Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions

Loading...
Thumbnail Image
File version

Version of Record (VoR)

Author(s)
Mu, Zi-Chun
Tan, Ya-Lan
Zhang, Ben-Gong
Liu, Jie
Shi, Ya-Zhou
Griffith University Author(s)
Primary Supervisor
Other Supervisors
Editor(s)

MacKerell, Alexander

Date
2022
Size
File type(s)
Location
Abstract

The three-dimensional (3D) structure and stability of DNA are essential to understand/control their biological functions and aid the development of novel materials. In this work, we present a coarse-grained (CG) model for DNA based on the RNA CG model proposed by us, to predict 3D structures and stability for both dsDNA and ssDNA from the sequence. Combined with a Monte Carlo simulated annealing algorithm and CG force fields involving the sequence-dependent base-pairing/stacking interactions and an implicit electrostatic potential, the present model successfully folds 20 dsDNAs (≤52nt) and 20 ssDNAs (≤74nt) into the corresponding native-like structures just from their sequences, with an overall mean RMSD of 3.4Å from the experimental structures. For DNAs with various lengths and sequences, the present model can make reliable predictions on stability, e.g., for 27 dsDNAs with/without bulge/internal loops and 24 ssDNAs including pseudoknot, the mean deviation of predicted melting temperatures from the corresponding experimental data is only ~2.0°C. Furthermore, the model also quantificationally predicts the effects of monovalent or divalent ions on the structure stability of ssDNAs/dsDNAs.

Journal Title

PLOS Computational Biology

Conference Title
Book Title
Edition
Volume

18

Issue

10

Thesis Type
Degree Program
School
Publisher link
Patent number
Funder(s)
Grant identifier(s)
Rights Statement
Rights Statement

© 2022 Mu et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Item Access Status
Note
Access the data
Related item(s)
Subject
Persistent link to this record
Citation

Mu, Z-C; Tan, Y-L; Zhang, B-G; Liu, J; Shi, Y-Z, Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions, PLOS Computational Biology, 2022, 18 (10), pp. e1010501

Collections