Kim Yong-Ick, Manalo Marlon N, Peréz Lisa M, LiWang Andy
Department of Biochemistry & Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
J Biomol NMR. 2006 Apr;34(4):229-36. doi: 10.1007/s10858-006-0021-y.
Density functional theory calculations of isolated Watson-Crick A:U and A:T base pairs predict that adenine 13C2 trans-hydrogen bond deuterium isotope shifts due to isotopic substitution at the pyrimidine H3, (2h)Delta13C2, 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)Delta13C2 is sensitive to hydrogen-bond strength. Calculated (2h)Delta13C2 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)Delta13C2 values. Thus, we show experimentally and computationally that the C7 methyl group of thymine has no measurable affect on (2h)Delta13C2 values. Furthermore, (2h)Delta13C2 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)Delta13C2 is context dependent and that this dependence is similar for RNA and DNA.
对孤立的沃森-克里克A:U和A:T碱基对进行的密度泛函理论计算预测，由于嘧啶H3处的同位素取代，腺嘌呤13C2反式氢键氘同位素位移(2h)Δ13C2对腺嘌呤N1与尿嘧啶或胸腺嘧啶N3之间的氢键距离敏感，这支持了(2h)Δ13C2对氢键强度敏感的观点。在给定的N1-N3距离下，孤立的A:U和A:T碱基对的计算(2h)Δ13C2值相同。用5-甲基尿苷取代RNA中的尿苷残基，并用脱氧尿苷取代DNA中的脱氧胸苷，不会使经验(2h)Δ13C2值发生统计学上的变化。因此，我们通过实验和计算表明，胸腺嘧啶的C7甲基对(2h)Δ13C2值没有可测量的影响。此外，修饰和未修饰RNA的(2h)Δ13C2值比修饰和未修饰DNA的更负，这支持了我们的假设，即RNA氢键比DNA的更强。这里还表明，(2h)Δ13C2依赖于上下文，并且这种依赖性在RNA和DNA中相似。
