Maffeo Christopher, Ngo Thuy T M, Ha Taekjip, Aksimentiev Aleksei
Department of Physics, University of Illinois at Urbana -Champaign, Urbana, Illinois, United States.
Center for Biophysics and Computational Biology, University of Illinois at Urbana -Champaign, Urbana, Illinois, United States.
J Chem Theory Comput. 2014 Aug 12;10(8):2891-2896. doi: 10.1021/ct500193u. Epub 2014 Jun 3.
A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force-extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT fragment via FRET while stretching the molecules using optical tweezers. The model offers straightforward generalization to systems containing double-stranded DNA and DNA binding proteins.
开发了一种简单的单链DNA（ssDNA）粗粒度模型，每个核苷酸仅具有两个位点，分别代表主链以及糖/碱基基团的质心。在该模型中，位点之间的相互作用通过列表形式的键合势来描述，这些势经过优化以重现原子分子动力学模拟中观察到的DNA溶液结构。各向同性势描述非键合相互作用，隐含地考虑了溶剂条件以匹配实验测定的ssDNA回转半径。该模型再现了非结构化DNA链在2个数量级的外加力范围内实验测量的力-伸长依赖性。通过在使用光镊拉伸分子时通过荧光共振能量转移（FRET）测量dT片段的端到端距离，证实了该模型的准确性。该模型可以直接推广到包含双链DNA和DNA结合蛋白的系统。
