Sponer J, Kypr J
Institute of Biophysics, Czech Academy of Sciences, Brno.
J Biomol Struct Dyn. 1993 Aug;11(1):27-41. doi: 10.1080/07391102.1993.10508707.
Empirical analyses of experimental data have recently revealed a strong correlation in B- and A-DNA crystal structures between rise of the base pair steps and their cup, or the difference between roll and cup. We show here using empirical potentials that a major part of this correlation can be explained by the base stacking forces. Our calculations further demonstrate that the correlation depends on the base sequence while the dependence is strongest with the C-G step. We also show that small values (which lie beyond resolution of the X-ray diffraction data obtained with the DNA fragment single crystals) of base pair stagger can completely substitute for the effects of roll in the correlation. The present and our previous studies demonstrate that the base pair buckle and stagger can substantially affect base stacking in DNA so that variability of these parameters cannot be neglected in the theoretical analysis of the base sequence effects on DNA conformation.
近期对实验数据的实证分析揭示了B型和A型DNA晶体结构中碱基对步移的上升与其杯状结构，或滚动与杯状结构之间的差异存在强相关性。我们在此利用经验势表明，这种相关性的主要部分可由碱基堆积力来解释。我们的计算进一步证明，这种相关性取决于碱基序列，而对于C-G步移，这种依赖性最强。我们还表明，碱基对交错的小值（超出用DNA片段单晶获得的X射线衍射数据的分辨率）可以完全替代相关性中滚动的影响。目前以及我们之前的研究表明，碱基对弯曲和交错会显著影响DNA中的碱基堆积，因此在对碱基序列对DNA构象影响的理论分析中，不能忽视这些参数的变异性。
