Olson W K, Marky N L, Jernigan R L, Zhurkin V B
Department of Chemistry, Rutgers, State University of New Jersey, Wright-Rieman Laboratories, New Brunswick 08903.
J Mol Biol. 1993 Jul 20;232(2):530-54. doi: 10.1006/jmbi.1993.1409.
Matrix-generator and Monte Carlo methods have been employed to study the influence of thermal fluctuations on the overall sizes and shapes of curved pieces of DNA. The DNA model involves the independent angular parameters relating successive base-pair steps: the sequence-dependent equilibrium values and fluctuations of the twist, tilt, and roll angles. The curved sequence under study is the (A5X5)n repeating polymer, the AA and XX steps having different equilibrium roll and twist values. Both planar circles and superhelices are analysed. Detailed comparison is made between the rigorous statistical mechanical representation of the DNA and simplified static models currently used in the literature. That is, a more realistic "flexible wedge" model is contrasted with the existing "static wedge" model of DNA curvature, which is demonstrated to be inadequate. The size of the coils is described by the unperturbed root-mean-square end-to-end distance and the shape by a ratio of the principal moments of the radius of gyration. The moment ratios indicate that when DNA is relatively short (e.g. its length is shorter than half a turn of the static superhelix), the flexible chains are more "short and thick" than the static structure. The end-to-end distances, however, are practically the same in the two models. For longer DNA fragments, the flexible chain is more extended in terms of the end-to-end distance and more globular in terms of the moment ratio. Thus, fluctuations "blur" the curvature of longer DNA fragments compared with static models. Furthermore, the overall average shape of slightly curved DNA subject to natural bending and twisting fluctuations is essentially indistinguishable from that of the corresponding "straight" DNA. Such configurational similarities are apparently responsible for the relative insensitivity of the polyacrylamide gel matrix to small degrees of DNA curvature. These findings raise serious questions regarding the quantitative estimation of wedge angles in DNA from electrophoretic experiments, based on static models. Comparison between planar circles and superhelices shows that when fluctuations are considered, the flexible circles are more spherical than the superhelices. The results imply that when DNA bending is exactly "in phase" with the helical repeat (i.e. when the DNA loop is exactly planar at 0 K), the DNA coil is packed more tightly than when bending and twisting are "out of phase" (and a superhelix is formed at 0 K). This finding is consistent with polyacrylamide gel electrophoresis data testifying to an increase in DNA retardation when twisting is more precisely "tuned".(ABSTRACT TRUNCATED AT 400 WORDS)
矩阵生成器和蒙特卡罗方法已被用于研究热涨落对弯曲DNA片段整体尺寸和形状的影响。DNA模型涉及连续碱基对步长的独立角参数：扭转、倾斜和滚动角的序列依赖性平衡值及涨落。所研究的弯曲序列是(A5X5)n重复聚合物，AA和XX步长具有不同的平衡滚动和扭转值。对平面圆和超螺旋都进行了分析。对DNA严格的统计力学表示与文献中目前使用的简化静态模型进行了详细比较。也就是说，将一个更现实的“柔性楔”模型与现有的DNA曲率“静态楔”模型进行了对比，结果表明后者是不充分的。线圈的尺寸用无扰均方根端到端距离来描述，形状用回转半径的主矩比来描述。矩比表明，当DNA相对较短时（例如其长度短于静态超螺旋半圈），柔性链比静态结构更“短而粗”。然而，两种模型中的端到端距离实际上是相同的。对于更长的DNA片段，柔性链在端到端距离方面更伸展，在矩比方面更呈球状。因此，与静态模型相比，涨落“模糊”了更长DNA片段的曲率。此外，受自然弯曲和扭转涨落影响的微弯DNA的整体平均形状与相应的“直”DNA基本无法区分。这种构型相似性显然是聚丙烯酰胺凝胶基质对小程度DNA曲率相对不敏感的原因。这些发现对基于静态模型从电泳实验定量估计DNA中的楔角提出了严重质疑。平面圆和超螺旋的比较表明，考虑涨落时，柔性圆比超螺旋更呈球形。结果表明，当DNA弯曲与螺旋重复完全“同相”时（即当DNA环在0K时完全平面），DNA线圈比弯曲和扭转“异相”时（且在0K时形成超螺旋）堆积得更紧密。这一发现与聚丙烯酰胺凝胶电泳数据一致，该数据证明当扭转更精确地“调谐”时DNA阻滞增加。（摘要截于400字）
