Direct Observation of Hydrogen Bonds in Nucleic Acid Base Pairs by Internucleotide ²<i>J</i>_NN Couplings

Abstract

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 scalar couplings across the hydrogen bond are observable for Watson−Crick base pairs in 15N-labeled RNA. These scalar couplings correlate the imino donor 15N nucleus and the corresponding acceptor 15N nucleus on the complementary base. The two-bond JNN 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 T1 domain of the potato spindle tuber viroid. In contrast, for non-Watson−Crick base pairs the hydrogen bond acceptor is usually not a nitrogen, but an oxygen atom, and thus, the two-bond JNN couplings are not observed.