1
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Zhang Z, Mlýnský V, Krepl M, Šponer J, Stadlbauer P. Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations. J Chem Inf Model 2024; 64:3896-3911. [PMID: 38630447 PMCID: PMC11094737 DOI: 10.1021/acs.jcim.4c00227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 05/14/2024]
Abstract
Guanine quadruplex (GQ) is a noncanonical nucleic acid structure formed by guanine-rich DNA and RNA sequences. Folding of GQs is a complex process, where several aspects remain elusive, despite being important for understanding structure formation and biological functions of GQs. Pulling experiments are a common tool for acquiring insights into the folding landscape of GQs. Herein, we applied a computational pulling strategy─steered molecular dynamics (SMD) simulations─in combination with standard molecular dynamics (MD) simulations to explore the unfolding landscapes of tetrameric parallel GQs. We identified anisotropic properties of elastic conformational changes, unfolding transitions, and GQ mechanical stabilities. Using a special set of structural parameters, we found that the vertical component of pulling force (perpendicular to the average G-quartet plane) plays a significant role in disrupting GQ structures and weakening their mechanical stabilities. We demonstrated that the magnitude of the vertical force component depends on the pulling anchor positions and the number of G-quartets. Typical unfolding transitions for tetrameric parallel GQs involve base unzipping, opening of the G-stem, strand slippage, and rotation to cross-like structures. The unzipping was detected as the first and dominant unfolding event, and it usually started at the 3'-end. Furthermore, results from both SMD and standard MD simulations indicate that partial spiral conformations serve as a transient ensemble during the (un)folding of GQs.
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Affiliation(s)
- Zhengyue Zhang
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
- CEITEC−Central
European Institute of Technology, Masaryk
University, Kamenice
5, Brno 625 00, Czech Republic
- National
Center for Biomolecular Research,
Faculty of Science, Masaryk University, Kamenice 5, Brno 625 00, Czech Republic
| | - Vojtěch Mlýnský
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Miroslav Krepl
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Jiří Šponer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics of the Czech Academy of Sciences, Královopolská 135, Brno 61200, Czech Republic
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2
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Ranjan N, Arya DP. Parallel G-quadruplex recognition by neomycin. Front Chem 2023; 11:1232514. [PMID: 37671393 PMCID: PMC10475565 DOI: 10.3389/fchem.2023.1232514] [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: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023] Open
Abstract
G-quadruplex-forming nucleic acids have evolved to have applications in biology, drug design, sensing, and nanotechnology, to name a few. Together with the structural understanding, several attempts have been made to discover and design new classes of chemical agents that target these structures in the hope of using them as future therapeutics. Here, we report the binding of aminoglycosides, in particular neomycin, to parallel G-quadruplexes that exist as G-quadruplex monomers, dimers, or compounds that have the propensity to form dimeric G-quadruplex structures. Using a combination of calorimetric and spectroscopic studies, we show that neomycin binds to the parallel G-quadruplex with affinities in the range of Ka ∼ 105-108 M-1, which depends on the base composition, ability to form dimeric G-quadruplex structures, salt, and pH of the buffer used. At pH 7.0, the binding of neomycin was found to be electrostatically driven potentially through the formation of ion pairs formed with the quadruplex. Lowering the pH resulted in neomycin's association constants in the range of Ka ∼ 106-107 M-1 in a salt dependent manner. Circular dichroism (CD) studies showed that neomycin's binding does not cause a change in the parallel conformation of the G-quadruplex, yet some binding-induced changes in the intensity of the CD signals were seen. A comparative binding study of neomycin and paromomycin using d(UG4T) showed paromomycin binding to be much weaker than neomycin, highlighting the importance of ring I in the recognition process. In toto, our results expanded the binding landscape of aminoglycosides where parallel G-quadruplexes have been discovered as one of the high-affinity sites. These results may offer a new understanding of some of the undesirable functions of aminoglycosides and help in the design of aminoglycoside-based G-quadruplex binders of high affinity.
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Affiliation(s)
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
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3
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Asha H, Green JA, Esposito L, Santoro F, Improta R. Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization. Chirality 2023; 35:298-310. [PMID: 36775278 DOI: 10.1002/chir.23540] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/14/2023]
Abstract
In this study, we exploit a recently developed fragment diabatization-based excitonic model, FrDEx, to simulate the electronic circular dichroism (ECD) spectra of three guanine-rich DNA sequences arranged in guanine quadruple helices with different topologies: thrombin binding aptamer (antiparallel), c-Myc promoter (parallel), and human telomeric sequence (3+1 hybrid). Starting from time-dependent density functional theory (TD-DFT) calculations with the M052X functional, we apply our protocol to parameterize the FrDEX Hamiltonian, which accounts for electron density overlap and includes both the coupling with charge transfer transitions and the effect of the surrounding bases on the local excitation of each chromophore. The TD-DFT/M052X spectral shapes are in good agreement with the experimental ones, the main source of discrepancy being related to the intrinsic error on the computed transition energies of guanine monomer. FrDEx spectra are fairly close to the reference TD-DFT ones, allowing a significant advance with respect to a more standard excitonic Hamiltonian. We also show that the ECD spectra are sensitive to the inclusion of the inner K + $$ {}^{+} $$ cation in the calculation.
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Affiliation(s)
- Haritha Asha
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - James A Green
- Institut für Physikalische Theoretische Chemie, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
| | | | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM-CNR), Area della Ricerca del CNR, Pisa, Italy
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4
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Cucinotta A, Kahlfuss C, Minoia A, Eyley S, Zwaenepoel K, Velpula G, Thielemans W, Lazzaroni R, Bulach V, Hosseini MW, Mali KS, De Feyter S. Metal Ion and Guest-Mediated Spontaneous Resolution and Solvent-Induced Chiral Symmetry Breaking in Guanine-Based Metallosupramolecular Networks. J Am Chem Soc 2023; 145:1194-1205. [PMID: 36576950 DOI: 10.1021/jacs.2c10933] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Two-dimensional (2D) chirality has been actively studied in view of numerous applications of chiral surfaces such as in chiral resolutions and enantioselective catalysis. Here, we report on the expression and amplification of chirality in hybrid 2D metallosupramolecular networks formed by a nucleobase derivative. Self-assembly of a guanine derivative appended with a pyridyl node was studied at the solution-graphite interface in the presence and absence of coordinating metal ions. In the absence of coordinating metal ions, a monolayer that is representative of a racemic compound was obtained. This system underwent spontaneous resolution upon addition of a coordinating ion and led to the formation of a racemic conglomerate. The spontaneous resolution could also be achieved upon addition of a suitable guest molecule. The mirror symmetry observed in the formation of the metallosupramolecular networks could be broken via the use of an enantiopure solvent, which led to the formation of a globally homochiral surface.
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Affiliation(s)
- Antonino Cucinotta
- Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Christophe Kahlfuss
- CMC UMR 7140, Université de Strasbourg, CNRS, 4 Rue Blaise Pascal, F-67000 Strasbourg, France
| | - Andrea Minoia
- Laboratory for Chemistry of Novel Materials, Materials Research Institute, University of Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Samuel Eyley
- Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, Campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Keanu Zwaenepoel
- Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Gangamallaiah Velpula
- Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Wim Thielemans
- Sustainable Materials Lab, Department of Chemical Engineering, KU Leuven, Campus Kulak Kortrijk, Etienne Sabbelaan 53, 8500 Kortrijk, Belgium
| | - Roberto Lazzaroni
- Laboratory for Chemistry of Novel Materials, Materials Research Institute, University of Mons, Place du Parc 20, 7000 Mons, Belgium
| | - Véronique Bulach
- CMC UMR 7140, Université de Strasbourg, CNRS, 4 Rue Blaise Pascal, F-67000 Strasbourg, France
| | - Mir Wais Hosseini
- CMC UMR 7140, Université de Strasbourg, CNRS, 4 Rue Blaise Pascal, F-67000 Strasbourg, France
| | - Kunal S Mali
- Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Steven De Feyter
- Division of Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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5
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Balanikas E, Gustavsson T, Markovitsi D. Fluorescence of Bimolecular Guanine Quadruplexes: From Femtoseconds to Nanoseconds. J Phys Chem B 2023; 127:172-179. [PMID: 36577031 DOI: 10.1021/acs.jpcb.2c07647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The paper deals with the fluorescence of guanine quadruplexes (G4) formed by association of two DNA strands d(GGGGTTTTGGGG) in the presence of K+ cations, noted as OXY/K+ in reference to the protozoon Oxytricha nova, whose telomere contains TTTTGGGG repeats. They were studied by steady-state and time-resolved techniques, time-correlated single photon counting, and fluorescence upconversion. The maximum of the OXY/K+ fluorescence spectrum is located at 334 nm, and the quantum yield is 5.8 × 10-4. About 75% of the photons are emitted before 100 ps and stem from ππ* states, possibly with a small contribution of charge transfer. Time-resolved fluorescence anisotropy measurements indicate that ultrafast (<330 fs) excitation transfer, due to internal conversion among exciton states, is more efficient in OXY/K+ compared to previously studied G4 structures. This is attributed to the arrangement of the peripheral thymines in two diagonal loops with restricted mobility, facilitating the interaction among them and with guanines. Thymines should also be responsible for a weak intensity excimer/exciplex emission band, peaking at 445 nm. Finally, the longest living fluorescence component (∼2.1 ns) is observed at the blue side of the spectrum. So far, high-energy long-lived emitting states had been reported only for double-stranded structures but not for G4.
