Brovarets' Ol'ha O, Hovorun Dmytro M
a Department of Molecular and Quantum Biophysics , Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine , 150 Akademika Zabolotnoho Str., Kyiv 03680 , Ukraine.
b Department of Molecular Biotechnology and Bioinformatics , Institute of High Technologies, Taras Shevchenko National University of Kyiv , 2-h Akademika Hlushkova Ave., Kyiv 03022 , Ukraine.
J Biomol Struct Dyn. 2015;33(11):2297-315. doi: 10.1080/07391102.2015.1046936. Epub 2015 Jun 23.
In this study, we have theoretically demonstrated the intrinsic ability of the wobble G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2) and Watson-Crick-like G*·T(WC) DNA base mispairs to interconvert into each other via the DPT tautomerization. We have established that among all these transitions, only one single G·T(w) ↔ G*·T(WC) pathway is eligible from a biological perspective. It involves short-lived intermediate - the G·T*(WC) base mispair - and is governed by the planar, highly stable, and zwitterionic [Formula: see text] transition state stabilized by the participation of the unique pattern of the five intermolecular O6(+)H⋯O4(-), O6(+)H⋯N3(-), N1(+)H⋯N3(-), N1(+)H⋯O2(-), and N2(+)H⋯O2(-) H-bonds. This non-dissociative G·T(w) ↔ G*·T(WC) tautomerization occurs without opening of the pair: Bases within mispair remain connected by 14 different patterns of the specific intermolecular interactions that successively change each other along the IRC. Novel kinetically controlled mechanism of the thermodynamically non-equilibrium spontaneous point GT/TG incorporation errors has been suggested. The mutagenic effect of the analogues of the nucleotide bases, in particular 5-bromouracil, can be attributed to the decreasing of the barrier of the acquisition by the wobble pair containing these compounds of the enzymatically competent Watson-Crick's geometry via the intrapair mutagenic tautomerization directly in the essentially hydrophobic recognition pocket of the replication DNA-polymerase machinery. Proposed approaches are able to explain experimental data, namely growth of the rate of the spontaneous point incorporation errors during DNA biosynthesis with increasing temperature.
在本研究中,我们从理论上证明了摆动G·T(w)/G*·T*(w)/G·T(w1)/G·T(w2)和类沃森-克里克G*·T(WC) DNA碱基错配通过双质子转移互变异构相互转化的内在能力。我们已经确定,在所有这些转变中,从生物学角度来看只有一条单一的G·T(w) ↔ G*·T(WC)途径是可行的。它涉及短寿命中间体——G·T*(WC)碱基错配——并由平面、高度稳定的两性离子[公式:见原文]过渡态控制,该过渡态通过独特的分子间O6(+)H⋯O4(-)、O6(+)H⋯N3(-)、N1(+)H⋯N3(-)、N1(+)H⋯O2(-)和N2(+)H⋯O2(-)氢键模式的参与而稳定。这种非解离性的G·T(w) ↔ G*·T(WC)互变异构在不打开碱基对的情况下发生:错配中的碱基通过14种不同的特定分子间相互作用模式保持连接,这些模式沿着反应坐标依次相互变化。提出了热力学非平衡自发点GT/TG掺入错误的新型动力学控制机制。核苷酸碱基类似物,特别是5-溴尿嘧啶的诱变作用,可归因于含有这些化合物的摆动对通过在复制DNA聚合酶机制的基本疏水识别口袋中直接进行的错配内诱变互变异构获得酶促活性的沃森-克里克几何形状的障碍降低。所提出的方法能够解释实验数据,即DNA生物合成过程中自发点掺入错误率随温度升高而增加的现象。