Cyclization of short DNA fragments and bending fluctuations of the double helix
Cyclization of short DNA fragments and bending fluctuations of the double helix
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DOI：
10.1073/pnas.0500983102
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发表时间：
2005-04-12
影响因子：
11.1
通讯作者：
Vologodskii, A
中科院分区：
文献类型：
--
作者：
Du, Q;Smith, C;Vologodskii, A
Cloutier 和 Widom [Cloutier, T. E. & Widom, J. (2004) Mol. Cell 14, 355-362]最近报道，长度约100 bp的短DNA片段的环化效率超出理论预期三个数量级。为了解决这种差异，我们尝试修改理论。我们研究了双螺旋相邻碱基对之间的角度分布如何影响环化效率。我们发现，只有在角度分布中加入尖锐的扭结才能提供所需的环化效率的提高。然而，我们没有找到适合不同长度 DNA 片段的所有环化数据的模型。因此，我们仔细地重新研究了100 bp DNA片段的环化实验，发现它们的环化效率与传统的DNA弯曲模型非常一致。我们还找到了我们的结果与 Cloutier 和 Widom 的结果之间差异的解释。
Cloutier and Widom [Cloutier, T. E. & Widom, J. (2004) Mol. Cell 14, 355-362] recently reported that the cyclization efficiency of short DNA fragments, about 100 bp in length, exceeds theoretical expectations by three orders of magnitude. In an effort to resolve this discrepancy, we tried modifying the theory. We investigated how the distribution of the angles between adjacent base pairs of the double helix affects the cyclization efficiency. We found that only the incorporation of sharp kinks in the angle distribution provides the desired increase of the cyclization efficiency. We did not find a model, however, that fits all cyclization data for DNA fragments of different lengths. Therefore, we carefully reinvestigated the cyclization of 100-bp DNA fragments experimentally and found their cyclization efficiency to be in remarkable agreement with the traditional model of DNA bending. We also found an explanation for the discrepancy between our results and those of Cloutier and Widom.