1
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Sabatucci A, Girella A, Di Bartolomeo M, Pucci M, Vismara M, Benatti B, Blacksell IA, Cooper D, Dainese E, D'Acquisto F, Dell'Osso B, D'Addario C. A possible role for G-quadruplexes formation and DNA methylation at IMOOD gene promoter in Obsessive Compulsive Disorder. Adv Biol Regul 2023; 89:100976. [PMID: 37572394 DOI: 10.1016/j.jbior.2023.100976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Obsessive Compulsive Disorder (OCD) is a mental health condition still classified and diagnosed with subjective interview-based assessments and which molecular clues have not completely been elucidated. We have recently identified a new regulator of anxiety and OCD-like behavior called Immuno-moodulin (IMOOD) and, here, we report that IMOOD gene promoter is differentially methylated in OCD subjects when compared to genomic material collected from healthy controls and this alteration is significantly correlated with the increased expression of the gene in OCD. We also demonstrated that IMOOD promoter can form G-quadruplexes and we suggest that, in homeostatic conditions, these structures could evoke DNA-methylation silencing the gene, whereas in pathological conditions, like OCD, could induce gene expression making the promoter more accessible to transcriptional factors. We here thus further suggest IMOOD as a new biomarker for OCD and also hypothesize new mechanisms of gene regulation.
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Affiliation(s)
- Annalaura Sabatucci
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Antonio Girella
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Martina Di Bartolomeo
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Mariangela Pucci
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Matteo Vismara
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milano, Italy
| | - Beatrice Benatti
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milano, Italy
| | - Isobel Alice Blacksell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dianne Cooper
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Enrico Dainese
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Fulvio D'Acquisto
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK; School of Life and Health Science, University of Roehampton, London, SW15, 4JD, UK
| | - Bernardo Dell'Osso
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milano, Italy; Department of Biomedical and Clinical Sciences "Luigi Sacco", Psychiatry Unit 2, ASST Sacco-Fatebenefratelli, Via G.B. Grassi, 74, 20157, Milan, Italy.
| | - Claudio D'Addario
- Department of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy; Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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2
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Fletcher M, Zhu J, Rubio-Sánchez R, Sandler SE, Nahas KA, Michele LD, Keyser UF, Tivony R. DNA-Based Optical Quantification of Ion Transport across Giant Vesicles. ACS NANO 2022; 16:17128-17138. [PMID: 36222833 PMCID: PMC9620405 DOI: 10.1021/acsnano.2c07496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Accurate measurements of ion permeability through cellular membranes remains challenging due to the lack of suitable ion-selective probes. Here we use giant unilamellar vesicles (GUVs) as membrane models for the direct visualization of mass translocation at the single-vesicle level. Ion transport is indicated with a fluorescently adjustable DNA-based sensor that accurately detects sub-millimolar variations in K+ concentration. In combination with microfluidics, we employed our DNA-based K+ sensor for extraction of the permeation coefficient of potassium ions. We measured K+ permeability coefficients at least 1 order of magnitude larger than previously reported values from bulk experiments and show that permeation rates across the lipid bilayer increase in the presence of octanol. In addition, an analysis of the K+ flux in different concentration gradients allows us to estimate the complementary H+ flux that dissipates the charge imbalance across the GUV membrane. Subsequently, we show that our sensor can quantify the K+ transport across prototypical cation-selective ion channels, gramicidin A and OmpF, revealing their relative H+/K+ selectivity. Our results show that gramicidin A is much more selective to protons than OmpF with a H+/K+ permeability ratio of ∼104.
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Affiliation(s)
- Marcus Fletcher
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Jinbo Zhu
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Roger Rubio-Sánchez
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Sarah E Sandler
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Kareem Al Nahas
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Lorenzo Di Michele
- Department
of Chemistry, Molecular Sciences Research Hub, Imperial College London, LondonW12 0BZ, U.K.
- fabriCELL,
Molecular Sciences Research Hub, Imperial
College London, LondonW12 0BZ, U.K.
| | - Ulrich F Keyser
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
| | - Ran Tivony
- Cavendish
Laboratory, University of Cambridge, J.J. Thomson Avenue, CambridgeCB3 0HE, U.K.
