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.

Journal of Biomolecular NMR
Yong-Ick KimAndy LiWang

Abstract

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.

References

Nov 1, 1992·Journal of Biomolecular NMR·M PiottoV Sklenár
Jul 2, 1996·Biochemistry·M EgliN Usman
Dec 10, 1996·Proceedings of the National Academy of Sciences of the United States of America·S O Shan, D Herschlag
Jan 1, 1997·Annual Review of Biochemistry·G J Narlikar, D Herschlag
Dec 30, 1998·The Journal of Hospital Infection·B L Atkins, I C Bowler
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Apr 1, 1996·Physical Review C: Nuclear Physics·A S MurphyD L Watson
Jun 15, 1992·Physical Review. B, Condensed Matter·J P Perdew, Y Wang
Mar 26, 2003·Journal of Biomolecular NMR·Ioannis VakonakisAndy C LiWang
Mar 16, 2004·Journal of Biomolecular NMR·Ioannis Vakonakis, Andy C LiWang
May 6, 2004·Journal of the American Chemical Society·Ioannis Vakonakis, Andy C LiWang
Aug 19, 2004·Journal of the American Chemical Society·Ellen M MoodyPhilip C Bevilacqua
Dec 23, 2004·Journal of the American Chemical Society·Marcel SwartF Matthias Bickelhaupt
Mar 25, 2005·Nucleic Acids Research·Pierre MignonPaul Geerlings
Dec 22, 2005·Journal of the American Chemical Society·Marlon N ManaloAndy LiWang

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Citations

May 21, 2009·Journal of Biomolecular NMR·Jens AbildgaardAndy LiWang
May 14, 2011·Physical Chemistry Chemical Physics : PCCP·Raphael F RibeiroDonald G Truhlar
May 1, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Poul Erik Hansen

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