The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes.
The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes.
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DNA 弹性杆模型及其在单核小体 DNA 小环三级结构中的应用。
DOI：
10.1016/s0006-3495(98)77960-3
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发表时间：
1998
影响因子：
3.4
通讯作者：
Tobias,I
中科院分区：
文献类型：
--
作者：
Swigon,D;Coleman,BD;Tobias,I
利用DNA弹性棒模型理论中平衡方程的显式解，开发了一种程序，用于寻找具有特定值的单个核小体中小圆的弹性能最小化的构型，这些值包括碱基对中的小圆大小、DNA围绕组蛋白核心颗粒的包裹程度、结合DNA的螺旋重复数和小圆的连接数。该程序允许确定最小能量构型不涉及自接触的flk积分值的集合（N,w,h0b），并给出了这些值的反软件曲线图。对于此处不感兴趣的范围，330<N<370，集合（N,w,h0b）是最重要的：当lkis不在（N,w,h0b）中时，与lkk相容的构型具有足够高的弹性能，以防止出现可观察到的拓扑异构体浓度lk，即拓扑异构体的平衡分布。通过设置核体外环的自由能差等于平衡弹性能差来计算的flk的平衡分布，发现在固定的假设下计算时非常接近于高斯分布，但在两个值之间波动的假设下计算时却远非高斯分布。给出的理论结果提出了一种从测量的flk平衡分布计算dna -组蛋白结合能的方法。
Explicit solutions to the equations of equilibrium in the theory of the elastic rod model for DNA are employed to develop a procedure for finding the configuration that minimizes the elastic energy of a minicircle in a mononucleosome with specified values of the minicircle sizeNin base pairs, the extentwof wrapping of DNA about the histone core particle, the helical repeath0bof the bound DNA, and the linking numberLkof the minicircle. The procedure permits a determination of the set(N,w,h0b) of integral values ofLkfor which the minimum energy configuration does not involve self-contact, and graphs of writhe versusware presented for such values ofLk. For the range ofNof interest here, 330<N<370, the set(N,w,h0b) is of primary importance: whenLkis not in(N,w,h0b), the configurations compatible withLkhave elastic energies high enough to preclude the occurrence of an observable concentration of topoisomerLkin an equilibrium distribution of topoisomers. Equilibrium distributions ofLk, calculated by setting differences in the free energy of the extranucleosomal loop equal to differences in equilibrium elastic energy, are found to be very close to Gaussian when computed under the assumption thatwis fixed, but far from Gaussian when it is assumed thatwfluctuates between two values. The theoretical results given suggest a method by which one may calculate DNA-histone binding energies from measured equilibrium distributions ofLk.
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影响因子：
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作者：
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