Brukner I, Jurukovski V, Savic A
Faculty of Sciences, Biology Department, University of Belgrade, Yugoslavia.
Nucleic Acids Res. 1990 Feb 25;18(4):891-4. doi: 10.1093/nar/18.4.891.
Two global helix parameters important for DNA-DNase I interaction are the geometry of the minor groove and the DNA stiffness that resists bending toward major groove. Thus, local averaging of P-O3' bonds cutting frequencies (InP) reflects global helix parameters revealed by DNase I. Using the approximation that locally averaged InP values depend only on the type of the dinucleotide steps involved in the region of interaction, we calculated the collective contribution (sigma Dd) for ten different dinucleotide steps. Our results suggest that, at the first approximation, global varying helix parameters revealed by DNase I, might be predicted from sequence. Obtained sigma Dd function can be used as a sequence-dependent measure of protein-induced DNA flexure in the direction towards the major groove, which is usually connected to widening of the minor groove. In the course of analysis of Mg2+ and Mn2+ dependent DNase I digestions, no significant difference was found, in spite of the supposed differences in enzyme activity. These results suggest that if the second Mn2(+)-dependent active site exists, its activity is lower than that of the first one.
对于DNA与DNase I相互作用而言，两个重要的全局螺旋参数是小沟的几何形状以及抵抗向大沟弯曲的DNA刚性。因此，P - O3'键切割频率（InP）的局部平均值反映了DNase I揭示的全局螺旋参数。利用局部平均InP值仅取决于相互作用区域中所涉及的二核苷酸步类型这一近似值，我们计算了十种不同二核苷酸步的集体贡献（σDd）。我们的结果表明，在一阶近似下，DNase I揭示的全局变化螺旋参数可能可从序列中预测。所获得的σDd函数可作为蛋白质诱导的DNA向大沟方向弯曲的序列依赖性度量，这通常与小沟变宽相关。在对Mg2 +和Mn2 +依赖性DNase I消化的分析过程中，尽管推测酶活性存在差异，但未发现显著差异。这些结果表明，如果存在第二个Mn2( + )依赖性活性位点，其活性低于第一个。
