Dornberger U, Leijon M, Fritzsche H
Institut für Molekularbiologie, Friedrich-Schiller-Universität, Winzerlaer Strasse 10, D-07745 Jena, Germany.
J Biol Chem. 1999 Mar 12;274(11):6957-62. doi: 10.1074/jbc.274.11.6957.
Sequence-dependent structural features of the DNA double helix have a strong influence on the base pair opening dynamics. Here we report a detailed study of the kinetics of base pair breathing in tracts of GC base pairs in DNA duplexes derived from 1H NMR measurements of the imino proton exchange rates upon titration with the exchange catalyst ammonia. In the limit of infinite exchange catalyst concentration, the exchange times of the guanine imino protons of the GC tracts extrapolate to much shorter base pair lifetimes than commonly observed for isolated GC base pairs. The base pair lifetimes in the GC tracts are below 5 ms for almost all of the base pairs. The unusually rapid base pair opening dynamics of GC tracts are in striking contrast to the behavior of AT tracts, where very long base pair lifetimes are observed. The implication of these findings for the structural principles governing spontaneous helix opening as well as the DNA-binding specificity of the cytosine-5-methyltransferases, where flipping of the cytosine base has been observed, are discussed.
DNA双螺旋的序列依赖性结构特征对碱基对打开动力学有强烈影响。在此，我们报告了一项详细研究，该研究通过用交换催化剂氨滴定后对亚氨基质子交换速率进行1H NMR测量，来研究源自DNA双链体中GC碱基对片段的碱基对呼吸动力学。在无限交换催化剂浓度的极限情况下，GC片段中鸟嘌呤亚氨基质子的交换时间外推得出的碱基对寿命比孤立GC碱基对通常观察到的要短得多。几乎所有碱基对在GC片段中的碱基对寿命都低于5毫秒。GC片段中异常快速的碱基对打开动力学与AT片段的行为形成鲜明对比，在AT片段中观察到非常长的碱基对寿命。讨论了这些发现对于控制自发螺旋打开的结构原理以及已观察到胞嘧啶碱基翻转的胞嘧啶-5-甲基转移酶的DNA结合特异性的意义。
