Direct observation of hydrogen bonds in nucleic acid base pairs by internucleotide 2JNN couplings

Hydrogen bonds play a key role in the stabilization of protein and nucleic acid secondary structure. Currently, most of the experimental evidence for the interaction of hydrogen bond donor and acceptor atoms is indirect. Here we show that scaler couplings across the hydrogen bond are observable for Watson-Crick base pairs in N-15-labeled RNA. These scalar couplings correlate the imino donor N-15 nucleus and the corresponding acceptor N-15 nucleus on the complementary base. The two-bond J(NN) couplings between the N3 of uridine and the N1 of adenosine, and between the N1 of guanosine and the N3 of cytidine, have values of approximately 7 Hz as determined by a novel quantitative J-correlation experiment for the 69-nucleotide TI domain of the potato spindle tuber viroid. In contrast, for non-Watson-Crick base pairs the hydrogen bond acceptor is usually nota nitrogen, but an oxygen atom, and thus, the two-bond J(NN) couplings are not observed.