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3
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Green AT, Pickard AJ, Li R, MacKerell AD, Bierbach U, Cho SS. Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes. J Phys Chem B 2022; 126:609-619. [PMID: 35026949 DOI: 10.1021/acs.jpcb.1c08340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA G-quadruplexes in human telomeres and gene promoters are being extensively studied for their role in controlling the growth of cancer cells. G-quadruplexes have been unambiguously shown to exist both in vitro and in vivo, including in the guanine (G)-rich DNA genes encoding pre-ribosomal RNA (pre-rRNA), which is transcribed in the cell's nucleolus. Recent studies strongly suggest that these DNA sequences ("rDNA"), and the transcribed rRNA, are a potential anticancer target through the inhibition of RNA polymerase I (Pol I) in ribosome biogenesis, but the structures of ribosomal G-quadruplexes at atomic resolution are unknown and very little biophysical characterization has been performed on them to date. In the present study, circular dichroism (CD) spectroscopy is used to show that two putative rDNA G-quadruplex sequences, NUC 19P and NUC 23P and their counterpart rRNAs, predominantly adopt parallel topologies, reminiscent of the analogous telomeric quadruplex structures. Based on this information, we modeled parallel topology atomistic structures of the putative ribosomal G-quadruplexes. We then validated and refined the modeled ribosomal G-quadruplex structures using all-atom molecular dynamics (MD) simulations with the CHARMM36 force field in the presence and absence of stabilizing K+. Motivated by preliminary MD simulations of the telomeric parallel G-quadruplex (TEL 24P) in which the K+ ion is expelled, we used updated CHARMM36 force field K+ parameters that were optimized, targeting the data from quantum mechanical calculations and the polarizable Drude model force field. In subsequent MD simulations with optimized CHARMM36 parameters, the K+ ions are predominantly in the G-quadruplex channel and the rDNA G-quadruplexes have more well-defined, predominantly parallel-topology structures as compared to rRNA. In addition, NUC 19P is more structured than NUC 23P, which contains extended loops. Results from this study set the structural foundation for understanding G-quadruplex functions and the design of novel chemotherapeutics against these nucleolar targets and can be readily extended to other DNA and RNA G-quadruplexes.
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Affiliation(s)
- Adam T Green
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Amanda J Pickard
- Department of Chemistry, Wake Forest University, Wake Downtown Campus, Winston-Salem, North Carolina 27101, United States
| | - Rongzhong Li
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina 27109, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Ulrich Bierbach
- Department of Chemistry, Wake Forest University, Wake Downtown Campus, Winston-Salem, North Carolina 27101, United States
| | - Samuel S Cho
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina 27109, United States.,Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina 27109, United States
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4
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Grün JT, Schwalbe H. Folding dynamics of polymorphic G-quadruplex structures. Biopolymers 2021; 113:e23477. [PMID: 34664713 DOI: 10.1002/bip.23477] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 12/14/2022]
Abstract
G-quadruplexes (G4), found in numerous places within the human genome, are involved in essential processes of cell regulation. Chromosomal DNA G4s are involved for example, in replication and transcription as first steps of gene expression. Hence, they influence a plethora of downstream processes. G4s possess an intricate structure that differs from canonical B-form DNA. Identical DNA G4 sequences can adopt multiple long-lived conformations, a phenomenon known as G4 polymorphism. A detailed understanding of the molecular mechanisms that drive G4 folding is essential to understand their ambivalent regulatory roles. Disentangling the inherent dynamic and polymorphic nature of G4 structures thus is key to unravel their biological functions and make them amenable as molecular targets in novel therapeutic approaches. We here review recent experimental approaches to monitor G4 folding and discuss structural aspects for possible folding pathways. Substantial progress in the understanding of G4 folding within the recent years now allows drawing comprehensive models of the complex folding energy landscape of G4s that we herein evaluate based on computational and experimental evidence.