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Affiliation(s)
| | - Thomas Gustavsson
- CEA, CNRS, LIDYL, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- CEA, CNRS, LIDYL, Université Paris-Saclay, F-91191 Gif-sur-Yvette, France.,CNRS, Institut de Chimie Physique, UMR8000, Université Paris-Saclay, 91405 Orsay, France
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6
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Dubrovin EV, Barinov NA, Klinov DV. Visualization of G-Quadruplexes, i-Motifs and Their Associates. Acta Naturae 2022; 14:4-18. [DOI: 10.32607/actanaturae.11705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/13/2022] [Indexed: 11/20/2022] Open
Abstract
The non-canonical structures formed by G- or C-rich DNA regions, such as quadruplexes and i-motifs, as well as their associates, have recently been attracting increasing attention both because of the arguments in favor of their existence in vivo and their potential application in nanobiotechnology. When studying the structure and properties of non-canonical forms of DNA, as well as when controlling the artificially created architectures based on them, visualization plays an important role. This review analyzes the methods used to visualize quadruplexes, i-motifs, and their associates with high spatial resolution: fluorescence microscopy, transmission electron microscopy (TEM), and atomic force microscopy (AFM). The key approaches to preparing specimens for the visualization of this type of structures are presented. Examples of visualization of non-canonical DNA structures having various morphologies, such as G-wires, G-loops, as well as individual quadruplexes, i-motifs and their associates, are considered. The potential for using AFM for visualizing non-canonical DNA structures is demonstrated.
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7
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Abstract
![]()
Oxidation of a guanine nucleotide in DNA yields an 8-oxoguanine
nucleotide (oxoG) and is a mutagenic event in the genome.
Due to different arrangements of hydrogen-bond donors and acceptors, oxoG can affect the secondary structure of nucleic acids. We
have investigated base pairing preferences of oxoG in the
core of a tetrahelical G-quadruplex structure, adopted by analogues
of d(TG4T). Using spectroscopic methods, we have shown
that G-quartets can be fully substituted with oxoG nucleobases
to form an oxoG-quartet with a revamped hydrogen-bonding
scheme. While an oxoG-quartet can be incorporated into
the G-quadruplex core without distorting the phosphodiester backbone,
larger dimensions of the central cavity change the cation localization
and exchange properties.
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Affiliation(s)
- Simon Aleksič
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Peter Podbevšek
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Janez Plavec
- Slovenian NMR Centre, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.,Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg OF 13, 1000 Ljubljana, Slovenia
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8
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Cueny RR, McMillan SD, Keck JL. G-quadruplexes in bacteria: insights into the regulatory roles and interacting proteins of non-canonical nucleic acid structures. Crit Rev Biochem Mol Biol 2022; 57:539-561. [PMID: 36999585 PMCID: PMC10336854 DOI: 10.1080/10409238.2023.2181310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 12/13/2022] [Accepted: 02/13/2023] [Indexed: 04/01/2023]
Abstract
G-quadruplexes (G4s) are highly stable, non-canonical DNA or RNA structures that can form in guanine-rich stretches of nucleic acids. G4-forming sequences have been found in all domains of life, and proteins that bind and/or resolve G4s have been discovered in both bacterial and eukaryotic organisms. G4s regulate a variety of cellular processes through inhibitory or stimulatory roles that depend upon their positions within genomes or transcripts. These include potential roles as impediments to genome replication, transcription, and translation or, in other contexts, as activators of genome stability, transcription, and recombination. This duality suggests that G4 sequences can aid cellular processes but that their presence can also be problematic. Despite their documented importance in bacterial species, G4s remain understudied in bacteria relative to eukaryotes. In this review, we highlight the roles of bacterial G4s by discussing their prevalence in bacterial genomes, the proteins that bind and unwind G4s in bacteria, and the processes regulated by bacterial G4s. We identify limitations in our current understanding of the functions of G4s in bacteria and describe new avenues for studying these remarkable nucleic acid structures.
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Affiliation(s)
- Rachel R. Cueny
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Sarah D. McMillan
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - James L. Keck
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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9
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Ngo KH, Liew CW, Lattmann S, Winnerdy FR, Phan AT. Crystal structures of an HIV-1 integrase aptamer: Formation of a water-mediated A•G•G•G•G pentad in an interlocked G-quadruplex. Biochem Biophys Res Commun 2022; 613:153-158. [DOI: 10.1016/j.bbrc.2022.04.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/27/2022]
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10
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Beseiso D, Chen EV, McCarthy SE, Martin KN, Gallagher EP, Miao J, Yatsunyk L. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2959-2972. [PMID: 35212369 PMCID: PMC8934647 DOI: 10.1093/nar/gkac091] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/13/2022] Open
Abstract
G-quadruplexes (GQs) are non-canonical DNA structures composed of stacks of stabilized G-tetrads. GQs play an important role in a variety of biological processes and may form at telomeres and oncogene promoters among other genomic locations. Here, we investigate nine variants of telomeric DNA from Tetrahymena thermophila with the repeat (TTGGGG)n. Biophysical data indicate that the sequences fold into stable four-tetrad GQs which adopt multiple conformations according to native PAGE. Excitingly, we solved the crystal structure of two variants, TET25 and TET26. The two variants differ by the presence of a 3′-T yet adopt different GQ conformations. TET25 forms a hybrid [3 + 1] GQ and exhibits a rare 5′-top snapback feature. Consequently, TET25 contains four loops: three lateral (TT, TT, and GTT) and one propeller (TT). TET26 folds into a parallel GQ with three TT propeller loops. To the best of our knowledge, TET25 and TET26 are the first reported hybrid and parallel four-tetrad unimolecular GQ structures. The results presented here expand the repertoire of available GQ structures and provide insight into the intricacy and plasticity of the 3D architecture adopted by telomeric repeats from T. thermophila and GQs in general.
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Affiliation(s)
- Dana Beseiso
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Erin V Chen
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Sawyer E McCarthy
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Kailey N Martin
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Elizabeth P Gallagher
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Department of Chemistry and Biochemistry, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA
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11
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Asha H, Stadlbauer P, Martínez-Fernández L, Banáš P, Šponer J, Improta R, Esposito L. Early steps of oxidative damage in DNA quadruplexes are position-dependent: Quantum mechanical and molecular dynamics analysis of human telomeric sequence containing ionized guanine. Int J Biol Macromol 2022; 194:882-894. [PMID: 34838862 DOI: 10.1016/j.ijbiomac.2021.11.143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/17/2022]
Abstract
Guanine radical cation (G•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)3 (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G•+ (Tel21+). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21+ systems, differing in the position of G•+ in the sequence. When G•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na+ ions and increase the solvent exposed surface of G•+. Analysis of solvation patterns of G•+ provides new insights on the main reactions of G•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.
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Affiliation(s)
- Haritha Asha
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Lara Martínez-Fernández
- Departamento de Quimica, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autonoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Pavel Banáš
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic; Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute, Palacký University, Křížkovského 8, 779 00 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
| | - Luciana Esposito
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, 80136 Napoli, Italy.
