Rivetti C, Walker C, Bustamante C
Institute of Molecular Biology, University of Oregon, Eugene, OR 97403, USA.
J Mol Biol. 1998 Jul 3;280(1):41-59. doi: 10.1006/jmbi.1998.1830.
The worm-like chain model has often been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA. The present study extends the applicability of the worm-like chain model to polymers containing bends or sections of different flexibility. Several cases have been explicitly considered: (i) polymers with a single bend; (ii) polymers with multiple coplanar bends; (iii) polymers with two non-coplanar bends; and (iv) polymers comprised of sections with different persistence lengths. Expressions describing the average conformation of such polymers in terms of the mean-square end-to-end distance have been derived for each case. For cases (i) and (iv), expressions for the projection of the end-to-end vector onto the initial orientation of the chain are presented. The expressions derived here have been used to investigate DNA molecules with sequence-induced bending (A-tracts). Mean-square end-to-end distance values determined from a large number of A-tract containing DNA molecules visualized by scanning force microscopy resulted in an average bend angle of 13.5 degrees per A-tract. A similar study was performed to characterize the flexibility of double-strandedDNA molecules containing a single-stranded region. Analysis of their mean-square end-to-end distance yielded a persistence length of 1.3 nm for single-stranded DNA.
蠕虫状链模型常被用于描述长的、本质上呈直线状的聚合物分子(包括DNA)的平均构象。本研究将蠕虫状链模型的适用性扩展到含有弯曲或不同柔性片段的聚合物。明确考虑了几种情况:(i)具有单个弯曲的聚合物;(ii)具有多个共面弯曲的聚合物;(iii)具有两个非共面弯曲的聚合物;以及(iv)由具有不同持久长度的片段组成的聚合物。针对每种情况,都推导出了用均方末端距来描述此类聚合物平均构象的表达式。对于情况(i)和(iv),给出了末端到末端向量在链的初始取向上的投影表达式。这里推导的表达式已用于研究具有序列诱导弯曲(A序列)的DNA分子。通过扫描力显微镜观察大量含有A序列的DNA分子所确定的均方末端距值,得出每个A序列的平均弯曲角度为13.5度。进行了一项类似的研究来表征含有单链区域的双链DNA分子的柔性。对其均方末端距的分析得出单链DNA的持久长度为1.3纳米。
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