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Affiliation(s)
- J Tassilo Grün
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot, Israel
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe-University, Frankfurt/M, Germany.,Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Frankfurt/M, Germany
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5
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Grün JT, Blümler A, Burkhart I, Wirmer-Bartoschek J, Heckel A, Schwalbe H. Unraveling the Kinetics of Spare-Tire DNA G-Quadruplex Folding. J Am Chem Soc 2021; 143:6185-6193. [PMID: 33872503 DOI: 10.1021/jacs.1c01089] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The folding of DNA G-quadruplexes (G4) is essential to regulate expression of oncogenes and involves polymorphic long-lived intermediate states. G4 formation requires four G-tracts, but human gene-promoters often contain multiple G-tracts that act as spare-tires. These additional G-tracts are highly conserved and add multiple layers of functional complexity, as they are crucial to maintain G4 function after oxidative damage. Herein, we unravel the folding dynamics of the G4 sequence containing five G-tracts from cMYC, the major proliferation-driving oncogene. We devise a general method to induce folding at constant experimental conditions using a photochemical trapping strategy. Our data dissect the individual kinetics and thermodynamics of the spare-tire mechanism of cMYC-G4.
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Affiliation(s)
- J Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Anja Blümler
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Ines Burkhart
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Alexander Heckel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt am Main, Frankfurt 60323, Germany.,Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt am Main, Frankfurt 60323, Germany
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6
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Chaires JB, Gray RD, Dean WL, Monsen R, DeLeeuw LW, Stribinskis V, Trent JO. Human POT1 unfolds G-quadruplexes by conformational selection. Nucleic Acids Res 2020; 48:4976-4991. [PMID: 32232414 PMCID: PMC7229828 DOI: 10.1093/nar/gkaa202] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 03/13/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
The reaction mechanism by which the shelterin protein POT1 (Protection of Telomeres 1) unfolds human telomeric G-quadruplex structures is not fully understood. We report here kinetic, thermodynamic, hydrodynamic and computational studies that show that a conformational selection mechanism, in which POT1 binding is coupled to an obligatory unfolding reaction, is the most plausible mechanism. Stopped-flow kinetic and spectroscopic titration studies, along with isothermal calorimetry, were used to show that binding of the single-strand oligonucleotide d[TTAGGGTTAG] to POT1 is both fast (80 ms) and strong (-10.1 ± 0.3 kcal mol-1). In sharp contrast, kinetic studies showed the binding of POT1 to an initially folded 24 nt G-quadruplex structure is four orders of magnitude slower. Fluorescence, circular dichroism and analytical ultracentrifugation studies showed that POT1 binding is coupled to quadruplex unfolding, with a final complex with a stoichiometry of 2 POT1 per 24 nt DNA. The binding isotherm for the POT1-quadruplex interaction was sigmoidal, indicative of a complex reaction. A conformational selection model that includes equilibrium constants for both G-quadruplex unfolding and POT1 binding to the resultant single-strand provided an excellent quantitative fit to the experimental binding data. POT1 unfolded and bound to any conformational form of human telomeric G-quadruplex (antiparallel, hybrid, parallel monomers or a 48 nt sequence with two contiguous quadruplexes), but did not avidly interact with duplex DNA or with other G-quadruplex structures. Finally, molecular dynamics simulations provided a detailed structural model of a 2:1 POT1:DNA complex that is fully consistent with experimental biophysical results.
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Affiliation(s)
- Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - William L Dean
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Robert Monsen
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Lynn W DeLeeuw
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - Vilius Stribinskis
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
| | - John O Trent
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202, USA
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7
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Voigt C, Dobrychlop M, Kruse E, Czerwoniec A, Kasprzak JM, Bytner P, Campo CD, Leeder WM, Bujnicki JM, Göringer HU. The OB-fold proteins of the Trypanosoma brucei editosome execute RNA-chaperone activity. Nucleic Acids Res 2019; 46:10353-10367. [PMID: 30060205 PMCID: PMC6212840 DOI: 10.1093/nar/gky668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 07/13/2018] [Indexed: 02/01/2023] Open
Abstract
Sequence-deficient mitochondrial pre-mRNAs in African trypanosomes are substrates of a U-nucleotide-specific RNA editing reaction to generate translation-competent mRNAs. The reaction is catalyzed by a macromolecular protein complex termed the editosome. Editosomes execute RNA-chaperone activity to overcome the highly folded nature of pre-edited substrate mRNAs. The molecular basis for this activity is unknown. Here we test five of the OB-fold proteins of the Trypanosoma brucei editosome as candidates. We demonstrate that all proteins execute RNA-chaperone activity albeit to different degrees. We further show that the activities correlate to the surface areas of the proteins and we map the protein-induced RNA-structure changes using SHAPE-chemical probing. To provide a structural context for our findings we calculate a coarse-grained model of the editosome. The model has a shell-like structure: Structurally well-defined protein domains are separated from an outer shell of intrinsically disordered protein domains, which suggests a surface-driven mechanism for the chaperone activity.
