Internucleotide Scalar Couplings Across Hydrogen Bonds in Watson−Crick and Hoogsteen Base Pairs of a DNA Triplex

Abstract

An extensive analysis of trans-hydrogen bond 2h J NN and 1h J HN scalar couplings, the covalent 1 J HN couplings, and the imino proton chemical shifts is presented for Hoogsteen−Watson−Crick T•A−T and C + •G−C triplets of an intramolecular DNA triplex. The 2h J NN coupling constants for the Watson−Crick base pairs have values ranging from 6 to 8 Hz, while the Hoogsteen base paired thymines and protonated cytidines have values of approximately 7 and 10 Hz, respectively. Distinct decreases of 2h J NN are observed at the triplex strand ends. Trans-hydrogen bond J correlations ( 1h J HN ) between the donor 1 H nucleus and the acceptor 15 N nucleus are observed for this triplex by a novel, simple quantitative J -correlation experiment. These one-bond 1h J HN couplings range between 1 and 3 Hz. A strong correlation is found between the chemical shift of the imino proton and the size of 2h J NN, with stronger J couplings corresponding to downfield chemical shifts. A similar, but inverse correlation is found between the proton chemical shift and the (absolute) size of the covalent 1 J HN constant. Methods of density functional theory were used to investigate the structural requirements for scalar J coupling and magnetic shielding associated with hydrogen bonding in nucleic acid base pairs. The dependencies of these NMR parameters on hydrogen bond distances were obtained for a representative base pair fragment. The results reproduce the trans-hydrogen bond coupling effect and the experimental correlations and suggest that the NMR parameters can be used to gain important insight into the nature of the hydrogen bond.