Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
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DOI：
10.1002/chem.200501239
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发表时间：
2006-03-20
影响因子：
4.3
通讯作者：
Hobza, P
中科院分区：
文献类型：
--
作者：
Sponer, J;Jurecka, P;Hobza, P
利用二阶Moller-Plesset （MP2）法、完全基集（CBS）外推法和三重(T)电子相关贡献的校正，对10个独特的B-DNA碱基对步骤和其他排列的基堆能进行了评估。将CBS(T)计算结果与10年前MP2/6-31G*(0.25)参考数据和AMBER力场进行比较。新的计算结果表明，与MP2/6-31G*(0.25)数据相比，层积稳定性有了适度的提高，层积能的序列依赖性变化惊人地大。绝对力场值与新参考数据的一致性较好，而量子化学（QM）与力场值之间的相对差异略有增加。然而，力场提供了很好的定性描述堆积，并且不需要引入额外的成对加性静电术语，如分布多极或面外电荷。在量子化学预测的碱基对垂直分离与晶体结构推导的碱基对垂直分离之间存在相当惊人的0.1埃的差异。对5‘-CG-3’阶跃的不同局部排列的评价表明，相对堆积能对计算水平具有敏感性。因此，描述局部DNA几何变化和堆叠之间的定量关系可能比通常假设的要复杂。参考计算通过对溶剂筛选效果的连续溶剂评估加以补充。
Base-stacking energies in ten unique B-DNA base-pair steps and some other arrangements were evaluated by the second-order Moller-Plesset (MP2) method, complete basis set (CBS) extrapolation, and correction for triple (T) electron-correlation contributions. The CBS(T) calculations were compared with decade-old MP2/6-31G*(0.25) reference data and AMBER force field. The new calculations show modest increases in stacking stabilization compared to the MP2/6-31G*(0.25) data and surprisingly large sequence-dependent variation of stacking energies. The absolute force-field values are in better agreement with the new reference data, while relative discrepancies between quantum-chemical (QM) and force-field values increase modestly. Nevertheless, the force field provides good qualitative description of stacking, and there is no need to introduce additional pair-additive electrostatic terms, such as distributed multipoles or out-of-plane charges. There is a rather surprising difference of about 0.1 angstrom between the vertical separation of base pairs predicted by quantum chemistry and derived from crystal structures. Evaluations of different local arrangements of the 5'-CG-3' step indicate a sensitivity of the relative stacking energies to the level of calculation. Thus, describing quantitative relations between local DNA geometrical variations and stacking may be more complicated than usually assumed. The reference calculations are complemented by continuum-solvent assessment of solvent-screening effects.