AI 中文总结
本研究基于TIS模型模拟短ssDNA同源聚体，揭示其在二价阳离子中持久长度符合德拜长度相关公式，而在四价精胺中几乎不随浓度变化，该发现有待实验验证。
AI 中文摘要
我们基于依赖序列的三相互作用位点（Three Interaction Site, TIS）模型，对短单链DNA（single stranded DNA, ssDNA）同源聚体进行模拟，以计算其在多价阳离子中的持久长度（$l_p$）。TIS模型考虑了堆积相互作用，静电相互作用则采用库仑势处理。我们发现，在二价阳离子$\boldsymbol{\rm Mg^{2+}}$和$\boldsymbol{\rm Ca^{2+}}$中，$\boldsymbol{\rm dT_{30}}$（T为胸腺嘧啶）和$\boldsymbol{\rm dA_{30}}$（A为腺嘌呤）的$l_p$可通过公式$l_p = l_p^0 + λκ^{-1}$（$l_p^0$为裸持久长度，$λ$为无量纲常数，$κ$为德拜长度的倒数）进行定量拟合。$l_p$对$κ$的这种依赖关系令人意外，因为该公式原本是针对长柔性聚电解质推导的，这类体系中电荷通过德拜-休克尔势相互作用。polyT和polyA的$l_p^0$值分别为0.4 nm和1.1 nm。值得注意的是，$l_p$几乎不随四价精胺（spermine）的浓度变化。目前尚无明确的理论解释，不过模拟结果显示，结合到ssDNA上的精胺分子数会在一个较小的数值上达到饱和。基于$\boldsymbol{\rm Spm^{4+}}$各向异性结构的体积排斥效应限制了其与磷酸基团的接触这一观点，可定性解释模拟结果。关于精胺中$l_p$的依赖关系预测仍有待实验验证。
英文摘要
We used simulations of short single stranded DNA (ssDNA) homopolymers, based on the sequence dependent Three Interaction Site (TIS) model, to calculate the persistence length ($l_p$) in polyvalent cations. The TIS model accounts for stacking interactions and electrostatic interactions are treated using the Coulomb potential. We find that $l_p$ for $\mathrm{dT_{30}}$ (T is thymine) and $\mathrm{dA_{30}}$ (A is adenine) is quantitatively fit using $l_p = l_p^0 + λκ^{-1}$ ($l_p^0$ is the bare persistence length, $λ$ is a dimensionless constant, and $κ$ is the inverse Debye length) in the divalent cations $\mathrm{Mg^{2+}}$ and $\mathrm{Ca^{2+}}$. The dependence of $l_p$ on $κ$ is surprising because it was derived for long flexible polyelectrolytes in which the charges interact via the Debye-Hückel potential. The $l_p^0$ values are 0.4 nm and 1.1 nm for polyT and polyA, respectively. Strikingly, $l_p$ is almost independent of the tetravalent spermine concentration. There is no clear theoretical explanation although simulations suggest that the number of spermine molecules that bind to the ssDNA saturates at a small value. A qualitative picture, based on the restrictions of access to the phosphate groups due to volume exclusion of the anisotropic structure of $\mathrm{Spm^{4+}}$, rationalizes the simulation results. The predicted dependence of $l_p$ in spermine awaits experimental test.