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12
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Marilovtseva EV, Studitsky VM. Guanine Quadruplexes in Cell Nucleus Metabolism. Mol Biol 2021. [DOI: 10.1134/s0026893321040075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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13
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Balanikas E, Martinez-Fernandez L, Improta R, Podbevšek P, Baldacchino G, Markovitsi D. The Structural Duality of Nucleobases in Guanine Quadruplexes Controls Their Low-Energy Photoionization. J Phys Chem Lett 2021; 12:8309-8313. [PMID: 34428044 DOI: 10.1021/acs.jpclett.1c01846] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Guanine quadruplexes are four-stranded DNA/RNA structures composed of a guanine core (vertically stacked guanine tetrads) and peripheral groups (dangling ends and/or loops). Such a dual structural arrangement of the nucleobases favors their photoionization at energies significantly lower than the guanine ionization potential. This effect is important with respect to the oxidative DNA damage and for applications in the field of optoelectronics. Photoionization quantum yields, determined at 266 nm by nanosecond transient absorption spectroscopy, strongly depend on both the type and position of the peripheral nucleobases. The highest value (1.5 × 10-2) is found for the tetramolecular structure (AG4A)4 in which adenines are intermittently stacked on the adjacent guanine tetrads, as determined by nuclear magnetic resonance spectroscopy. Quantum chemistry calculations show that peripheral nucleobases interfere in a key step preceding electron ejection: charge separation, initiated by the population of charge transfer states during the relaxation of electronic excited states.
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Affiliation(s)
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Peter Podbevšek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia
| | - Gérard Baldacchino
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CEA, CNRS, LIDYL, F-91191 Gif-sur-Yvette, France
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14
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Park G, Kang B, Park SV, Lee D, Oh SS. A unified computational view of DNA duplex, triplex, quadruplex and their donor-acceptor interactions. Nucleic Acids Res 2021; 49:4919-4933. [PMID: 33893806 PMCID: PMC8136788 DOI: 10.1093/nar/gkab285] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/07/2021] [Accepted: 04/14/2021] [Indexed: 01/09/2023] Open
Abstract
DNA can assume various structures as a result of interactions at atomic and molecular levels (e.g., hydrogen bonds, π–π stacking interactions, and electrostatic potentials), so understanding of the consequences of these interactions could guide development of ways to produce elaborate programmable DNA for applications in bio- and nanotechnology. We conducted advanced ab initio calculations to investigate nucleobase model structures by componentizing their donor-acceptor interactions. By unifying computational conditions, we compared the independent interactions of DNA duplexes, triplexes, and quadruplexes, which led us to evaluate a stability trend among Watson–Crick and Hoogsteen base pairing, stacking, and even ion binding. For a realistic solution-like environment, the influence of water molecules was carefully considered, and the potassium-ion preference of G-quadruplex was first analyzed at an ab initio level by considering both base-base and ion-water interactions. We devised new structure factors including hydrogen bond length, glycosidic vector angle, and twist angle, which were highly effective for comparison between computationally-predicted and experimentally-determined structures; we clarified the function of phosphate backbone during nucleobase ordering. The simulated tendency of net interaction energies agreed well with that of real world, and this agreement validates the potential of ab initio study to guide programming of complicated DNA constructs.
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Affiliation(s)
- Gyuri Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Donghwa Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea.,Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea.,School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
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15
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Alenaizan A, Borca CH, Karunakaran SC, Kendall AK, Stubbs G, Schuster GB, Sherrill CD, Hud NV. X-ray Fiber Diffraction and Computational Analyses of Stacked Hexads in Supramolecular Polymers: Insight into Self-Assembly in Water by Prospective Prebiotic Nucleobases. J Am Chem Soc 2021; 143:6079-6094. [DOI: 10.1021/jacs.0c12010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Carlos H. Borca
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Suneesh C. Karunakaran
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
| | - Amy K. Kendall
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Gerald Stubbs
- Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Gary B. Schuster
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
- Center for Computational Molecular Science and Technology, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0765, United States
| | - Nicholas V. Hud
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
- NSF-NASA Center for Chemical Evolution, Atlanta, Georgia 30332-0400, United States
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16
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Das P, Ngo KH, Winnerdy FR, Maity A, Bakalar B, Mechulam Y, Schmitt E, Phan AT. Bulges in left-handed G-quadruplexes. Nucleic Acids Res 2021; 49:1724-1736. [PMID: 33503265 PMCID: PMC7897477 DOI: 10.1093/nar/gkaa1259] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/10/2020] [Accepted: 12/18/2020] [Indexed: 12/03/2022] Open
Abstract
G-quadruplex (G4) DNA structures with a left-handed backbone progression have unique and conserved structural features. Studies on sequence dependency of the structures revealed the prerequisites and some minimal motifs required for left-handed G4 formation. To extend the boundaries, we explore the adaptability of left-handed G4s towards the existence of bulges. Here we present two X-ray crystal structures and an NMR solution structure of left-handed G4s accommodating one, two and three bulges. Bulges in left-handed G4s show distinct characteristics as compared to those in right-handed G4s. The elucidation of intricate structural details will help in understanding the possible roles and limitations of these unique structures.
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Affiliation(s)
- Poulomi Das
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Khac Huy Ngo
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule (BIOC), Ecole Polytechnique, CNRS-UMR7654, Institut Polytechnique de Paris, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.,NTU Institute of Structural Biology, Nanyang Technological University, Singapore 636921, Singapore
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17
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Li K, Yatsunyk L, Neidle S. Water spines and networks in G-quadruplex structures. Nucleic Acids Res 2021; 49:519-528. [PMID: 33290519 PMCID: PMC7797044 DOI: 10.1093/nar/gkaa1177] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/12/2022] Open
Abstract
Quadruplex DNAs can fold into a variety of distinct topologies, depending in part on loop types and orientations of individual strands, as shown by high-resolution crystal and NMR structures. Crystal structures also show associated water molecules. We report here on an analysis of the hydration arrangements around selected folded quadruplex DNAs, which has revealed several prominent features that re-occur in related structures. Many of the primary-sphere water molecules are found in the grooves and loop regions of these structures. At least one groove in anti-parallel and hybrid quadruplex structures is long and narrow and contains an extensive spine of linked primary-sphere water molecules. This spine is analogous to but fundamentally distinct from the well-characterized spine observed in the minor groove of A/T-rich duplex DNA, in that every water molecule in the continuous quadruplex spines makes a direct hydrogen bond contact with groove atoms, principally phosphate oxygen atoms lining groove walls and guanine base nitrogen atoms on the groove floor. By contrast, parallel quadruplexes do not have extended grooves, but primary-sphere water molecules still cluster in them and are especially associated with the loops, helping to stabilize loop conformations.
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Affiliation(s)
- Kevin Li
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Liliya Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, London WC1N 1AX, UK
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18
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Xi H, Juhas M, Zhang Y. G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection. Biosens Bioelectron 2020; 167:112494. [PMID: 32791468 PMCID: PMC7403137 DOI: 10.1016/j.bios.2020.112494] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/26/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022]
Abstract
G-quadruplex is a non-canonical nucleic acid structure formed by the folding of guanine rich DNA or RNA. The conformation and function of G-quadruplex are determined by a number of factors, including the number and polarity of nucleotide strands, the type of cations and the binding targets. Recent studies led to the discovery of additional advantageous attributes of G-quadruplex with the potential to be used in novel biosensors, such as improved ligand binding and unique folding properties. G-quadruplex based biosensor can detect various substances, such as metal ions, organic macromolecules, proteins and nucleic acids with improved affinity and specificity compared to standard biosensors. The recently developed G-quadruplex based biosensors include electrochemical and optical biosensors. A novel G-quadruplex based biosensors also show better performance and broader applications in the detection of a wide spectrum of pathogens, including SARS-CoV-2, the causative agent of COVID-19 disease. This review highlights the latest developments in the field of G-quadruplex based biosensors, with particular focus on the G-quadruplex sequences and recent applications and the potential of G-quadruplex based biosensors in SARS-CoV-2 detection.
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Affiliation(s)
- Hui Xi
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China.
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19
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Ida J, Kuzuya A, Choong YS, Lim TS. An intermolecular-split G-quadruplex DNAzyme sensor for dengue virus detection. RSC Adv 2020; 10:33040-33051. [PMID: 35515051 PMCID: PMC9056686 DOI: 10.1039/d0ra05439a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/23/2020] [Indexed: 01/12/2023] Open
Abstract
Nucleic acids have special ability to organize themselves into various non-canonical structures, including a four-stranded DNA structure termed G-quadruplex (G4) that has been utilized for diagnostic and therapeutic applications. Herein, we report the ability of G4 to distinguish dengue virus (DENV) based on its serotypes (DENV-1, DENV-2, DENV-3 and DENV-4) using a split G4-hemin DNAzyme configuration. In this system, two separate G-rich oligonucleotides are brought together upon target DNA strand hybridization to form a three-way junction architecture, allowing the formation of a G4 structure. The G4 formation in complexation with hemin can thus provide a signal readout by generating a DNAzyme that is able to catalyze H2O2-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) diammonium salt (ABTS). This results in a change of color providing a sensing platform for the colorimetric detection of DENV. In our approach, betaine and dimethyl sulfoxide were utilized for better G4 generation by enhancing the target-probe hybridization. In addition to this serotype-specific assay, a multi-probe cocktail assay, which is an all-in-one assay was also examined for DENV detection. The system highlights the potential of split G-quadruplex configurations for the development of DNA-based detection and serotyping systems in the future.
