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arXiv · 2501.11891

3D structure and stability prediction of DNA with multi-way junctions in ionic solutions

Xunxun Wang·Ya-Zhou Shi
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Abstract

Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more refined electrostatic energy term, the replica-exchange Monte Carlo algorithm, and the weighted histogram analysis method. The enhanced model predicts the 3D structures and stability of DNA with multi-way junctions (three-way and four-way) in various ionic environments, going beyond traditional single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). Our model demonstrates remarkable accuracy in predicting the structures of DNAs with multi-way junctions from sequences and offers reliable estimates of their thermal stability across a range of sequences and lengths, with both monovalent and divalent salts. Notably, our analysis of the thermally unfolding pathways reveals that the stability of DNA with multi-way junctions is strongly influenced by the relative stabilities of their unfolded intermediate states, providing key insights into DNA structure-function relationships.

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Xunxun Wang, Ya-Zhou Shi. 2025-01-21. 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions. https://arxiv.org/abs/2501.11891

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