Department of Mechanical Engineering, Kanto Gakuin University , 1-50-1 Mutsuura-higashi, Kanazawa-ku, Yokohama 236-8501, Japan.
Department of Mechanical and Aerospace Engineering, Seoul National University , 1 Gwanak-ro, Daehak-dong, Gwanak-gu, Seoul 08826, Republic of Korea.
J Phys Chem B. 2017 May 18;121(19):5033-5039. doi: 10.1021/acs.jpcb.7b03931. Epub 2017 May 10.
A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads-spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the nonbond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35.3° and 120.3 bp, confirming that the proposed model successfully realized the experimentally observed double-stranded DNA structure. Moreover, the model with electrostatic interaction was discussed. From calculation results, we confirmed that the dependency of the salt concentration on the persistence length of the nCG-dsDNA model at the 30% charge is in good agreement with the Poisson-Boltzmann theoretical model.
提出了一种新的粗粒度分子动力学双链 DNA 模型（nCG-dsDNA 模型），使用改进的珠-弹簧模型。在这个模型中，核苷酸由磷酸、糖和碱基组成，被替换为一个单个珠子。创建了一个具有 202 个碱基对的双链模型，以调整键、非键、堆积、角度弯曲和静电相互作用的参数。在没有静电相互作用的情况下，模型的平均扭曲角度和持久长度计算为 35.3°和 120.3 bp，这证实了所提出的模型成功地实现了实验观察到的双链 DNA 结构。此外，还讨论了具有静电相互作用的模型。从计算结果中，我们确认了盐浓度对 30%电荷下 nCG-dsDNA 模型持久长度的依赖性与泊松-玻尔兹曼理论模型非常吻合。
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