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Affiliation(s)
- Christin Voigt
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Mateusz Dobrychlop
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Elisabeth Kruse
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Anna Czerwoniec
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Joanna M Kasprzak
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Patrycja Bytner
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland
| | - Cristian Del Campo
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - W-Matthias Leeder
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
| | - Janusz M Bujnicki
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.,Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - H Ulrich Göringer
- Molecular Genetics, Darmstadt University of Technology, Darmstadt, Germany
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8
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Effects of Central Loop Length and Metal Ions on the Thermal Stability of G-Quadruplexes. Molecules 2019; 24:molecules24101863. [PMID: 31096553 PMCID: PMC6571788 DOI: 10.3390/molecules24101863] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/03/2023] Open
Abstract
The central loop of G-quadruplex molecular beacons is a key element to sense target DNA or RNA sequences. In this study, circular dichroism spectroscopy (CD), thermal difference spectrum (TDS), non-denatured non-denaturing gel electrophoresis, and thermal stability analysis were used to investigate the effect of the central loop length on G-quadruplex features. Two series of G-quadruplexes, AG3TTAG3-(TTA)n-G3TTAG3T (n = 1–8) (named TTA series) and AG3TTTG3-(TTA)n-G3TTTG3T (n = 1–8) (named TTT series) were examined in K+ and Na+ solutions, respectively. CD and TDS spectral data indicated that TTA series adopted an antiparallel G-quadruplex structure in Na+ solution and a hybrid G-quadruplex structure in K+ solution respectively. TTT series exhibited a hybrid G-quadruplex structure in both Na+ and K+ solutions. UV melting curves indicated that the stability of G-quadruplex in both series was reduced by the elongation of central loop. Thermal stability analysis concluded that the G-quadruplex destabilization with long central loop is an entropy-driven process due to more flexible and longer central loops.
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9
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Marchand A, Gabelica V. Folding and misfolding pathways of G-quadruplex DNA. Nucleic Acids Res 2016; 44:10999-11012. [PMID: 27924036 PMCID: PMC5159560 DOI: 10.1093/nar/gkw970] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/07/2016] [Accepted: 10/15/2016] [Indexed: 12/13/2022] Open
Abstract
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K+ binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K+ at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel. Flanking bases increase the K+ binding cooperativity. To decipher the folding pathways, we investigated the kinetics of K+ binding to telomeric (hybrid) and c-myc (parallel) G-quadruplexes. G-quadruplexes fold via branched pathways with multiple parallel reactions. Up to six states (one ensemble without K+, two ensembles with 1-K+ and three ensembles with 2-K+) are separated based on their formation rates and ion mobility spectrometry. All G-quadruplexes first form long-lived misfolded structures (off-pathway compared to the most stable structures) containing one K+ and two quartets in an antiparallel stacking arrangement. The results highlight the particular ruggedness of G-quadruplex nucleic acid folding landscapes. Misfolded structures can play important roles for designing artificial G-quadruplex based structures, and for conformational selection by ligands or proteins in a biological context.
