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从头预测离子溶液中单链和双链 DNA 的 3D 结构和稳定性。

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

机构信息

Research Center of Nonlinear Science, School of Mathematical & Physical Sciences, Wuhan Textile University, Wuhan, China.

School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China.

出版信息

PLoS Comput Biol. 2022 Oct 19;18(10):e1010501. doi: 10.1371/journal.pcbi.1010501. eCollection 2022 Oct.

DOI:10.1371/journal.pcbi.1010501
PMID:36260618
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9621594/
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.

摘要

三维（3D）结构和 DNA 的稳定性对于理解/控制其生物功能和帮助开发新型材料至关重要。在这项工作中，我们提出了一种基于我们提出的 RNA CG 模型的 DNA 粗粒（CG）模型，以从序列预测双链 DNA（dsDNA）和单链 DNA（ssDNA）的 3D 结构和稳定性。结合蒙特卡罗模拟退火算法和 CG 力场，该力场涉及序列依赖性碱基对/堆积相互作用和隐式静电势，该模型成功地将 20 个 dsDNA（≤52nt）和 20 个 ssDNA（≤74nt）折叠成相应的天然样结构，仅从其序列来看，整体平均均方根偏差为 3.4Å，与实验结构相比。对于具有各种长度和序列的 DNA，该模型可以对稳定性进行可靠的预测，例如，对于具有/不具有凸起/内环的 27 个 dsDNA 和包括假结在内的 24 个 ssDNA，预测的熔化温度与相应实验数据的平均偏差仅约为 2.0°C。此外，该模型还定量预测了单价或二价离子对 ssDNA/dsDNA 结构稳定性的影响。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/b0fa68ce5dd3/pcbi.1010501.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/cf81f02c5cbf/pcbi.1010501.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/f5b012505a5b/pcbi.1010501.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/66d22f3ed3a7/pcbi.1010501.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/f9ace0a19a2c/pcbi.1010501.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/a1aea891b113/pcbi.1010501.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/17a49a8e354d/pcbi.1010501.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/f21170aeea7b/pcbi.1010501.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/b0fa68ce5dd3/pcbi.1010501.g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/cf81f02c5cbf/pcbi.1010501.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/f5b012505a5b/pcbi.1010501.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/66d22f3ed3a7/pcbi.1010501.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/f9ace0a19a2c/pcbi.1010501.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/a1aea891b113/pcbi.1010501.g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/17a49a8e354d/pcbi.1010501.g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/f21170aeea7b/pcbi.1010501.g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/26ee/9621594/b0fa68ce5dd3/pcbi.1010501.g008.jpg

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