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Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University 3-3-35 Yamate, Suita Osaka 564-8680 Japan
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia 11800 Penang Malaysia +60-4-653-4803 +60-4-653-4852
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia 11800 Penang Malaysia
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20
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Yuan WF, Wan LY, Peng H, Zhong YM, Cai WL, Zhang YQ, Ai WB, Wu JF. The influencing factors and functions of DNA G-quadruplexes. Cell Biochem Funct 2020; 38:524-532. [PMID: 32056246 PMCID: PMC7383576 DOI: 10.1002/cbf.3505] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 12/28/2022]
Abstract
G‐quadruplexes form folded structures because of tandem repeats of guanine sequences in DNA or RNA. They adopt a variety of conformations, depending on many factors, including the type of loops and cations, the nucleotide strand number, and the main strand polarity of the G‐quadruplex. Meanwhile, the different conformations of G‐quadruplexes have certain influences on their biological functions, such as the inhibition of transcription, translation, and DNA replication. In addition, G‐quadruplex binding proteins also affect the structure and function of G‐quadruplexes. Some chemically synthesized G‐quadruplex sequences have been shown to have biological activities. For example, bimolecular G‐quadruplexes of AS1411 act as targets of exogenous drugs that inhibit the proliferation of malignant tumours. G‐quadruplexes are also used as vehicles to deliver nanoparticles. Thus, it is important to identify the factors that influence G‐quadruplex structures and maintain the stability of G‐quadruplexes. Herein, we mainly discuss the factors influencing G‐quadruplexes and the synthetic G‐quadruplex, AS1411. Significance of the study This review summarizes the factors that influence G‐quadruplexes and the functions of the synthetic G‐quadruplex, AS1411. It also discusses the use of G‐quadruplexes for drug delivery in tumour therapy.
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Affiliation(s)
- Wen-Fang Yuan
- Medical College, China Three Gorges University, Yichang, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Lin-Yan Wan
- The People's Hospital, China Three Gorges University, Yichang, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Hu Peng
- Medical College, China Three Gorges University, Yichang, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.,Surgeon, The Yiling Hospital of Yichang, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Yuan-Mei Zhong
- Medical College, China Three Gorges University, Yichang, China
| | - Wen-Li Cai
- Medical College, China Three Gorges University, Yichang, China
| | - Yan-Qiong Zhang
- Medical College, China Three Gorges University, Yichang, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Wen-Bing Ai
- Surgeon, The Yiling Hospital of Yichang, Yichang, China
| | - Jiang-Feng Wu
- Medical College, China Three Gorges University, Yichang, China.,The People's Hospital, China Three Gorges University, Yichang, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.,Surgeon, The Yiling Hospital of Yichang, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
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21
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Nguyen GTH, Leung WY, Tran TN, Wang H, Murray V, Donald WA. Mechanism for the Binding of Netropsin to Hairpin DNA Revealed Using Nanoscale Ion Emitters in Native Mass Spectrometry. Anal Chem 2019; 92:1130-1137. [PMID: 31778608 DOI: 10.1021/acs.analchem.9b04209] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Netropsin is one of the first ligands to be discovered that selectively binds to the minor groove of DNA and is actively used as a scaffold for developing potential anticancer and antibiotic agents. The mechanism by which netropsin binds to hairpin DNA remains controversial with two competing mechanisms having been proposed. In one mechanism, netropsin binding induces a hairpin-to-duplex DNA transition. Alternatively, netropsin binds in two thermodynamically different modes at a single duplexed AATT site. Here, results from native mass spectrometry (MS) with nanoscale ion emitters indicate that netropsin can simultaneously and sequentially bind to both hairpin and duplex DNA. Duplex DNA was not detected using conventional MS with larger emitters because nanoscale emitters significantly reduce the extent of salt adduction to ligand-DNA complex ions, including in the presence of relatively high concentrations of nonvolatile salts. Based on native MS and polyacrylamide gel electrophoresis results, the abundances of hairpin and duplex DNA are unaffected by the addition of netropsin. By native MS, the binding affinities for five ligand-DNA and DNA-DNA interactions can be rapidly obtained simultaneously. This research indicates a "simultaneous binding mechanism" for the interactions of netropsin with DNA.
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Affiliation(s)
- Giang T H Nguyen
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Wai Yu Leung
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Thinh N Tran
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Huixin Wang
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia.,Mark Wainwright Analytical Centre , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - Vincent Murray
- School of Biotechnology and Biomolecular Sciences , University of New South Wales , Sydney New South Wales 2052 , Australia
| | - William A Donald
- School of Chemistry , University of New South Wales , Sydney New South Wales 2052 , Australia
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22
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Yett A, Lin LY, Beseiso D, Miao J, Yatsunyk LA. N-methyl mesoporphyrin IX as a highly selective light-up probe for G-quadruplex DNA. J PORPHYR PHTHALOCYA 2019; 23:1195-1215. [PMID: 34385812 PMCID: PMC8356643 DOI: 10.1142/s1088424619300179] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
N-methyl mesoporphyrin IX (NMM) is a water-soluble, non-symmetric porphyrin with excellent optical properties and unparalleled selectivity for G-quadruplex (GQ) DNA. G-quadruplexes are non-canonical DNA structures formed by guanine-rich sequences. They are implicated in genomic stability, longevity, and cancer. The ability of NMM to selectively recognize GQ structures makes it a valuable scaffold for designing novel GQ binders. In this review, we survey the literature describing the GQ-binding properties of NMM as well as its wide utility in chemistry and biology. We start with the discovery of the GQ-binding properties of NMM and the development of NMM-binding aptamers. We then discuss the optical properties of NMM, focusing on the light-switch effect - high fluorescence of NMM induced upon its binding to GQ DNA. Additionally, we examine the affinity and selectivity of NMM for GQs, as well as its ability to stabilize GQ structures and favor parallel GQ conformations. Furthermore, a portion of the review is dedicated to the applications of NMM-GQ complexes as biosensors for heavy metals, small molecules (e.g. ATP and pesticides), DNA, and proteins. Finally and importantly, we discuss the utility of NMM as a probe to investigate the roles of GQs in biological processes.
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Affiliation(s)
- Ariana Yett
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Linda Yingqi Lin
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Dana Beseiso
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Joanne Miao
- Swarthmore College, Department of Chemistry and Biochemistry, 500 College Ave, Swarthmore, PA 19081, USA
| | - Liliya A. Yatsunyk
- Correspondence to: Liliya A. Yatsunyk, Swarthmore College, 500 College Ave, Swarthmore, PA 19081, USA. tel.: 610-328-8558,
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23
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Winnerdy FR, Bakalar B, Maity A, Vandana JJ, Mechulam Y, Schmitt E, Phan AT. NMR solution and X-ray crystal structures of a DNA molecule containing both right- and left-handed parallel-stranded G-quadruplexes. Nucleic Acids Res 2019; 47:8272-8281. [PMID: 31216034 PMCID: PMC6735952 DOI: 10.1093/nar/gkz349] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/16/2019] [Accepted: 06/13/2019] [Indexed: 01/29/2023] Open
Abstract
Analogous to the B- and Z-DNA structures in double-helix DNA, there exist both right- and left-handed quadruple-helix (G-quadruplex) DNA. Numerous conformations of right-handed and a few left-handed G-quadruplexes were previously observed, yet they were always identified separately. Here, we present the NMR solution and X-ray crystal structures of a right- and left-handed hybrid G-quadruplex. The structure reveals a stacking interaction between two G-quadruplex blocks with different helical orientations and displays features of both right- and left-handed G-quadruplexes. An analysis of loop mutations suggests that single-nucleotide loops are preferred or even required for the left-handed G-quadruplex formation. The discovery of a right- and left-handed hybrid G-quadruplex further expands the polymorphism of G-quadruplexes and is potentially useful in designing a left-to-right junction in G-quadruplex engineering.
