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Islam B, Stadlbauer P, Vorlíčková M, Mergny JL, Otyepka M, Šponer J. Stability of Two-Quartet G-Quadruplexes and Their Dimers in Atomistic Simulations. J Chem Theory Comput 2020; 16:3447-3463. [PMID: 32163706 DOI: 10.1021/acs.jctc.9b01068] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-quadruplexes (GQs) are four-stranded noncanonical DNA and RNA architectures that can be formed by guanine-rich sequences. The stability of GQs increases with the number of G-quartets, and three G-quartets generally form stable GQs. However, the stability of two-quartet GQs is an open issue. To understand the intrinsic stability of two-quartet GQ stems, we have carried out a series of unbiased molecular dynamics (MD) simulations (505 μs in total) of two- and four-quartet DNA and RNA GQs, with attention paid mainly to parallel-stranded arrangements. We used AMBER DNA parmOL15 and RNA parmOL3 force fields and tested different ion and water models. Two-quartet parallel-stranded DNA GQs unfolded in all the simulations, while the equivalent RNA GQ was stable in most of the simulations. GQs composed of two stacked units of two-quartet GQs were stable for both DNA and RNA. The simulations suggest that a minimum of three quartets are needed to form an intrinsically stable all-anti parallel-stranded DNA GQ. Parallel two-quartet DNA GQ may exist if substantially stabilized by another molecule or structural element, including multimerization. On the other hand, we predict that isolated RNA two-quartet parallel GQs may form, albeit being weakly stable. We also show that ionic parameters and water models should be chosen with caution because some parameter combinations can cause spurious instability of GQ stems. Some in-so-far unnoticed limitations of force-field description of multiple ions inside the GQs are discussed, which compromise the capability of simulations to fully capture the effect of increase in the number of quartets on the GQ stability.
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Affiliation(s)
- Barira Islam
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Michaela Vorlíčková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jean-Louis Mergny
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Michal Otyepka
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic.,Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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Singh A, Joshi S, Kukreti S. Cationic porphyrins as destabilizer of a G-quadruplex located at the promoter of human MYH7 β gene. J Biomol Struct Dyn 2019; 38:4801-4816. [PMID: 31809672 DOI: 10.1080/07391102.2019.1689850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
G-quadruplex (GQ) architecture is adopted by guanine rich sequences, present throughout the eukaryotic genome including promoter locations and telomeric ends. The in vivo presence indicates their involvement and role in various biological processes. Various small ligands have been developed to interact and stabilize/destabilize G-quadruplex structures. Cationic porphyrins are among the most studied ligands, reported to bind and stabilize G-quadruplexes. Herein, we report the recognition and destabilization of a parallel G-quadruplex by porphyrins (TMPyP3 and TMPyP4). This G-quadruplex forming 23-nt G-rich sequence is in the promoter region of Human Myosin Heavy Chain β gene (MYH7β). Presence of various putative regulatory sequence elements (TATA Box, CCAAT, SP-1) located in the vicinity of this quadruplex motif, highlight its regulatory implications. Biophysical methods as Circular Dichroism Spectroscopy, UV-Absorption Spectroscopy, UV-Thermal Denaturation and Fluorescence Spectroscopy (steady as well as Time Resolved) have been used for studying the interaction and binding parameters. It is proposed that porphyrins have a destabilizing effect on the G-quadruplexes with parallel topology and a stronger binding specifically via intercalation mode is needed to cause destabilization. The study deals with better understanding and insights of DNA-Drug interactions in biological systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Savita Joshi
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
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Islam B, Stadlbauer P, Krepl M, Havrila M, Haider S, Sponer J. Structural Dynamics of Lateral and Diagonal Loops of Human Telomeric G-Quadruplexes in Extended MD Simulations. J Chem Theory Comput 2018; 14:5011-5026. [DOI: 10.1021/acs.jctc.8b00543] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Barira Islam
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Miroslav Krepl
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Marek Havrila
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Shozeb Haider
- UCL School of
Pharmacy, 29-39 Brunswick Square, London WC1N 1AX, U.K
| | - Jiri Sponer
- Institute of Biophysics
of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
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Zhang X, Bao L, Wu YY, Zhu XL, Tan ZJ. Radial distribution function of semiflexible oligomers with stretching flexibility. J Chem Phys 2018; 147:054901. [PMID: 28789545 DOI: 10.1063/1.4991689] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The radial distribution of the end-to-end distance Ree is crucial for quantifying the global size and flexibility of a linear polymer. For semiflexible polymers, several analytical formulas have been derived for the radial distribution of Ree ignoring the stretching flexibility. However, for semiflexible oligomers, such as DNA or RNA, the stretching flexibility can be rather pronounced and can significantly affect the radial distribution of Ree. In this study, we obtained an extended formula that includes the stretch modulus to describe the distribution of Ree for semiflexible oligomers on the basis of previous formulas for semiflexible polymers without stretching flexibility. The extended formula was validated by extensive Monte Carlo simulations over wide ranges of the stretch modulus and persistence length, as well as all-atom molecular dynamics simulations of short DNAs and RNAs. Additionally, our analyses showed that the effect of stretching flexibility on the distribution of Ree becomes negligible for DNAs longer than ∼130 base pairs and RNAs longer than ∼240 base pairs.
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Affiliation(s)
- Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Lei Bao
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Yuan-Yan Wu
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics and Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro and Nano-Structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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Abstract
Minima of the electric field and positions of K+ and Na+ (zero of the x-coordinate is the center of the cavity).
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Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici
- ICCOM – UOS Pisa
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
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Islam B, Stadlbauer P, Neidle S, Haider S, Sponer J. Can We Execute Reliable MM-PBSA Free Energy Computations of Relative Stabilities of Different Guanine Quadruplex Folds? J Phys Chem B 2016; 120:2899-912. [DOI: 10.1021/acs.jpcb.6b01059] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Barira Islam
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Petr Stadlbauer
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Stephen Neidle
- UCL School of Pharmacy, 29-39
Brunswick Square, London WC1N 1AX, U.K
| | - Shozeb Haider
- UCL School of Pharmacy, 29-39
Brunswick Square, London WC1N 1AX, U.K
| | - Jiri Sponer
- 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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