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Affiliation(s)
- Adrien Marchand
- INSERM, CNRS, Univ. Bordeaux, U1212 / UMR5320 - Acides Nucléiques: Régulations Naturelle et Artificielle, IECB, 2 rue Robert Escarpit, 33607 Pessac, France
| | - Valérie Gabelica
- INSERM, CNRS, Univ. Bordeaux, U1212 / UMR5320 - Acides Nucléiques: Régulations Naturelle et Artificielle, IECB, 2 rue Robert Escarpit, 33607 Pessac, France
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10
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Kim BG, Long J, Dubins DN, Chalikian TV. Ionic Effects on VEGF G-Quadruplex Stability. J Phys Chem B 2016; 120:4963-71. [DOI: 10.1021/acs.jpcb.6b03731] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Byul G. Kim
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Ji Long
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - David N. Dubins
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Tigran V. Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty
of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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11
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Largy E, Marchand A, Amrane S, Gabelica V, Mergny JL. Quadruplex Turncoats: Cation-Dependent Folding and Stability of Quadruplex-DNA Double Switches. J Am Chem Soc 2016; 138:2780-92. [PMID: 26837276 DOI: 10.1021/jacs.5b13130] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Quadruplex (G4) nucleic acids, a family of secondary structures formed by guanine-rich sequences, exhibit an important structural polymorphism. We demonstrate here that G-rich DNA sequences may function as a double switch based on different triggers, provided that their quadruplex structures and stability display a high dependence on cation nature and concentration. A first switch is based on a remarkable antiparallel-to-parallel conversion, taking place in a few seconds at room temperature by addition of low KCl amounts to a sodium-rich sample. The second switch involves the conversion of alternative antiparallel quadruplex structures binding only one cation, formed in the presence of sub-millimolar potassium or strontium concentrations, to parallel structures by increasing the cation concentration. Incidentally, extremely low K(+) or Sr(2+) concentrations (≤5 equiv) are sufficient to induce G4 formation in a buffer devoid of other G4-promoting cations, and we suggest that the alternative structures observed contain only two tetrads. Such DNA systems are biological relevant targets, can be used in nanotechnology applications, and are valuable methodological tools for understanding DNA quadruplex folding, notably at low cation concentrations. We demonstrate that this behavior is not restricted to a narrow set of sequences but can also be found for other G-quadruplex-forming motifs, arguing for widespread applications.
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Affiliation(s)
- Eric Largy
- U1212, ARNA Laboratory, Inserm , F-33000 Bordeaux, France.,IECB, ARNA Laboratory, Université de Bordeaux , F-33600 Pessac, France.,UMR 5320, ARNA Laboratory, CNRS , F-33600 Pessac, France
| | - Adrien Marchand
- U1212, ARNA Laboratory, Inserm , F-33000 Bordeaux, France.,IECB, ARNA Laboratory, Université de Bordeaux , F-33600 Pessac, France.,UMR 5320, ARNA Laboratory, CNRS , F-33600 Pessac, France
| | - Samir Amrane
- U1212, ARNA Laboratory, Inserm , F-33000 Bordeaux, France.,IECB, ARNA Laboratory, Université de Bordeaux , F-33600 Pessac, France.,UMR 5320, ARNA Laboratory, CNRS , F-33600 Pessac, France
| | - Valérie Gabelica
- U1212, ARNA Laboratory, Inserm , F-33000 Bordeaux, France.,IECB, ARNA Laboratory, Université de Bordeaux , F-33600 Pessac, France.,UMR 5320, ARNA Laboratory, CNRS , F-33600 Pessac, France
| | - Jean-Louis Mergny
- U1212, ARNA Laboratory, Inserm , F-33000 Bordeaux, France.,IECB, ARNA Laboratory, Université de Bordeaux , F-33600 Pessac, France.,UMR 5320, ARNA Laboratory, CNRS , F-33600 Pessac, France
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12
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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Novotný J, Yurenko YP, Kulhánek P, Marek R. Tailoring the properties of quadruplex nucleobases for biological and nanomaterial applications. Phys Chem Chem Phys 2015; 16:15241-8. [PMID: 24939211 DOI: 10.1039/c4cp00541d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Guanine DNA quadruplexes are interesting and important biological objects because they represent potential targets for regulatory drugs. Their use as building blocks for biomaterial applications is also being investigated. This contribution reports the in silico design of artificial building blocks derived from xanthine. Methods of quantum chemistry were used to evaluate the properties of xanthine structures relative to those containing guanine, the natural reference used. Tailoring the xanthine core showed that the base stacking and the ion coordination were significantly enhanced in the designed systems, while the ion-transport properties were not affected. Our study suggests that the 9-deaza-8-haloxanthine bases (where the halogen is fluorine or chlorine) are highly promising candidates for the development of artificial quadruplexes and quadruplex-active ligands.
