Enhanced sampling molecular dynamics simulations correctly predict the diverse activities of a series of stiff-stilbene G-quadruplex DNA ligands

Enhanced sampling molecular dynamics simulations and solution-phase experiments come together to demonstrate the diverse effects of G4-interactive small molecules.

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Molecular Dynamics Simulations to Provide New Insights into the Asymmetrical Ammonium Ion Movement Inside of the [d(G3T4G4)]2 G-Quadruplex DNA Structure

The Journal of Physical Chemistry B ◽

10.1021/jp304760k ◽

2012 ◽

Vol 116 (31) ◽

pp. 9363-9370 ◽

Cited By ~ 23

Author(s):

Parisa Akhshi ◽

Gregory Acton ◽

Gang Wu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Dna Structure ◽

Ammonium Ion ◽

Quadruplex Dna ◽

Ion Movement ◽

G Quadruplex ◽

Dynamics Simulations

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Toward a full structural characterization of G-quadruplex DNA in aqueous solution: Molecular dynamics simulations of four G-quadruplex molecules

Journal of Molecular Structure THEOCHEM ◽

10.1016/j.theochem.2010.04.035 ◽

2010 ◽

Vol 952 (1-3) ◽

pp. 96-102 ◽

Cited By ~ 13

Author(s):

Ming-Hui Li ◽

Quan Luo ◽

Xiang-Gui Xue ◽

Ze-Sheng Li

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Molecular Dynamics Simulations ◽

Structural Characterization ◽

Quadruplex Dna ◽

G Quadruplex ◽

Dynamics Simulations

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Binding of anticancer drug daunomycin to a TGGGGT G-quadruplex DNA probed by all-atom molecular dynamics simulations: additional pure groove binding mode and implications on designing more selective G-quadruplex ligands

Journal of Molecular Modeling ◽

10.1007/s00894-017-3417-6 ◽

2017 ◽

Vol 23 (9) ◽

Cited By ~ 13

Author(s):

Zhanhang Shen ◽

Kelly A. Mulholland ◽

Yujun Zheng ◽

Chun Wu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Anticancer Drug ◽

Binding Mode ◽

Groove Binding ◽

Quadruplex Dna ◽

G Quadruplex ◽

Dynamics Simulations ◽

Groove Binding Mode

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Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2017.1323013 ◽

2017 ◽

Vol 36 (6) ◽

pp. 1369-1401 ◽

Cited By ~ 11

Author(s):

R. Radhika ◽

R. Shankar ◽

S. Vijayakumar ◽

P. Kolandaivel

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Quantum Chemical ◽

Base Pairs ◽

Quadruplex Dna ◽

Dna Base ◽

Dna Base Pairs ◽

G Quadruplex ◽

Dynamics Simulations

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Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA

Nucleic Acids Research ◽

10.1093/nar/gkw160 ◽

2016 ◽

Vol 44 (7) ◽

pp. 3020-3030 ◽

Cited By ~ 15

Author(s):

Mateusz Kogut ◽

Cyprian Kleist ◽

Jacek Czub

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Structural Unit ◽

Quadruplex Dna ◽

G Quadruplex ◽

Balance Of Forces ◽

Dynamics Simulations

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Binding of Telomestatin to a Telomeric G-Quadruplex DNA Probed by All-Atom Molecular Dynamics Simulations with Explicit Solvent

Journal of Chemical Information and Modeling ◽

10.1021/acs.jcim.6b00473 ◽

2016 ◽

Vol 56 (10) ◽

pp. 2093-2102 ◽

Cited By ~ 19

Author(s):

Kelly Mulholland ◽

Chun Wu

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Quadruplex Dna ◽

Explicit Solvent ◽

G Quadruplex ◽

Dynamics Simulations

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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

Journal of Biomolecular Structure and Dynamics ◽

10.1080/07391102.2019.1574239 ◽

2019 ◽

Vol 38 (2) ◽

pp. 317-339 ◽

Cited By ~ 11

Author(s):

S. Vinnarasi ◽

R. Radhika ◽

S. Vijayakumar ◽

R. Shankar

Keyword(s):

Molecular Dynamics ◽

Molecular Dynamics Simulations ◽

Quantum Chemical ◽

Quadruplex Dna ◽

Anti Cancer ◽

G Quadruplex ◽

Dynamics Simulations ◽

Structural Insights ◽

Cancer Activity

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Umbrella sampling molecular dynamics simulations reveal concerted ion movement through G-quadruplex DNA channels

Physical Chemistry Chemical Physics ◽

10.1039/c7cp01028a ◽

2017 ◽

Vol 19 (18) ◽

pp. 11017-11025 ◽

Cited By ~ 12

Author(s):

Parisa Akhshi ◽

Gang Wu

Keyword(s):

Molecular Dynamics ◽

Ion Transport ◽

Molecular Dynamics Simulations ◽

Md Simulations ◽

Umbrella Sampling ◽

Potential Of Mean Force ◽

Quadruplex Dna ◽

Ion Movement ◽

G Quadruplex ◽

Dynamics Simulations

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].

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