Structural elasticity of double-strand DNAs is very important for their biological functions such as DNA-ligand binding and DNA-protein recognition. By all-atom molecular dynamics simulations, we investigated the bending elasticity of DNA with three typical sequences including poly(A)-poly(T) (AA-TT), poly(AT)-poly(TA) (AT-TA), and a generic sequence (GENE). Our calculations indicate that, AA-TT has an apparently larger bending persistence length (P ∼63 nm) than GENE (P ∼49 nm) and AT-TA (P ∼48 nm) while the persistence length of AT-TA is only very slightly smaller than that of GENE, which agrees well with those from existing works. Moreover, through extensive electrostatic calculations, we found that the sequence-dependent bending elasticity is attributed to the sequence-dependent electrostatic bending energy for AA-TT, AT-TA and GENE, which is coupled to their backbone structures. Particularly, the apparently stronger bending stiffness of AA-TT is attributed to its narrower minor groove. Interestingly, for the three DNAs, we predicted the non-electrostatic persistence length of ∼17 nm, thus electrostatic interaction makes the major contribution to DNA bending elasticity. The mechanism of electrostatic energy dominating sequence effect in DNA bending elasticity is furtherly illustrated through the electrostatic calculations for a grooved coarse-grained DNA model where minor groove width and other microscopic structural parameters can be artificially adjusted.

双链 DNA 的结构弹性对其生物学功能非常重要，例如 DNA-配体结合和 DNA-蛋白质识别。通过全原子分子动力学模拟，我们研究了具有三种典型序列的 DNA 的弯曲弹性，包括 poly(A)-poly(T) (AA-TT)、poly(AT)-poly(TA) (AT-TA)、和一个通用序列（GENE）。我们的计算表明，AA-TT 的弯曲持续长度（P ∼63 nm）明显大于 GENE（P ∼49 nm）和 AT-TA（P∼48 nm)，而 AT-TA 的持续长度仅比 GENE 的稍小，这与现有工作的结果非常吻合。此外，通过广泛的静电计算，我们发现序列相关的弯曲弹性归因于 AA-TT、AT-TA 和 GENE 的序列相关静电弯曲能，这与它们的骨架结构耦合。特别是，AA-TT 明显更强的弯曲刚度归因于其更窄的小凹槽。有趣的是，对于这三种 DNA，我们预测非静电持续长度约为 17 nm，因此静电相互作用对 DNA 弯曲弹性做出了主要贡献。