Elastic stability of DNA configurations. I. General theory.
Elastic stability of DNA configurations. I. General theory.
复制标题
DOI：
10.1103/physreve.61.747
复制
发表时间：
2000
期刊：
影响因子：
--
通讯作者：
I. Tobias;D. Swigon;B. D. Coleman
中科院分区：
文献类型：
--
作者：
I. Tobias;D. Swigon;B. D. Coleman
结果在DNA的弹性杆模型的理论，其中有一些判据能使人们确定计算的DNA片段的平衡构型是否稳定，在这个意义上，它给出片段的弹性能和作用于其上的力的势能之和的局部最小值。导出的稳定性判据适用于质粒和具有强锚定末端的线性片段条件他们的效用是说明与一个例子，从理论的配置的一个DNA miniplasmid在一个monopolysome的nucleosomal环，重点放在一方面，切口和连接的影响，和弹性系数的比例的变化，对平衡配置的稳定性。在该示例中，使用显式解的方法的扩展来计算所研究的配置，在这种情况下，弹性杆建模的DNA片段被认为是不可穿透的，因此排除的体积效应和自接触产生的力被考虑在内。
Results are presented in the theory of the elastic rod model for DNA, among which are criteria enabling one to determine whether a calculated equilibrium configuration of a DNA segment is stable in the sense that it gives a local minimum to the sum of the segment's elastic energy and the potential of forces acting on it. The derived stability criteria are applicable to plasmids and to linear segments subject to strong anchoring end conditions. Their utility is illustrated with an example from the theory of configurations of the extranucleosomal loop of a DNA miniplasmid in a mononucleosome, with emphasis placed on the influence that nicking and ligation on one hand, and changes in the ratio of elastic coefficients on the other, have on the stability of equilibrium configurations. In that example, the configurations studied are calculated using an extension of the method of explicit solutions to cases in which the elastic rod modeling a DNA segment is considered impenetrable, and hence excluded volume effects and forces arising from self-contact are taken into account.