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Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1 J NH measurements in ethanol–water mixtures

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Abstract

Hydrogen-bond lengths of nucleic acids are (1) longer in DNA than in RNA, and (2) sequence dependent. The physicochemical basis for these variations in hydrogen-bond lengths is unknown, however. Here, the notion that hydration plays a significant role in nucleic acid hydrogen-bond lengths is tested. Watson–Crick N1...N3 hydrogen-bond lengths of several DNA and RNA duplexes are gauged using imino 1 J NH measurements, and ethanol is used as a cosolvent to lower water activity. We find that 1 J NH values of DNA and RNA become less negative with added ethanol, which suggests that mild dehydration reduces hydrogen-bond lengths even as the overall thermal stabilities of these duplexes decrease. The 1 J NH of DNA are increased in 8 mol% ethanol to those of RNA in water, which suggests that the greater hydration of DNA plays a significant role in its longer hydrogen bonds. The data also suggest that ethanol-induced dehydration is greater for the more hydrated G:C base pairs and thereby results in greater hydrogen-bond shortening than for the less hydrated A:T/U base pairs of DNA and RNA.

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Acknowledgements

We thank Elihu Ihms for helpful discussions, and Lisa M. Pérez, Yun Wei and Peter Cornish for technical assistance. We are also grateful for the financial support provided by the Robert A. Welch Foundation Grant A-1471. The NMR instrumentation at Texas A&M University was supported by National Science Foundation Grant DBI-9970232 and by the Texas Agriculture Experiment Station.

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Authors and Affiliations

  1. Department of Biochemistry & Biophysics, Texas A&M University, 2128 TAMU, College Station, TX, 77843-2128, USA

    Marlon N. Manalo, Xiangming Kong & Andy LiWang

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  1. Marlon N. Manalo
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  2. Xiangming Kong
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  3. Andy LiWang
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Correspondence to Andy LiWang.

Electronic supplementary material

Tables of 1 J NH, imino proton chemical shifts, and T m values in water and ethanol–water mixtures, and calculated energies of isolated Watson–Crick base pairs; 1H spectra of imino regions of DNA and RNA; plots of T m as a function of ethanol concentration; correlation plot of imino proton line widths in water and 8 mol% ethanol; plots of isotropic chemical shifts of imino protons in water and 8 mol% ethanol; selection of Gaussian input files.

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Manalo, M.N., Kong, X. & LiWang, A. Sensitivity of hydrogen bonds of DNA and RNA to hydration, as gauged by 1 J NH measurements in ethanol–water mixtures. J Biomol NMR 37, 257–263 (2007). https://doi.org/10.1007/s10858-006-9132-8

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  • DOI: https://doi.org/10.1007/s10858-006-9132-8

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