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Affiliation(s)
- Jan Novotný
- CEITEC - Central European Institute of Technology, Masaryk University, Kamenice 5/A4, Brno, CZ-625 00, Czech Republic.
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Islam B, Stadlbauer P, Krepl M, Koca J, Neidle S, Haider S, Sponer J. Extended molecular dynamics of a c-kit promoter quadruplex. Nucleic Acids Res 2015; 43:8673-93. [PMID: 26245347 PMCID: PMC4605300 DOI: 10.1093/nar/gkv785] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/21/2015] [Indexed: 01/29/2023] Open
Abstract
The 22-mer c-kit promoter sequence folds into a parallel-stranded quadruplex with a unique structure, which has been elucidated by crystallographic and NMR methods and shows a high degree of structural conservation. We have carried out a series of extended (up to 10 μs long, ∼50 μs in total) molecular dynamics simulations to explore conformational stability and loop dynamics of this quadruplex. Unfolding no-salt simulations are consistent with a multi-pathway model of quadruplex folding and identify the single-nucleotide propeller loops as the most fragile part of the quadruplex. Thus, formation of propeller loops represents a peculiar atomistic aspect of quadruplex folding. Unbiased simulations reveal μs-scale transitions in the loops, which emphasizes the need for extended simulations in studies of quadruplex loops. We identify ion binding in the loops which may contribute to quadruplex stability. The long lateral-propeller loop is internally very stable but extensively fluctuates as a rigid entity. It creates a size-adaptable cleft between the loop and the stem, which can facilitate ligand binding. The stability gain by forming the internal network of GA base pairs and stacks of this loop may be dictating which of the many possible quadruplex topologies is observed in the ground state by this promoter quadruplex.
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Affiliation(s)
- Barira Islam
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
| | - Jaroslav Koca
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic National Center for Biomolecular Research, Faculty of Science, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Stephen Neidle
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiri Sponer
- Central European Institute of Technology (CEITEC), Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
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Rebič M, Mocci F, Laaksonen A, Uličný J. Multiscale simulations of human telomeric G-quadruplex DNA. J Phys Chem B 2014; 119:105-13. [PMID: 25469629 DOI: 10.1021/jp5103274] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We present a coarse-grain (CG) model of human telomeric G-quadruplex, obtained using the inverse Monte Carlo (IMC) and iterative Boltzmann inversion (IBI) techniques implemented within the software package called MagiC. As a starting point, the 2HY9 human telomeric [3 + 1] hybrid, a 26-nucleobase sequence, was modeled performing a 1 μs long atomistic molecular dynamics (MD) simulation. The chosen quadruplex includes two kinds of loops and all possible combinations of relative orientations of guanine strands that can be found in quadruplexes. The effective CG potential for a one bead per nucleotide model has been developed from the radial distribution functions of this reference system. The obtained potentials take into account explicitly the interaction with counterions, while the effect of the solvent is included implicitly. The structural properties of the obtained CG model of the quadruplex provided a perfect match to those resulting from the reference atomistic MD simulation. The same set of interaction potentials was then used to simulate at the CG level another quadruplex topology (PDB id 1KF1 ) that can be formed by the human telomeric DNA sequence. This quadruplex differs from 2HY9 in the loop topology and G-strand relative orientation. The results of the CG MD simulations of 1KF1 are very encouraging and suggest that the CG model based on 2HY9 can be used to simulate quadruplexes with different topologies. The CG model was further applied to a higher order human telomeric quadruplex formed by the repetition, 20 times, of the 1KF1 quadruplex structure. In all cases, the developed model, which to the best of our knowledge is the first model of quadruplexes at the CG level presented in the literature, reproduces the main structural features remarkably well.
