Nussinov R, Shapiro B, Lipkin L E, Maizel J V
J Mol Biol. 1984 Aug 25;177(4):591-607. doi: 10.1016/0022-2836(84)90039-1.
Helical-twist, roll and torsion-angle variations calculated by the Calladine (1982)-Dickerson (1983) rules were scanned along several nucleotide sequences for which DNAase I cleavage data are available. It has been shown that for short synthetic oligomers DNAase I cuts preferentially at positions of high helical twist (Dickerson & Drew, 1981; Lomonossoff et al., 1981). Our calculations indicate that DNAase I sensitive and hypersensitive sites in chromatin are correlated with regions of successive, large, helical-twist angle variations from regular B-DNA. In many cases these regions exhibit large variations in base-pair roll and backbone torsion angles as well. It has been suggested that DNAase I cuts in the vicinity of cruciforms. However, it was recently demonstrated by Courey & Wang (1983) and Gellert et al. (1983) that such cruciform formation in a negatively supercoiled DNA is kinetically forbidden under physiological conditions. We thus propose that clustering of large twist-angle (and/or roll and backbone torsion angle) variations may be among the conformational features recognized by the enzyme. Specific cuts can then preferentially occur at base-pair steps with high helical twists.
通过卡拉迪恩（1982年）-迪克森（1983年）规则计算出的螺旋扭曲、滚动和扭转角变化，沿着几个有DNA酶I切割数据的核苷酸序列进行了扫描。研究表明，对于短的合成寡聚物，DNA酶I优先在高螺旋扭曲的位置切割（迪克森和德鲁，1981年；洛莫诺索夫等人，1981年）。我们的计算表明，染色质中DNA酶I敏感和超敏感位点与规则B-DNA中连续的、大的螺旋扭曲角变化区域相关。在许多情况下，这些区域的碱基对滚动和主链扭转角也有很大变化。有人提出DNA酶I在十字形结构附近切割。然而，库里和王（1983年）以及盖勒特等人（1983年）最近证明，在生理条件下，负超螺旋DNA中的这种十字形结构形成在动力学上是被禁止的。因此，我们提出大扭转角（和/或滚动和主链扭转角）变化的聚集可能是该酶识别的构象特征之一。然后，特异性切割可以优先发生在具有高螺旋扭曲的碱基对步骤处。
