DNA G-quadruplex structures obtained through MD-based folding procedure

Description

The dataset contains structures of DNA G-quadruplexes (G4s), obtained through steered molecular dynamics simulations, for 128 oligonucleotides capable of forming 3- and 2-tetrad G4s. The general sequence of the oligonucleotides is GxTiGxTjGxTkGx, where x = 3 or 2 for 3- and 2-tetrad G4s, respectively, while i, j, and k vary independently from 1 to 4, representing the length of loop regions. Each sequence was folded into 26 G4 topologies, and for each topology, all possible tetrad polarity patterns were considered (8 or 4 such patterns for 3- and 2-tetrad G4s, respectively). Lists of all obtained structures, with specifications of whether the given structures are properly folded, can be found in the files ‘List_of_three-tetrad_structures.csv’ and ‘List_of_two-tetrad_structures.csv’ for 3- and 2-tetrad G4s, respectively. Additionally, pictures showing all obtained structures and movies visualizing the folding simulation for exemplary G4s are attached.

Dataset file

G4_structures.tar.gz

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CC BY

Attribution
Software:: VMD, PyMol

Details

Year of publication:

2024

Verification date:

2024-12-03

Dataset language:

English

Fields of science:

chemical sciences (Natural sciences)

DOI:

10.34808/fcyz-w866

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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