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

Author:

Akhshi Parisa1234,Wu Gang1234ORCID

Affiliation:

1. Department of Chemistry

2. Queen's University

3. Kingston

4. Canada

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].

Funder

Natural Sciences and Engineering Research Council of Canada

Publisher

Royal Society of Chemistry (RSC)

Subject

Physical and Theoretical Chemistry,General Physics and Astronomy

Reference88 articles.

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3. Guanine Quartets: Structure and Application, ed. L. Spindler and W. Fritzsche, The Royal Society of Chemistry, Cambridge, UK, 2013

4. The High-Resolution Crystal Structure of a Parallel-Stranded Guanine Tetraplex

5. The crystal structure of a parallel-stranded guanine tetraplex at 0.95Å resolution

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