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Affiliation(s)
- Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Blaž Bakalar
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Arijit Maity
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - J Jeya Vandana
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
| | - Yves Mechulam
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, Palaiseau 91128, France
| | - Emmanuelle Schmitt
- Laboratoire de Biochimie, UMR 7654, CNRS, Ecole Polytechnique, Palaiseau 91128, France
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore
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24
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Kolesnikova S, Curtis EA. Structure and Function of Multimeric G-Quadruplexes. Molecules 2019; 24:molecules24173074. [PMID: 31450559 PMCID: PMC6749722 DOI: 10.3390/molecules24173074] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/21/2019] [Accepted: 08/22/2019] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes are noncanonical nucleic acid structures formed from stacked guanine tetrads. They are frequently used as building blocks and functional elements in fields such as synthetic biology and also thought to play widespread biological roles. G-quadruplexes are often studied as monomers, but can also form a variety of higher-order structures. This increases the structural and functional diversity of G-quadruplexes, and recent evidence suggests that it could also be biologically important. In this review, we describe the types of multimeric topologies adopted by G-quadruplexes and highlight what is known about their sequence requirements. We also summarize the limited information available about potential biological roles of multimeric G-quadruplexes and suggest new approaches that could facilitate future studies of these structures.
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Affiliation(s)
- Sofia Kolesnikova
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Edward A Curtis
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 166 10 Prague, Czech Republic.
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25
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Guédin A, Lin LY, Armane S, Lacroix L, Mergny JL, Thore S, Yatsunyk LA. Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome. Nucleic Acids Res 2019; 46:5297-5307. [PMID: 29718337 PMCID: PMC6007418 DOI: 10.1093/nar/gky290] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022] Open
Abstract
Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249–1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson–Crick base pair and a A–T–A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.
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Affiliation(s)
- Aurore Guédin
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | | | - Samir Armane
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
| | | | - Jean-Louis Mergny
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France.,Institute of Biophysics of the CAS, v.v.i., Kraálovopolskaá 135, 612 65 Brno, Czech Republic
| | - Stéphane Thore
- ARNA Laboratory, Inserm U1212, CNRS UMR 5320, Université de Bordeaux, Bordeaux, France
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26
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Ida J, Chan SK, Glökler J, Lim YY, Choong YS, Lim TS. G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing. Molecules 2019; 24:E1079. [PMID: 30893817 PMCID: PMC6471233 DOI: 10.3390/molecules24061079] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/14/2019] [Accepted: 03/16/2019] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.
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Affiliation(s)
- Jeunice Ida
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Soo Khim Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Jörn Glökler
- Division of Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Hochschulring 1, 15745 Wildau, Germany.
| | - Yee Ying Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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27
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Vinnarasi S, Radhika R, Vijayakumar S, Shankar R. Structural insights into the anti-cancer activity of quercetin on G-tetrad, mixed G-tetrad, and G-quadruplex DNA using quantum chemical and molecular dynamics simulations. J Biomol Struct Dyn 2019; 38:317-339. [PMID: 30794082 DOI: 10.1080/07391102.2019.1574239] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Human telomerase referred as 'terminal transferase' is a nucleoprotein enzyme which inhibits the disintegration of telomere length and act as a drug target for the anticancer therapy. The tandem repeating structure of telomere sequence forms the guanine-rich quadruplex structures that stabilize stacked tetrads. In our present work, we have investigated the interaction of quercetin with DNA tetrads using DFT. Geometrical analysis revealed that the influence of quercetin drug induces the structural changes into the DNA tetrads. Among DNA tetrads, the quercetin stacked with GCGC tetrad has the highest interaction energy of -88.08 kcal/mol. The binding mode and the structural stability are verified by the absorption spectroscopy method. The longer wavelength was found at 380 nm and it exhibits bathochromic shift. The findings help us to understand the binding nature of quercetin drug with DNA tetrads and it also inhibits the telomerase activity. Further, the quercetin drug interacted with G-quadruplex DNA by using molecular dynamics (MD) simulation studies for 100 ns simulation at different temperatures and different pH levels (T = 298 K, 320 K and pH = 7.4, 5.4). The structural stability of the quercetin with G-quadruplex structure is confirmed by RMSD. For the acidic condition (pH = 5.4), the binding affinity is higher toward G-quadruplex DNA, this result resembles that the quercetin drug is well interacted with G-quadruplex DNA at acidic condition (pH = 7.4) than the neutral condition. The obtained results show that quercetin drug stabilizes the G-quadruplex DNA, which regulates telomerase enzyme and it potentially acts as a novel anti-cancer agent.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Vinnarasi
- Department of Physics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - R Radhika
- Department of Physics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - S Vijayakumar
- Department of Medical Physics, Bharathiar University, Coimbatore, Tamil Nadu, India
| | - R Shankar
- Department of Physics, Bharathiar University, Coimbatore, Tamil Nadu, India
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28
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Sharawy M, Consta S. Effect of the chemical environment of the DNA guanine quadruplex on the free energy of binding of Na and K ions. J Chem Phys 2019; 149:225102. [PMID: 30553268 DOI: 10.1063/1.5050534] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Guanine quadruplex (G-quadruplex) structures play a vital role in stabilizing the DNA genome and in protecting healthy cells from transforming into cancer cells. The structural stability of G-quadruplexes is greatly enhanced by the binding of monovalent cations such as Na+ or K+ into the interior axial channel. We computationally study the free energy of binding of Na+ and K+ ions to two intramolecular G-quadruplexes that differ considerably in their degree of rigidity and the presence or absence of terminal nucleotides. The goal of our study is two-fold. On the one hand, we study the free energy of binding every ion, which complements the experimental findings that report the average free energy for replacing Na+ with K+ ions. On the other hand, we examine the role of the G-quadruplex structure in the binding free energy. In the study, we employ all-atom molecular dynamics simulations and the alchemical transformation method for the computation of the free energies. To compare the cation-dependent contribution to the structural stability of G-quadruplexes, we use a two-step approach to calculate the individual free energy difference ΔG of binding two Na+ and two K+ to two G-quadruplexes: the unimolecular DNA d[T2GT2(G3T)3] (Protein Data Bank ID 2M4P) and the human telomeric DNA d[AGGG(TTAGGG)3] (PDB ID 1KF1). In contrast to the experimental studies that estimate the average free energy of binding, we find a varying difference of approximately 2-9 kcal/mol between the free energy contribution of binding the first and second cation, Na+ or K+. Furthermore, we found that the free energy of binding K+ is not affected by the chemical nature of the two quadruplexes. By contrast, Na+ showed dependency on the G-quadruplex structure; the relatively small size allows Na+ to explore larger configurational space than K+. Numerical results presented here may offer reference values for future design of cationic drug-like ligands that replace the metal ions in G-quadruplexes.
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Affiliation(s)
- Mahmoud Sharawy
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
| | - Styliani Consta
- Department of Chemistry, The University of Western Ontario, London, Ontario N6A 5B7, Canada
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29
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Zheng KW, Zhang JY, Tan Z. Characterization of Co-transcriptional Formation of G-Quadruplexes in Double-Stranded DNA. Methods Mol Biol 2019; 2035:243-255. [PMID: 31444754 DOI: 10.1007/978-1-4939-9666-7_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In vitro transcription of double-stranded DNA (dsDNA) induces a formation of two types of G-quadruplexes, intramolecular DNA G-quadruplexes or DNA:RNA hybrid G-quadruplexes, in clusters of guanine tracts. The formation of G-quadruplexes can be characterized by native PEG polyacrylamide gel electrophoresis, DMS footprinting, and ligand-induced photocleavage footprinting. The type of G-quadruplexes can be distinguished by transcription with 7-deaza-GTP (dzGTP) or 4-thio-uridine-5'-triphosphate (4SU) to detect the participation of RNA transcript.
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Affiliation(s)
- Ke-Wei Zheng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.
| | - Jia-Yu Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China.
| | - Zheng Tan
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
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30
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Andrałojć W, Małgowska M, Sarzyńska J, Pasternak K, Szpotkowski K, Kierzek R, Gdaniec Z. Unraveling the structural basis for the exceptional stability of RNA G-quadruplexes capped by a uridine tetrad at the 3' terminus. RNA (NEW YORK, N.Y.) 2019; 25:121-134. [PMID: 30341177 PMCID: PMC6298561 DOI: 10.1261/rna.068163.118] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/16/2018] [Indexed: 05/24/2023]
Abstract
Uridine tetrads (U-tetrads) are a structural element encountered in RNA G-quadruplexes, for example, in the structures formed by the biologically relevant human telomeric repeat RNA. For these molecules, an unexpectedly strong stabilizing influence of a U-tetrad forming at the 3' terminus of a quadruplex was reported. Here we present the high-resolution solution NMR structure of the r(UGGUGGU)4 quadruplex which, in our opinion, provides an explanation for this stabilization. Our structure features a distinctive, abrupt chain reversal just prior to the 3' uridine tetrad. Similar "reversed U-tetrads" were already observed in the crystalline phase. However, our NMR structure coupled with extensive explicit solvent molecular dynamics (MD) simulations identifies some key features of this motif that up to now remained overlooked. These include the presence of an exceptionally stable 2'OH to phosphate hydrogen bond, as well as the formation of an additional K+ binding pocket in the quadruplex groove.
