Bhattacharyya D, Bansal M
Molecular Biophysics Unit, Indian Institute of Science, Bangalore.
J Biomol Struct Dyn. 1990 Dec;8(3):539-72. doi: 10.1080/07391102.1990.10507828.
The importance and usefulness of local doublet parameters in understanding sequence dependent effects has been described for A- and B-DNA oligonucleotide crystal structures. Each of the two sets of local parameters described by us in the NUPARM algorithm, namely the local doublet parameters, calculated with reference to the mean z-axis, and the local helical parameters, calculated with reference to the local helix axis, is sufficient to describe the oligonucleotide structures, with the local helical parameters giving a slightly magnified picture of the variations in the structures. The values of local doublet parameters calculated by NUPARM algorithm are similar to those calculated by NEWHELIX90 program, only if the oligonucleotide fragment is not too distorted. The mean values obtained using all the available data for B-DNA crystals are not significantly different from those obtained when a limited data set is used, consisting only of structures with a data resolution of better than 2.4 A and without any bound drug molecule. Thus the variation observed in the oligonucleotide crystals appears to be independent of the quality of their crystallinity. No strong correlation is seen between any pair of local doublet parameters but the local helical parameters are interrelated by geometric relationships. An interesting feature that emerges from this analysis is that the local rise along the z-axis is highly correlated with the difference in the buckle values of the two basepairs in the doublet, as suggested earlier for the dodecamer structures (Bansal and Bhattacharyya, in Structure & Methods: DNA & RNA, Vol. 3 (Eds., R.H. Sarma and M.H. Sarma), pp. 139-153 (1990)). In fact the local rise values become almost constant for both A- and B-forms, if a correction is applied for the buckling of the basepairs. In B-DNA the AA, AT, TA and GA basepair sequences generally have a smaller local rise (3.25 A) compared to the other sequences (3.4 A) and this seems to be an intrinsic feature of basepair stacking interaction and not related to any other local doublet parameter. The roll angles in B-DNA oligonucleotides have small values (less than +/- 8 degrees), while mean local twist varies from 24 degrees to 45 degrees. The CA/TG doublet sequences show two types of preferred geometries, one with positive roll, small positive slide and reduced twist and another with negative roll, large positive slide and increased twist.(ABSTRACT TRUNCATED AT 400 WORDS)
在理解序列依赖性效应方面，局部双联体参数对于A - 和B - DNA寡核苷酸晶体结构的重要性及实用性已得到描述。我们在NUPARM算法中描述的两组局部参数，即相对于平均z轴计算的局部双联体参数，以及相对于局部螺旋轴计算的局部螺旋参数，每一组都足以描述寡核苷酸结构，其中局部螺旋参数给出了结构变化的稍放大图像。仅当寡核苷酸片段没有过度扭曲时，通过NUPARM算法计算的局部双联体参数值才与通过NEWHELIX90程序计算的值相似。使用B - DNA晶体的所有可用数据获得的平均值与使用仅由数据分辨率优于2.4 Å且无任何结合药物分子的结构组成的有限数据集时获得的平均值没有显著差异。因此，在寡核苷酸晶体中观察到的变化似乎与它们的结晶度质量无关。任何一对局部双联体参数之间都没有强相关性，但局部螺旋参数通过几何关系相互关联。从该分析中出现的一个有趣特征是，如之前对十二聚体结构所建议的那样（Bansal和Bhattacharyya，《结构与方法：DNA与RNA》，第3卷（编者：R.H. Sarma和M.H. Sarma），第139 - 153页（1990年）），沿着z轴的局部上升与双联体中两个碱基对的弯曲值差异高度相关。实际上，如果对碱基对的弯曲进行校正，对于A - 和B - 形式，局部上升值几乎变得恒定。在B - DNA中，与其他序列（3.4 Å）相比，AA、AT、TA和GA碱基对序列通常具有较小的局部上升（3.25 Å），这似乎是碱基对堆积相互作用的一个固有特征，与任何其他局部双联体参数无关。B - DNA寡核苷酸中的滚动角值较小（小于±8度），而平均局部扭曲从24度到45度不等。CA/TG双联体序列显示出两种类型的优选几何形状，一种具有正滚动、小正滑动和减小的扭曲，另一种具有负滚动、大正滑动和增加的扭曲。（摘要截断于400字）