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Affiliation(s)
- Matúš Rebič
- Department of Biophysics, Faculty of Science, P. J. Šafárik University , Jesenná 5, 041 54 Košice, Slovakia
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Verdian-Doghaei A, Housaindokht MR, Bozorgmehr MR, Abnous K. Conformational switch of insulin-binding aptamer into G-quadruplex induced by K⁺ and Na⁺: an experimental and theoretical approach. J Biomol Struct Dyn 2014; 33:1153-63. [PMID: 24933356 DOI: 10.1080/07391102.2014.935482] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Guanine-rich sequences can form the G-quadruplex structure in the presence of specific metal ions. Here, circular dichroism, UV-vis absorption, fluorescence, and molecular dynamics simulation studies revealed that insulin-binding aptamer (IBA) could form an intramolecular G-quadruplex structure after binding K(+). Circular dichroism (CD) spectra demonstrated that IBA could fold into a parallel G-quadruplex with a strong positive peak at 263 nm. Analysis of equilibrium titration data revealed that cation binding was cooperative with the Hill coefficient of 2.01 in K(+) and 1.90 in Na(+). Thermal denaturation assays indicated that K(+)-induced G-quadruplex is more stable than Na(+)-induced structure. Folding of IBA into G-quadruplex leading to the contact quenching occurs as a result of the formation of a nonfluorescent complex between donor and acceptor. Based on fluorescence quenching of IBA folding, a potassium-sensing aptasensor in the range of 0-1.4 mM was proposed. Since the quenching process was predominantly static, the binding constant and the number of binding sites were determined. In this research, based on the experimental data, the initial model of IBA G-quadruplex was constructed by molecular modeling method. The modeling structure of IBA is an intramolecular parallel-strand quadruplex conformation with two guanine tetrads. The extended molecular dynamics simulation for the model indicated that the G-quadruplex maintains its structure very well in aqueous solution in presence of K(+) in the central cavity. In contrast, it was demonstrated that the G-quadruplex structure of model in the water collapses in absence of this cation.
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Affiliation(s)
- A Verdian-Doghaei
- a Biophysical Chemistry Laboratory, Department of Chemistry, Faculty of Science , Ferdowsi University of Mashhad , Mashhad , Iran
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Marchand A, Gabelica V. Native electrospray mass spectrometry of DNA G-quadruplexes in potassium solution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1146-54. [PMID: 24781455 PMCID: PMC4055847 DOI: 10.1007/s13361-014-0890-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/11/2014] [Accepted: 03/17/2014] [Indexed: 05/25/2023]
Abstract
A commonly used electrolyte in electrospray mass spectrometry (ESI-MS) of biomolecules is ammonium acetate (NH4OAc). Although some nucleic acid structures such as duplexes require only proper physiological ionic strength (whatever the monovalent ions) to be properly folded in ESI-MS conditions, the folding of some other nucleic acid structures such as DNA G-quadruplexes also depends on direct binding of specific cations. Here, we developed ESI-MS compatible conditions that allow one to observe DNA G-quaduplexes with K(+) ions specifically bound between G-quartets. NH4OAc was replaced with trimethylammonium acetate (TMAA), at concentrations up to 150 mM to provide physiological ionic strength, and the solution was doped with KCl at concentrations up to 1 mM. The trimethylammonium ion is too large to coordinate between G-quartets, where only K(+) ions bind. Compared with the equivalent NH4OAc/KCl mixtures, the TMAA/KCl mixtures provide cleaner spectra by suppressing the nonspecific adducts, and favor the formation of similar stacking arrangements as in 100 mM KCl (physiologically relevant cation) for the polymorphic human telomeric DNA G-quadruplexes. This new sample preparation method can be exploited to determine the number of potassium binding sites in new sequences, to screen ligand binding to the structures favored in potassium, and to transfer potassium-bound G-quadruplexes to the mass spectrometer for gas-phase structural probing, as illustrated herein with ion mobility spectrometry experiments.
