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arXiv 1503.03344physics.bio-phcond-mat.softcond-mat.stat-mechphysics.comp-phphysics.med-ph
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具有有限长度效应的短DNA螺旋的灵活性：从碱基对到数十个碱基对

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

Yuan-Yan Wu, Lei Bao, Xi Zhang, Zhi-Jie Tan

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32 pages, 9 figures,Supplementary Material
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摘要：

DNA短螺旋的柔性对于核小体的形成、DNA与蛋白质的识别等生物学功能具有重要意义。最近的实验表明，几十个碱基对（bps）的短DNA可能具有明显高于千个碱基对（bps）的DNA的灵活性，但这种高灵活性仍有争议。本文采用全原子分子动力学模拟和蒙特卡罗模拟，采用蠕虫链模型，研究了有限长（5 ~ 50 bp）的短DNA的柔性。我们的微观分析表明，短DNA具有明显的高柔性，这归因于每个螺旋末端的~6 bp的显著强的弯曲和拉伸柔性。相应地，随着DNA长度从10 bp增加到50 bp，短DNA的表观持续长度lp从~ 29 nm逐渐增加到~ 45 nm，与已有的实验数据一致。进一步的分析表明，每个螺旋末端不含~6 bp的短DNA具有与千bp DNA相似的柔性，可以用lp~ 50 nm的蠕虫链模型来描述。

英文摘要：

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.

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