Sponer J, Gabb H A, Leszczynski J, Hobza P
J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic.
Biophys J. 1997 Jul;73(1):76-87. doi: 10.1016/S0006-3495(97)78049-4.
Base-stacking interactions in canonical and crystal B-DNA and in Z-DNA steps are studied using the ab initio quantum-chemical method with inclusion of electron correlation. The stacking energies in canonical B-DNA base-pair steps vary from -9.5 kcal/mol (GG) to -13.2 kcal/mol (GC). The many-body nonadditivity term, although rather small in absolute value, influences the sequence dependence of stacking energy. The base-stacking energies calculated for CGC and a hypothetical TAT sequence in Z-configuration are similar to those in B-DNA. Comparison with older quantum-chemical studies shows that they do not provide even a qualitatively correct description of base stacking. We also evaluate the base-(deoxy)ribose stacking geometry that occurs in Z-DNA and in nucleotides linked by 2',5'-phosphodiester bonds. Although the molecular orbital analysis does not rule out the charge-transfer n-pi* interaction of the sugar 04' with the aromatic base, the base-sugar contact is stabilized by dispersion energy similar to that of stacked bases. The stabilization amounts to almost 4 kcal/mol and is thus comparable to that afforded by normal base-base stacking. This enhancement of the total stacking interaction could contribute to the propensity of short d(CG)n sequences to adopt the Z-conformation.
使用包含电子相关的从头算量子化学方法，研究了经典和晶体B-DNA以及Z-DNA步中的碱基堆积相互作用。经典B-DNA碱基对步中的堆积能量在-9.5千卡/摩尔（GG）至-13.2千卡/摩尔（GC）之间变化。多体非加和项虽然绝对值相当小，但会影响堆积能量的序列依赖性。在Z构型中为CGC和假设的TAT序列计算的碱基堆积能量与B-DNA中的相似。与早期量子化学研究的比较表明，它们甚至没有提供对碱基堆积的定性正确描述。我们还评估了Z-DNA以及通过2',5'-磷酸二酯键连接的核苷酸中发生的碱基-（脱氧）核糖堆积几何结构。尽管分子轨道分析不排除糖04'与芳香碱基之间的电荷转移n-π*相互作用，但碱基-糖接触通过与堆积碱基类似的色散能而稳定。这种稳定作用几乎达到4千卡/摩尔，因此与正常碱基-碱基堆积所提供的稳定作用相当。总堆积相互作用的这种增强可能有助于短d(CG)n序列倾向于采用Z构象。
