Computational and empirical trans-hydrogen bond deuterium isotope shifts suggest that N1-N3 A:U hydrogen bonds of RNA are shorter than those of A:T hydrogen bonds of DNA
Computational and empirical trans-hydrogen bond deuterium isotope shifts suggest that N1-N3 A:U hydrogen bonds of RNA are shorter than those of A:T hydrogen bonds of DNA
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DOI：
10.1007/s10858-006-0021-y
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发表时间：
2006-04-01
影响因子：
2.7
通讯作者：
LiWang, A
中科院分区：
文献类型：
--
作者：
Kim, YI;Manalo, MN;LiWang, A
孤立的沃森-克里克A的密度泛函理论计算：U和A：T碱基对预测，由于嘧啶H3处的同位素取代，腺嘌呤（13）C2反式氢键氘同位素位移，（2 h）Δ（13）C2，对腺嘌呤的N1和尿嘧啶或胸腺嘧啶的N3之间的氢键距离敏感，这支持了（2 h）Δ（13）C2对氢键强度敏感的观点。对于孤立的A：U和A：T碱基对，在给定的N1-N3距离处计算的（2 h）Delta（13）C2值相同。用5-甲基尿苷取代RNA中的尿苷残基和用脱氧尿苷取代DNA中的脱氧胸苷不会使经验（2 h）Δ（13）C2值发生统计学偏移。因此，我们通过实验和计算表明，胸腺嘧啶的C7甲基对（2 h）Delta（13）C2值没有可测量的影响。此外，修饰和未修饰的RNA的（2 h）Delta（13）C2值比修饰和未修饰的DNA的更负，这支持了我们的假设，RNA氢键比DNA的更强。这里还表明，（2 h）Δ（13）C2是上下文依赖性的，并且这种依赖性对于RNA和DNA是相似的。
Density functional theory calculations of isolated Watson - Crick A: U and A: T base pairs predict that adenine (13)C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, (2h)Delta(13)C2, are sensitive to the hydrogen-bond distance between the N1 of adenine and the N3 of uracil or thymine, which supports the notion that (2h)Delta(13)C2 is sensitive to hydrogen-bond strength. Calculated (2h)Delta(13)C2 values at a given N1-N3 distance are the same for isolated A:U and A:T base pairs. Replacing uridine residues in RNA with 5-methyl uridine and substituting deoxythymidines in DNA with deoxyuridines do not statistically shift empirical (2h)Delta(13)C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on (2h)Delta(13)C2 values. Furthermore, (2h)Delta(13)C2 values of modified and unmodified RNA are more negative than those of modified and unmodified DNA, which supports our hypothesis that RNA hydrogen bonds are stronger than those of DNA. It is also shown here that (2h)Delta(13)C2 is context dependent and that this dependence is similar for RNA and DNA.