimachi Chuo-ku, Kobe 650-0047 Japan
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43
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Ruan TL, Davis SJ, Powell BM, Harbeck CP, Habdas J, Habdas P, Yatsunyk LA. Lowering the overall charge on TMPyP4 improves its selectivity for G-quadruplex DNA. Biochimie 2017; 132:121-130. [DOI: 10.1016/j.biochi.2016.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022]
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44
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Stadlbauer P, Mazzanti L, Cragnolini T, Wales DJ, Derreumaux P, Pasquali S, Šponer J. Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes. J Chem Theory Comput 2016; 12:6077-6097. [DOI: 10.1021/acs.jctc.6b00667] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Petr Stadlbauer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
- Regional
Centre of Advanced Technologies and Materials, Departments of Physical
Chemistry, Faculty of Science, Palacký University, 17. listopadu
1192/12, 771 46 Olomouc, Czech Republic
| | - Liuba Mazzanti
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Tristan Cragnolini
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J. Wales
- Department
of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Philippe Derreumaux
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Samuela Pasquali
- Laboratoire
de Biochimie Théorique, IBPC, CNRS UPR9080, Université Sorbonne Paris Cite, Paris Diderot, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Jiří Šponer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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45
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Aznauryan M, Søndergaard S, Noer SL, Schiøtt B, Birkedal V. A direct view of the complex multi-pathway folding of telomeric G-quadruplexes. Nucleic Acids Res 2016; 44:11024-11032. [PMID: 27799468 PMCID: PMC5159523 DOI: 10.1093/nar/gkw1010] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 10/14/2016] [Accepted: 10/24/2016] [Indexed: 01/28/2023] Open
Abstract
G-quadruplexes (G4s) are DNA secondary structures that are capable of forming and function in vivo. The propensity of G4s to exhibit extreme polymorphism and complex dynamics is likely to influence their cellular function, yet a clear microscopic picture of their folding process is lacking. Here we employed single-molecule FRET microscopy to obtain a direct view of the folding and underlying conformational dynamics of G4s formed by the human telomeric sequence in potassium containing solutions. Our experiments allowed detecting several folded states that are populated in the course of G4 folding and determining their folding energetics and timescales. Combining the single-molecule data with molecular dynamics simulations enabled obtaining a structural description of the experimentally observed folded states. Our work thus provides a comprehensive thermodynamic and kinetic description of the folding of G4s that proceeds through a complex multi-route pathway, involving several marginally stable conformational states.
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Affiliation(s)
- Mikayel Aznauryan
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Siri Søndergaard
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Sofie L Noer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark
| | - Birgit Schiøtt
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark.,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark .,Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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46
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Marchand A, Gabelica V. Folding and misfolding pathways of G-quadruplex DNA. Nucleic Acids Res 2016; 44:10999-11012. [PMID: 27924036 PMCID: PMC5159560 DOI: 10.1093/nar/gkw970] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/07/2016] [Accepted: 10/15/2016] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K+ binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K+ at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel. Flanking bases increase the K+ binding cooperativity. To decipher the folding pathways, we investigated the kinetics of K+ binding to telomeric (hybrid) and c-myc (parallel) G-quadruplexes. G-quadruplexes fold via branched pathways with multiple parallel reactions. Up to six states (one ensemble without K+, two ensembles with 1-K+ and three ensembles with 2-K+) are separated based on their formation rates and ion mobility spectrometry. All G-quadruplexes first form long-lived misfolded structures (off-pathway compared to the most stable structures) containing one K+ and two quartets in an antiparallel stacking arrangement. The results highlight the particular ruggedness of G-quadruplex nucleic acid folding landscapes. Misfolded structures can play important roles for designing artificial G-quadruplex based structures, and for conformational selection by ligands or proteins in a biological context.
