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 αres (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.
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机译:本文从理论上研究了限制超螺旋DNA结构域的三级结构对连接能和构象转变开始的影响。最重要的三级约束来自体内基因组DNA的核小体缠绕。在其三级结构受到限制的DNA中,构象转变在平衡时以较小的极端超螺旋发生,而在未约束分子中,残余连接差α res sub>(超螺旋形变形的一部分未被过渡吸收) )可以在扭曲和弯曲之间自由分配。在刚性保持的三级结构的极端情况下,该分析预测,B-Z跃迁将发生在驱动溶液中相同跃迁所需的超螺旋密度的大约一半处,而其他因素则保持不变。这表明,在体内比在溶液中更适度的超螺旋形变形可能发生超螺旋形转变。还讨论了凝胶条件对三级结构约束过渡行为的影响。
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