Hydrogen bonding of the 2′ OH in RNA

Abstract

The high resolution PMR spectra of single and double stranded RNA and transfer RNA all exhibit resonances from exchangeable protons at about 6.8 ppm. This resonance at 6.8 ppm can be assigned to the 2′ OH since (i) resonances from all other exchangeable protons are otherwise accounted for, (ii) the resonance position is the same (±0.2 ppm) in all RNA indicating that it is from a proton in the backbone, (iii) the resonance is only observed from RNA at low temperature, and (iv) the resonance shifts upfield with the addition of dimethylsulfoxide to samples originally in water such that the extrapolation of the resonance position to neat dimethylsulfoxide is about 5.6 ppm which is approximately the resonance position of the 2′ OH proton of mononucleosides in dimethylsulfoxide. The 2′ OH is hydrogen bonded since the resonance position in RNA is shifted more than one ppm downfield from that of the mononucleoside in dimethylsulfoxide and the rate of exchange of the 2′ OH is considerably slower in RNA than in the monomer units. Examination of the PMR of mononucleosides in water dimethylsulfoxide mixtures, where the exchange is slow, shows that the resonance position of the 2′ OH hydrogen bonded to water is about 6.5 ppm. These PMR results indicate that the 2′ OH proton is hydrogen bonded to water. Examination of molecular models of RNA indicate a bound water molecule which can function as the acceptor of the 2′ OH hydrogen bond is properly situated to act as the donor in a hydrogen bond to the 3′ phosphate. The existence of this hydrogen bonding helps to explain some of the differences in conformation and thermal stability of RNA and DNA.