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Affiliation(s)
- Adrien Marchand
- INSERM, CNRS, Univ. Bordeaux, U1212 / UMR5320 - Acides Nucléiques: Régulations Naturelle et Artificielle, IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Valérie Gabelica
- INSERM, CNRS, Univ. Bordeaux, U1212 / UMR5320 - Acides Nucléiques: Régulations Naturelle et Artificielle, IECB, 2 rue Robert Escarpit, 33607 Pessac, France
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47
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Wang X, Pei L, Fan X, Shi S. [Ru(L) 2 (3-tppp)] 2+ (L = bpy, phen) stabilizes two different forms of the human telomeric G-quadruplex DNA. INORG CHEM COMMUN 2016. [DOI: 10.1016/j.inoche.2016.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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48
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Bončina M, Vesnaver G, Chaires JB, Lah J. Unraveling the Thermodynamics of the Folding and Interconversion of Human Telomere G-Quadruplexes. Angew Chem Int Ed Engl 2016; 55:10340-4. [PMID: 27484724 DOI: 10.1002/anie.201605350] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Indexed: 12/22/2022]
Abstract
Why human telomere DNA fragments fold into different G-quadruplex structures with parallel, hybrid, and antiparallel strand orientations depending on the temperature and concentration of co-solutes remains poorly understood. Similarly, the formation of intermediate structures along the folding or interconversion pathways is not well understood. Herein, we address these questions by introducing a conceptual framework, based on the global thermodynamic analysis of DSC and CD spectroscopy data, which led to a detailed description of the topological phase space (phase diagram) of the stability of the human telomere fragment 5'-AGGG(TTAGGG)3 -3' (Tel22). This framework clarifies the driving forces of quadruplex folding and interconversion processes over a wide range of temperatures and ion (K(+) , Na(+) ) and polyethylene glycol (PEG) concentrations and demonstrates their linkage to the human telomere DNA structural features.
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Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Gorazd Vesnaver
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia
| | - Jonathan Brad Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY, 40202, USA.
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana, Slovenia.
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49
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Bončina M, Vesnaver G, Chaires JB, Lah J. Unraveling the Thermodynamics of the Folding and Interconversion of Human Telomere G-Quadruplexes. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605350] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Matjaž Bončina
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Gorazd Vesnaver
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
| | - Jonathan Brad Chaires
- James Graham Brown Cancer Center; University of Louisville; 505 S. Hancock St. Louisville KY 40202 USA
| | - Jurij Lah
- Faculty of Chemistry and Chemical Technology; University of Ljubljana; Večna pot 113 Ljubljana Slovenia
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50
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Tian Y, Zhang L, Shen J, Wu L, He H, Ma DL, Leung CH, Wu W, Fan Q, Huang W, Wang L. An Individual Nanocube-Based Plasmonic Biosensor for Real-Time Monitoring the Structural Switch of the Telomeric G-Quadruplex. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2913-2920. [PMID: 27106517 DOI: 10.1002/smll.201600041] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/08/2016] [Indexed: 06/05/2023]
Abstract
Promoted by the localized surface plasmon resonance nanotechnology, a simple and sensitive plasmonic aptamer nanosensor (nanoaptasensor) on an individual Au@Ag core-shell nanocube (Au@Ag NC) has been proposed for real-time monitoring of the formation process of G-quadruplex structures and label-free analysis of potassium ions (K(+) ). In particular, the analysis of the thermodynamic parameters indicates that there are two types of binding states accompanied with a remarkable change of free energy (ΔG) in the sequential folding process of telomere DNA sequence. This nanoaptasensor has raised promising applications in monitoring the dynamic process of the structural switch of the G-quadruplex.
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Affiliation(s)
- Yuanyuan Tian
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lei Zhang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Jingjing Shen
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lingzhi Wu
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Hongzhang He
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
| | - Weibing Wu
- Jiangsu Provincial Key Lab of Pulp and Paper Science and Technology, Nanjing Forestry University, Nanjing, 210037, China
| | - Quli Fan
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Wei Huang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, 30 South Puzhu Road, Nanjing, 211816, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts & Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
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