Initial geometries and MD trajectories of right- and left-handed G-quadruplexes

Description

Dataset contains initial geometries of 12 monomeric, 2-tetrad G-quadruplexes featuring three different loop lengths (T1, T2 and T3), adapted by the sequence GGTnGGTnGGTnGG where n=(1-3). For each loop length variant two directions of strand progression (clockwise (+) and anti-clockwise (-)) and two helicities (left-handed (LH) and right-handed (RH)) were considered. All structures are solvated in water with K+ and CL- ions. Additionally, dataset contains MD-generated folded-state ensembles of energetically accessible folds. Ensembles were obtained by concatenaiting folded-state parts of trajectories from independent MD runs for each system.

Dataset file

initial_structures_and_folded_state_ensembles.tar.gz

2.0 GB, S3 ETag 1f3b809d8a6666c81d8d15a7e9f04577-5, downloads: 73

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CC BY

Attribution
Software:: VMD, PyMol

Details

Year of publication:

2023

Verification date:

2023-11-24

Dataset language:

English

Fields of science:

chemical sciences (Natural sciences)

DOI:

10.34808/w2df-6642

Funding:

Exploring the sequence-structure relationship as a starting point for the design of DNA G-quadruplexes with a given topology -- an integrative approach combining molecular simulations with experimental methods

Verified by:

Gdańsk University of Technology

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