Benham C J
Mathematics Department, University of Kentucky, Lexington 40506.
Nucleic Acids Res. 1987 Dec 10;15(23):9985-95. doi: 10.1093/nar/15.23.9985.
This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transitions are shown to occur at equilibrium at less extreme superhelicities in DNA whose tertiary structure is restrained than in unrestrained molecules where the residual linking difference alpha res (that part of the superhelical deformation which is not absorbed by transitions) may be freely partitioned between twisting and bending. In the extreme case of a rigidly held tertiary structure, this analysis predicts that the B-Z transition will occur at roughly half the superhelix density needed to drive the same transition in solution, other factors remaining fixed. This suggests that superhelical transitions may occur at more moderate superhelical deformations in vivo than in solution. The influence on transition behavior of the tertiary structural restraints imposed by gel conditions also are discussed.
本文从理论上研究了超螺旋DNA结构域三级结构的限制对连接能和构象转变起始的影响。最重要的三级限制源于体内基因组DNA的核小体缠绕。结果表明，与未受限制的分子相比，三级结构受到限制的DNA在平衡状态下，在不那么极端的超螺旋度下就会发生构象转变。在未受限制的分子中，残余连接差αres（即未被转变吸收的超螺旋变形部分）可以在扭曲和弯曲之间自由分配。在三级结构被严格固定的极端情况下，该分析预测，B-Z转变将在驱动溶液中相同转变所需超螺旋密度的大约一半时发生，其他因素保持不变。这表明，与溶液中相比，体内超螺旋转变可能在更适度的超螺旋变形下发生。还讨论了凝胶条件对三级结构限制的转变行为的影响。
