Individual basepair stability of DNA and RNA studied by NMR-detected solvent exchange.
In this study, we have optimized NMR methodology to determine the thermodynamic parameters of basepair opening in DNA and RNA duplexes by characterizing the temperature dependence of imino proton exchange rates of individual basepairs. Contributions of the nuclear Overhauser effect to exchange rates measured with inversion recovery experiments are quantified, and the influence of intrinsic and external catalysis exchange mechanisms on the imino proton exchange rates is analyzed. Basepairs in DNA and RNA have an approximately equal stability, and the enthalpy and entropy values of their basepair dissociation are correlated linearly. Furthermore, the compensation temperature, T(c), which is derived from the slope of the correlation, coincides with the melting temperature, and duplex unfolding occurs at that temperature where all basepairs are equally thermodynamically stable. The impact of protium-deuterium exchange of the imino hydrogen on the free energy of RNA basepair opening is investigated, and it is found that two A·U basepairs show distinct fractionation factors.
Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University, Frankfurt/Main, Germany.
Hannah S
HS
Steinert
Jörg
J
Rinnenthal
Harald
H
Schwalbe
D020029:Base Pairing; D001483:Base Sequence; D002384:Catalysis; D005591:Chemical Fractionation; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D003903:Deuterium; D041961:Deuterium Exchange Measurement; D019277:Entropy; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D009692:Nucleic Acid Heteroduplexes; D011522:Protons; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D059370:RNA Folding; D020871:RNA Stability; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
D009692:Nucleic Acid Heteroduplexes; D011522:Protons; D012997:Solvents; D012313:RNA; D004247:DNA; D003903:Deuterium