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Affiliation(s)
- Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Magdalena Małgowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Joanna Sarzyńska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Karol Pasternak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Kamil Szpotkowski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
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31
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Pal S, Paul S. Conformational deviation of Thrombin binding G-quadruplex aptamer (TBA) in presence of divalent cation Sr 2+: A classical molecular dynamics simulation study. Int J Biol Macromol 2018; 121:350-363. [PMID: 30308284 DOI: 10.1016/j.ijbiomac.2018.09.102] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Revised: 08/27/2018] [Accepted: 09/17/2018] [Indexed: 11/28/2022]
Abstract
Thrombin binding TBA-G-quadruplex aptamer (TBA) plays a major role in blood coagulation cascade. The 15-mer TBA sequence tends to form four-stranded TBA-G-quadruplex structure. In this research work, a series of explicit solvent classical MD simulations of the TBA is carried out using different salt (SrCl2) concentrations (0, 50, 100 and 200 mM). Here we have also testified the effect of salt concentration of divalent cation Sr2+ on the conformational change of quadruplex DNA. The structural deviations, fluctuations, torsional angles and the affinity of the ion are explored at different salt concentrations. It is found that the conformation of TBA-G-quadruplex at 0 mM and 50 mM salt concentrations, is very much different than the other salt concentrations (100 mM and 200 mM). Also observed are as follows: (i) no exchange of Sr2+ ion between inside and outside of the channel, (ii) an enhancement in the Sr2+ ion density around the phosphate region of the loop residues as salt concentration increases and (iii) the stacking of T3 and T4 residues of loop-1 that appears up to 50 mM concentration, vanishes as the salt concentration is increased further.
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Affiliation(s)
- Saikat Pal
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India.
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32
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Solís-Calero C, Augusto TM, Carvalho HF. Human-specific features of the G-quadruplex in the androgen receptor gene promoter: A comparative structural and dynamics study. J Steroid Biochem Mol Biol 2018; 182:95-105. [PMID: 29709633 DOI: 10.1016/j.jsbmb.2018.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 04/22/2018] [Accepted: 04/23/2018] [Indexed: 10/17/2022]
Abstract
The androgen receptor (AR) promoter contains guanine-rich regions that are able to fold into polymorphic G-quadruplex (GQ) structures, and whose deletion decreases AR gene transcription. Our attention was focused on this region because of the frequent termination of sequencing reactions during promoter methylation studies. UV and circular dichroism (CD) spectroscopy of synthetic oligonucleotides encompassing these guanine-rich regions suggested a parallel quadruplex topology with three guanine quartets and three side loops in the three cases. Melting curves revealed a lower thermostability of the human GQ compared to the rat/mouse QG structures, which is attributed to the presence of a longer central loop in the former. One molecular model is proposed for the highly similar sequences in the rat/mouse. Due to the polymorphism resulting from possible arrangements of the guanine tracts, two models were derived for the human GQ. Molecular dynamics (MD) simulations determined that both models for the human GQ had higher flexibility and lower stability than the rodent GQ models. These properties result from the presence of a longer central loop in the human GQ models, which contains 11 and 13 nucleotides, in comparison to the 2-nucleotide long loop in the rat/mouse GQ. Overall, the unveiled structural and dynamics features provide sufficient detail for the intelligent design of drugs targeting the human AR promoter.
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Affiliation(s)
- Christian Solís-Calero
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Taize M Augusto
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Hernandes F Carvalho
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil.
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33
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Meier M, Moya-Torres A, Krahn NJ, McDougall MD, Orriss GL, McRae EK, Booy EP, McEleney K, Patel TR, McKenna SA, Stetefeld J. Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. Nucleic Acids Res 2018; 46:5319-5331. [PMID: 29718405 PMCID: PMC6007744 DOI: 10.1093/nar/gky307] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 04/05/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
The identification of four-stranded G-quadruplexes (G4s) has highlighted the fact that DNA has additional spatial organisations at its disposal other than double-stranded helices. Recently, it became clear that the formation of G4s is not limited to the traditional G3+NL1G3+NL2G3+NL3G3+ sequence motif. Instead, the G3 triplets can be interrupted by deoxythymidylate (DNA) or uridylate (RNA) where the base forms a bulge that loops out from the G-quadruplex core. Here, we report the first high-resolution X-ray structure of a unique unimolecular DNA G4 with a cytosine bulge. The G4 forms a dimer that is stacked via its 5'-tetrads. Analytical ultracentrifugation, static light scattering and small angle X-ray scattering confirmed that the G4 adapts a predominantly dimeric structure in solution. We provide a comprehensive comparison of previously published G4 structures containing bulges and report a special γ torsion angle range preferentially populated by the G4 core guanylates adjacent to bulges. Since the penalty for introducing bulges appears to be negligible, it should be possible to functionalize G4s by introducing artificial or modified nucleotides at such positions. The presence of the bulge alters the surface of the DNA, providing an opportunity to develop drugs that can specifically target individual G4s.
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Affiliation(s)
- Markus Meier
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Aniel Moya-Torres
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Natalie J Krahn
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Matthew D McDougall
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - George L Orriss
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Ewan K S McRae
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Kevin McEleney
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
- DiscoveryLab, Medical Sciences Building, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
- Department of Microbiology, Immunology and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 1N4, Alberta, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Jörg Stetefeld
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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34
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Akhshi P, Wu G. Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels. Phys Chem Chem Phys 2018; 19:11017-11025. [PMID: 28327752 DOI: 10.1039/c7cp01028a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system. We anticipate that these modern free-energy methods will be useful tools in evaluating ion transport properties of other G-quadruplex DNA channels.
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Affiliation(s)
- Parisa Akhshi
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada.
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35
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Gülbakan B, Barylyuk K, Schneider P, Pillong M, Schneider G, Zenobi R. Native Electrospray Ionization Mass Spectrometry Reveals Multiple Facets of Aptamer–Ligand Interactions: From Mechanism to Binding Constants. J Am Chem Soc 2018; 140:7486-7497. [DOI: 10.1021/jacs.7b13044] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Basri Gülbakan
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
- Hacettepe University Institute of Child Health, Ihsan Dogramaci Children’s Hospital, Sıhhiye Square, 06100 Ankara, Turkey
| | - Konstantin Barylyuk
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Max Pillong
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Gisbert Schneider
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Bioscience, ETH Zürich, CH-8093 Zürich, Switzerland
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36
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Qiao JQ, Cao ZM, Liang C, Chen HJ, Zheng WJ, Lian HZ. Study on the polymorphism of G-quadruplexes by reversed-phase HPLC and LC–MS. J Chromatogr A 2018; 1542:61-71. [DOI: 10.1016/j.chroma.2018.02.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 02/03/2018] [Accepted: 02/11/2018] [Indexed: 12/16/2022]
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37
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Donohue MP, Szalai VA. Distance measurements between paramagnetic ligands bound to parallel stranded guanine quadruplexes. Phys Chem Chem Phys 2018; 18:15447-55. [PMID: 27218217 DOI: 10.1039/c6cp01121g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Aside from a double helix, deoxyribonucleic acid (DNA) folds into non-canonical structures, one of which is the guanine quadruplex. Cationic porphyrins bind guanine quadruplexes, but the effects of ligand binding on the structure of guanine quadruplexes with more than four contiguous guanine quartets remains to be fully elucidated. Double electron-electron resonance (DEER) spectroscopy conducted at 9.5 GHz (X-band) using broadband, shaped inversion pulses was used to measure the distances between cationic copper porphyrins bound to model parallel-stranded guanine quadruplexes with increasing numbers of guanine quartets. A single Gaussian component was found to best model the time domain datasets, characteristic of a 2 : 1 binding stoichiometry between the porphyrins and each quadruplex. The measured Cu(2+)-Cu(2+) distances were found to be linearly proportional with the number of guanines. Rather unexpectedly, the ligand end-stacking distance was found to monotonically decreases the overall quadruplex length was extended, suggesting a conformational change in the quadruplex secondary structure dependent upon the number of successive guanine quartets.
