Dickerson R E, Kopka M L, Pjura P
Molecular Biology Institute, University of California, Los Angeles 90024.
J Biomol Struct Dyn. 1983 Dec;1(3):755-71. doi: 10.1080/07391102.1983.10507480.
Bending in double-helical B-DNA apparently occurs only by rolling adjacent base pairs over one another along their long axes. The lifting apart of ends that would be required by tilt or wedge angle contributions is too costly in free energy and does not occur. Roll angles at base steps can be positive (compression of major groove) or negative (compression of minor groove), with the former somewhat easier. Individual steps may advance or oppose the overall direction of bend, or make lateral excursions, but the result of this series of "random roll" steps is the production of a net bending in the helix axis. Because the natural roll points for bending in a given plane occur every 5 base pairs, one would expect that double-helical DNA wrapped around a nucleosome core would exhibit bends with the same periodicity. Alternate bends might be particularly acute where the major groove faced the nucleosome core and was compressed against it. The "annealed kinking" model proposed by Fratini et al. (J. Biol. Chem. 257, 14686 (1982) was suggested from the observation that a major bend at a natural roll point is flanked by decreasing roll angles at the steps to either side, as though local strain was being minimized by somewhat blurring the bend out rather than keeping it localized. The random walk model suggested in this paper would describe this as a decreased roll angle as the helix step rotates toward a direction perpendicular to the overall bend. Bending of DNA is seen to be a more stochastic process than had been suspected. Detailed analysis of every helix step reveals both side excursions and backward or retrograde motion, as in any random walk situation. Yet these isolated steps counteract one another, to leave behind a residuum of overall bending in a specific direction.
双螺旋B型DNA的弯曲显然仅通过相邻碱基对沿其长轴相互滚动而发生。倾斜或楔角贡献所要求的末端拉开在自由能方面成本过高，因而不会发生。碱基步的滚动角可以是正的（大沟压缩）或负的（小沟压缩），前者相对更容易些。各个步可以推进或对抗整体弯曲方向，或者进行横向偏移，但这一系列“随机滚动”步的结果是在螺旋轴上产生净弯曲。由于在给定平面内弯曲的自然滚动点每5个碱基对出现一次，人们会预期缠绕在核小体核心周围的双螺旋DNA会呈现出相同周期性的弯曲。当大沟面向核小体核心并被挤压时，交替的弯曲可能会特别尖锐。Fratini等人（《生物化学杂志》257, 14686 (1982)）提出的“退火扭结”模型是基于这样的观察：在自然滚动点处的一个主要弯曲两侧的步的滚动角逐渐减小，就好像局部应变通过使弯曲稍微模糊而不是保持其局部化来最小化。本文提出的随机游走模型将此描述为当螺旋步朝着垂直于整体弯曲的方向旋转时滚动角减小。DNA的弯曲被认为是一个比之前所怀疑的更具随机性的过程。对每个螺旋步的详细分析揭示了侧向偏移以及向后或逆行运动，如同在任何随机游走情况中一样。然而这些孤立的步相互抵消，从而在特定方向上留下整体弯曲的残余。
