标题： 短DNA螺旋的灵活性与有限长度效应：从碱基对到数十个碱基对 显示英文标题

标题： Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs

摘要： 短DNA螺旋的柔韧性对于生物功能如核小体形成和DNA-蛋白质识别非常重要。 最近的实验表明，数十个碱基对（bps）的短DNA可能比千碱基对的DNA具有明显更高的柔韧性，但关于这种高柔韧性的争论仍在继续。 在本研究中，我们通过全原子分子动力学模拟和基于蠕虫样链模型的蒙特卡洛模拟，研究了长度为5到50 bps的短DNA的柔韧性。 我们的微观分析表明，短DNA具有明显的高柔韧性，这归因于每个螺旋末端约6 bps处显著强烈的弯曲和拉伸柔韧性。 相应地，随着DNA长度从10到50 bps增加，短DNA的表观持久长度lp逐渐从约29nm增加到约45nm，这与现有的实验数据一致。 我们的进一步分析表明，排除每个螺旋末端约6 bps的短DNA具有与千碱基对相似的柔韧性，并可以通过持久长度lp~50nm的蠕虫样链模型进行描述。 显示英文摘要

摘要： Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5 to 50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ~6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ~29nm to ~45nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ~6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp~50nm.