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Affiliation(s)
- Adrien Marchand
- University Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France
- INSERM, U869, ARNA Laboratory, F-33000 Bordeaux, France
| | - Valerie Gabelica
- University Bordeaux, IECB, ARNA Laboratory, F-33600 Pessac, France
- INSERM, U869, ARNA Laboratory, F-33000 Bordeaux, France
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Stadlbauer P, Krepl M, Cheatham TE, Koča J, Šponer J. Structural dynamics of possible late-stage intermediates in folding of quadruplex DNA studied by molecular simulations. Nucleic Acids Res 2013; 41:7128-43. [PMID: 23700306 PMCID: PMC3737530 DOI: 10.1093/nar/gkt412] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/18/2013] [Accepted: 04/24/2013] [Indexed: 12/31/2022] Open
Abstract
Explicit solvent molecular dynamics simulations have been used to complement preceding experimental and computational studies of folding of guanine quadruplexes (G-DNA). We initiate early stages of unfolding of several G-DNAs by simulating them under no-salt conditions and then try to fold them back using standard excess salt simulations. There is a significant difference between G-DNAs with all-anti parallel stranded stems and those with stems containing mixtures of syn and anti guanosines. The most natural rearrangement for all-anti stems is a vertical mutual slippage of the strands. This leads to stems with reduced numbers of tetrads during unfolding and a reduction of strand slippage during refolding. The presence of syn nucleotides prevents mutual strand slippage; therefore, the antiparallel and hybrid quadruplexes initiate unfolding via separation of the individual strands. The simulations confirm the capability of G-DNA molecules to adopt numerous stable locally and globally misfolded structures. The key point for a proper individual folding attempt appears to be correct prior distribution of syn and anti nucleotides in all four G-strands. The results suggest that at the level of individual molecules, G-DNA folding is an extremely multi-pathway process that is slowed by numerous misfolding arrangements stabilized on highly variable timescales.
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Affiliation(s)
- Petr Stadlbauer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Thomas E. Cheatham
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jaroslav Koča
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic, Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84124, USA and CEITEC – Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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Islam B, Sgobba M, Laughton C, Orozco M, Sponer J, Neidle S, Haider S. Conformational dynamics of the human propeller telomeric DNA quadruplex on a microsecond time scale. Nucleic Acids Res 2013; 41:2723-35. [PMID: 23293000 PMCID: PMC3575793 DOI: 10.1093/nar/gks1331] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 11/26/2012] [Accepted: 11/27/2012] [Indexed: 01/12/2023] Open
Abstract
The human telomeric DNA sequence with four repeats can fold into a parallel-stranded propeller-type topology. NMR structures solved under molecular crowding experiments correlate with the crystal structures found with crystal-packing interactions that are effectively equivalent to molecular crowding. This topology has been used for rationalization of ligand design and occurs experimentally in a number of complexes with a diversity of ligands, at least in the crystalline state. Although G-quartet stems have been well characterized, the interactions of the TTA loop with the G-quartets are much less defined. To better understand the conformational variability and structural dynamics of the propeller-type topology, we performed molecular dynamics simulations in explicit solvent up to 1.5 μs. The analysis provides a detailed atomistic account of the dynamic nature of the TTA loops highlighting their interactions with the G-quartets including formation of an A:A base pair, triad, pentad and hexad. The results present a threshold in quadruplex simulations, with regards to understanding the flexible nature of the sugar-phosphate backbone in formation of unusual architecture within the topology. Furthermore, this study stresses the importance of simulation time in sampling conformational space for this topology.
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Affiliation(s)
- Barira Islam
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Miriam Sgobba
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Charlie Laughton
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Modesto Orozco
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Jiri Sponer
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Stephen Neidle
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- Centre for Cancer Research and Cell Biology, Queen’s University of Belfast, Belfast BT9 7BL, UK, School of Pharmacy, Nottingham University, University Park, Nottingham NG7 2RD, UK, Institute of Research in Biomedicine, Barcelona 08028, Spain, Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovoplka 135, Brno 612 65, Czech Republic, Central European Institute of Technology, Campus Bohunice, Kamenice 5, Brno 625 00, Czech Republic and University College London, School of Pharmacy, Brunswick Square, London WC1N 1AX, UK
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