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Affiliation(s)
- M P Donohue
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA. and Maryland NanoCenter, University of Maryland, College Park, MD 20742, USA
| | - V A Szalai
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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38
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Gao M, Harish B, Berghaus M, Seymen R, Arns L, McCallum SA, Royer CA, Winter R. Temperature and pressure limits of guanosine monophosphate self-assemblies. Sci Rep 2017; 7:9864. [PMID: 28852183 PMCID: PMC5574928 DOI: 10.1038/s41598-017-10689-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/14/2017] [Indexed: 12/31/2022] Open
Abstract
Guanosine monophosphate, among the nucleotides, has the unique property to self-associate and form nanoscale cylinders consisting of hydrogen-bonded G-quartet disks, which are stacked on top of one another. Such self-assemblies describe not only the basic structural motif of G-quadruplexes formed by, e.g., telomeric DNA sequences, but are also interesting targets for supramolecular chemistry and nanotechnology. The G-quartet stacks serve as an excellent model to understand the fundamentals of their molecular self-association and to unveil their application spectrum. However, the thermodynamic stability of such self-assemblies over an extended temperature and pressure range is largely unexplored. Here, we report a combined FTIR and NMR study on the temperature and pressure stability of G-quartet stacks formed by disodium guanosine 5′-monophosphate (Na25′-GMP). We found that under abyssal conditions, where temperatures as low as 5 °C and pressures up to 1 kbar are reached, the self-association of Na25′-GMP is most favoured. Beyond those conditions, the G-quartet stacks dissociate laterally into monomer stacks without significantly changing the longitudinal dimension. Among the tested alkali cations, K+ is the most efficient one to elevate the temperature as well as the pressure limits of GMP self-assembly.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Balasubramanian Harish
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, United States
| | - Melanie Berghaus
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Rana Seymen
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Loana Arns
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Scott A McCallum
- NMR Facility Center for Biotechnology and Interdisciplinary Science, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Catherine A Royer
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, United States
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany.
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39
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Generation, repair and replication of guanine oxidation products. Genes Environ 2017; 39:21. [PMID: 28781714 PMCID: PMC5537945 DOI: 10.1186/s41021-017-0081-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 05/16/2017] [Indexed: 02/07/2023] Open
Abstract
Guanine is the most readily oxidized of the four DNA bases, and guanine oxidation products cause G:C-T:A and G:C-C:G transversions through DNA replication. 8-Oxo-7,8-dihydroguanine (8-oxoG) causes G:C-T:A transversions but not G:C-C:G transversions, and is more readily oxidized than guanine. This review covers four major findings. (i) 2,2,4-Triamino-5(2H)-oxazolone (Oz) is produced from guanine and 8-oxoG under various oxidative conditions. Guanine is incorporated opposite Oz by DNA polymerases, except REV1. (ii) Several enzymes exhibit incision activity towards Oz. (iii) Since the redox potential of GG is lower than that of G, contiguous GG sequences are more readily oxidized by a one-electron oxidant than a single guanine, and OzOz is produced from GG in double-stranded DNA. Unlike most DNA polymerases, DNA polymerase ζ efficiently extends the primer up to full-length across OzOz. (iv) In quadruplex DNA, 3′-guanine is mainly damaged by one-electron oxidation in quadruplex DNA, and this damage depends on the highest occupied molecular orbital (HOMO). The oxidation products in quadruplex DNA are different from those in single-stranded or double-stranded DNA.
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40
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Havrila M, Stadlbauer P, Islam B, Otyepka M, Šponer J. Effect of Monovalent Ion Parameters on Molecular Dynamics Simulations of G-Quadruplexes. J Chem Theory Comput 2017; 13:3911-3926. [PMID: 28657760 DOI: 10.1021/acs.jctc.7b00257] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
G-quadruplexes (GQs) are key noncanonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (∼580 μs in total) of GQs with 11 monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations, and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model; however, test simulations with TIP3P and OPC water models are also reported. The identity and parametrization of ions strongly affect behavior of a tetramolecular d[GGG]4 GQ, which is unstable with several ion parametrizations. The remaining studied RNA and DNA GQs are structurally stable, though the G-tetrad geometries are always deformed by bifurcated H-bonding in a parametrization-specific manner. Thus, basic 10-μs-scale simulations of fully folded GQs can be safely done with a number of cation parametrizations. However, there are parametrization-specific differences and basic force-field errors affecting the quantitative description of ion-tetrad interactions, which may significantly affect studies of the ion-binding processes and description of the GQ folding landscape. Our d[GGG]4 simulations indirectly suggest that such studies will also be sensitive to the water models. During exchanges with bulk water, the Na+ ions move inside the GQs in a concerted manner, while larger relocations of the K+ ions are typically separated. We suggest that the Joung-Cheatham SPC/E K+ parameters represent a safe choice in simulation studies of GQs, though variation of ion parameters can be used for specific simulation goals.
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Affiliation(s)
- Marek Havrila
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - 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, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Barira Islam
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC - Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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41
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Kulikov K, Nozinovic S, Kath-Schorr S. The 5'-AG 5 CC-3' Fragment from the Human CPEB3 Ribozyme Forms an Ultrastable Parallel RNA G-Quadruplex. Chembiochem 2017; 18:969-973. [PMID: 28296179 DOI: 10.1002/cbic.201700028] [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: 01/20/2017] [Indexed: 11/07/2022]
Abstract
An unusually thermostable G-quadruplex is formed by a sequence fragment of a naturally occurring ribozyme, the human CPEB3 ribozyme. Strong evidence is provided for the formation of a uniquely stable intermolecular G-quadruplex structure consisting of five tetrad layers, by using CD spectroscopy, UV melting curves, 2D NMR spectroscopy, and gel shift analysis. The cationic porphyrin TMPyP4 destabilizes the complex.
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Affiliation(s)
- Katharina Kulikov
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Senada Nozinovic
- Institute for Inorganic Chemistry, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology & Medicinal Chemistry Unit, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
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42
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Radhika R, Shankar R, Vijayakumar S, Kolandaivel P. Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations. J Biomol Struct Dyn 2017; 36:1369-1401. [PMID: 28436311 DOI: 10.1080/07391102.2017.1323013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The theoretical studies on DNA with the anticancer drug 6-Mercaptopurine (6-MP) are investigated using theoretical methods to shed light on drug designing. Among the DNA base pairs considered, 6-MP is stacked with GC with the highest interaction energy of -46.19 kcal/mol. Structural parameters revealed that structure of the DNA base pairs is deviated from the planarity of the equilibrium position due to the formation of hydrogen bonds and stacking interactions with 6-MP. These deviations are verified through the systematic comparison between X-H bond contraction and elongation and the associated blue shift and red shift values by both NBO analysis and vibrational analysis. Bent's rule is verified for the C-H bond contraction in the 6-MP interacted base pairs. The AIM results disclose that the higher values of electron density (ρ) and Laplacian of electron density (∇2ρ) indicate the increased overlap between the orbitals that represent the strong interaction and positive values of the total electron density show the closed-shell interaction. The relative sensitivity of the chemical shift values for the DNA base pairs with 6-MP is investigated to confirm the hydrogen bond strength. Molecular dynamics simulation studies of G-quadruplex DNA d(TGGGGT)4 with 6-MP revealed that the incorporation of 6-MP appears to cause local distortions and destabilize the G-quadruplex DNA.
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Affiliation(s)
- R Radhika
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - R Shankar
- a Department of Physics , Bharathiar University , Coimbatore , India
| | - S Vijayakumar
- b Department of Medical Physics , Bharathiar University , Coimbatore , India
| | - P Kolandaivel
- a Department of Physics , Bharathiar University , Coimbatore , India
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Yurenko YP, Novotný J, Marek R. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. Chemistry 2017; 23:5573-5584. [PMID: 28225208 DOI: 10.1002/chem.201700236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Indexed: 12/30/2022]
Abstract
The topology and energetics of guanine (G) quadruplexes is governed by supramolecular interactions within their strands. In this work, an extensive quantum mechanical (QM) study has been performed to analyze supramolecular interactions that shape the stems of (4+0) parallel (P) and (2+2) antiparallel (AP) quadruplex systems. The large-scale (≈400 atoms) models of P and AP were constructed from high-quality experimental structures. The results provide evidence that each of the P and AP structures is shaped by a distinct network of supramolecular interactions. Analysis of electron topological characteristics of hydrogen bonds in P and AP systems indicates that the P model benefits from stronger intratetrad hydrogen bonding. For intertetrad stacking interactions, both noncovalent interaction plot and energy decomposition analysis approaches suggest that the stem of the P quadruplex benefits more from stacking than that of the AP stem; the difference in energetic stabilization for the two topologies is about 10 %. Stronger hydrogen-bonding and stacking interactions in the stem of the P quadruplex, relative to those in the AP system, can be an important indicator to explain the experimental observations that guanine-rich oligonucleotides tend to form all-parallel stems with an all-anti orientation of nucleobases. However, in addition to intrinsic stabilization, partial desolvation effects, which affect the energetics and dynamics of the G-quadruplex folding process, call for further investigations.
