3D structure and stability prediction of DNA with multi-way junctions in ionic solutions
Fuente:
arXiv
Guardado en:
| Autores principales: | , |
|---|---|
| Formato: | Preprint |
| Publicado: |
2025
|
| Materias: | |
| Acceso en línea: | |
| Etiquetas: |
Agregar Etiqueta
Sin Etiquetas, Sea el primero en etiquetar este registro!
|
| _version_ | 1866929683225903104 |
|---|---|
| author | Wang, Xunxun Shi, Ya-Zhou |
| author_facet | Wang, Xunxun Shi, Ya-Zhou |
| contents | 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2501_11891 |
| institution | arXiv |
| publishDate | 2025 |
| record_format | arxiv |
| spellingShingle | 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions Wang, Xunxun Shi, Ya-Zhou Soft Condensed Matter 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. |
| title | 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions |
| topic | Soft Condensed Matter |
| url | https://arxiv.org/abs/2501.11891 |