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Affiliation(s)
- Yevgen P Yurenko
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| | - Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
| | - Radek Marek
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic
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Lecours MJ, Marchand A, Anwar A, Guetta C, Hopkins WS, Gabelica V. What stoichiometries determined by mass spectrometry reveal about the ligand binding mode to G-quadruplex nucleic acids. Biochim Biophys Acta Gen Subj 2017; 1861:1353-1361. [PMID: 28087374 DOI: 10.1016/j.bbagen.2017.01.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 11/27/2022]
Abstract
G-quadruplexes (G4s) have become important drug targets to regulate gene expression and telomere maintenance. Many studies on G4 ligand binding focus on determining the ligand binding affinities and selectivities. Ligands, however, can also affect the G4 conformation. Here we explain how to use electrospray ionization mass spectrometry (ESI-MS) to monitor simultaneously ligand binding and cation binding stoichiometries. The changes in potassium binding stoichiometry upon ligand binding hint at ligand-induced conformational changes involving a modification of the number of G-quartets. We investigated the interaction of three quadruplex ligands (PhenDC3, 360A and Pyridostatin) with a variety of G4s. Electrospray mass spectrometry makes it easy to detect K+ displacement (interpreted as quartet disruption) upon ligand binding, and to determine how many ligand molecules must be bound for the quartet opening to occur. The reasons for ligand-induced conversion to antiparallel structures with fewer quartets are discussed. Conversely, K+ intake (hence quartet formation) was detected upon ligand binding to G-rich sequences that did not form quadruplexes in 1mM K+ alone. This demonstrates the value of mass spectrometry for assessing not only ligand binding, but also ligand-induced rearrangements in the target sequence. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Michael J Lecours
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Adrien Marchand
- INSERM, CNRS, Université de Bordeaux, Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Ahdia Anwar
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Corinne Guetta
- Institut Curie, CNRS, INSERM, Univ. Paris Sud, Laboratoire de Chimie, modélisation et imagerie pour la biologie (CMIB, U1196, UMR9187), Orsay, France
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Valérie Gabelica
- INSERM, CNRS, Université de Bordeaux, Laboratoire Acides Nucléiques: Régulations Naturelle et Artificielle (ARNA, U1212, UMR5320), IECB, 2 rue Robert Escarpit, 33607 Pessac, France.
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45
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Cerón-Carrasco JP, Jacquemin D. Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors. Phys Chem Chem Phys 2017; 19:9358-9365. [DOI: 10.1039/c7cp01034f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.
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Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics and High Performance Computing Research Group (BIO-HPC)
- Universidad Católica San Antonio de Murcia (UCAM)
- Murcia
- Spain
| | - Denis Jacquemin
- CEISAM
- UMR CNRS 6230
- BP 92208
- Université de Nantes
- 44322 Nantes Cedex 3
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46
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Pandey S, Agarwala P, Maiti S. Targeting RNA G-Quadruplexes for Potential Therapeutic Applications. TOPICS IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1007/7355_2016_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Bhattacharyya D, Mirihana Arachchilage G, Basu S. Metal Cations in G-Quadruplex Folding and Stability. Front Chem 2016; 4:38. [PMID: 27668212 PMCID: PMC5016522 DOI: 10.3389/fchem.2016.00038] [Citation(s) in RCA: 364] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/25/2016] [Indexed: 12/23/2022] Open
Abstract
This review is focused on the structural and physicochemical aspects of metal cation coordination to G-Quadruplexes (GQ) and their effects on GQ stability and conformation. G-quadruplex structures are non-canonical secondary structures formed by both DNA and RNA. G-quadruplexes regulate a wide range of important biochemical processes. Besides the sequence requirements, the coordination of monovalent cations in the GQ is essential for its formation and determines the stability and polymorphism of GQ structures. The nature, location, and dynamics of the cation coordination and their impact on the overall GQ stability are dependent on several factors such as the ionic radii, hydration energy, and the bonding strength to the O6 of guanines. The intracellular monovalent cation concentration and the localized ion concentrations determine the formation of GQs and can potentially dictate their regulatory roles. A wide range of biochemical and biophysical studies on an array of GQ enabling sequences have generated at a minimum the knowledge base that allows us to often predict the stability of GQs in the presence of the physiologically relevant metal ions, however, prediction of conformation of such GQs is still out of the realm.
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Affiliation(s)
| | | | - Soumitra Basu
- Department of Chemistry and Biochemistry, Kent State UniversityKent, OH, USA
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48
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Gao Y, Wu S, Ye X. The effects of monovalent metal ions on the conformation of human telomere DNA using analytical ultracentrifugation. SOFT MATTER 2016; 12:5959-5967. [PMID: 27329676 DOI: 10.1039/c6sm01010e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A human telomere DNA segment (HT-DNA) can fold into a G-quadruplex in the presence of some monovalent cations. These cations can interact with the phosphate groups of the DNA segment and/or with the O6 oxygen atom of guanines, which are called non-specific interactions and specific interactions, respectively. However, until now how these two interactions affect the structure of HT-DNA has not been well understood. In this study, a combination of analytical ultracentrifugation (AUC) and circular dichroism (CD) was used to explore the effects of these two interactions on the structure of a 22-mer single-stranded DNA with a sequence of 5'-AGGG(TTAGGG)3-3'. The results showed that the standard sedimentation coefficient (s20,w) of HT-DNA starts to increase when the concentration of potassium ions (CK(+)) is higher than 10.0 µM due to the formation of a G-quadruplex through specific interactions. Whereas, for a control DNA, a higher CK(+) value of 1.0 mM was needed for increasing s20,w due to non-specific interactions. Moreover, potassium ions could promote the formation of the G-quadruplex much more easily than lithium, sodium and cesium ions, presumably due to its appropriate size in the dehydrated state and easier dehydration. The molar mass of DNA at different cation concentrations was nearly a constant and close to the theoretical value of the molar mass of monomeric HT-DNA, indicating that what we observed is the structural change of individual DNA chains.
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Affiliation(s)
- Yating Gao
- Hefei National Laboratory for Physical Sciences at the Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui 230026, China.
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Balaratnam S, Basu S. Divalent cation-aided identification of physico-chemical properties of metal ions that stabilize RNA G-quadruplexes. Biopolymers 2016; 103:376-86. [PMID: 25807937 DOI: 10.1002/bip.22628] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 02/02/2023]
Abstract
DNA and RNA sequences rich in guanosines (G) can form a four-stranded secondary structure known as a G-quadruplex (GQ), which plays a role in regulation of gene expression at the transcription and translation level. Both DNA and RNA GQs typically use the monovalent K(+) ion for stabilization of the structures. However, the fundamental reasons for K(+) acting as the most stabilizing metal ion for RNA GQs are not known. To identify the properties of a metal ion that stabilizes an RNA GQ we investigated the effect of alkaline earth metal cations and a set of divalent transition metal ions on two previously identified highly stable RNA GQs. Our results based upon circular dichroism and RNase T1 structure mapping data reveal that the RNA GQs are destabilized in the presence of the tested divalent metal cations. The destabilizing effect of a divalent metal cation is reversible upon increasing K(+) concentration. Results show that ionic radius, hydration energy, and binding strength towards the hard ligand (guanine O(6)) are important factors that determine a metal ion's ability to stabilize an RNA GQ. Additionally, the tested set of divalent metal cations incongruously affects RNA and DNA GQs.
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Affiliation(s)
- Sumirtha Balaratnam
- Department of Chemistry and Biochemistry, Kent State University, Kent, OH, 44242
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50
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Gkionis K, Kruse H, Šponer J. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. J Chem Theory Comput 2016; 12:2000-16. [DOI: 10.1021/acs.jctc.5b01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Konstantinos Gkionis
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
- CEITEC
− Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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