Probing rare and short-lived conformational states in nucleic acids using off-resonance carbonyl and guanidino carbon R1ρ relaxation dispersion

Chemical exchange-based NMR techniques provide powerful approaches for characterizing lowly-populated and short-lived conformational states in nucleic acids. Among possible probes, the nucleobase carbonyl and guanidino carbons stand out due to the sensitivity of their chemical shifts to hydrogen bonding and keto–enol tautomerization. However, chemical exchange measurements targeting these carbon nuclei have not yet been reported in studies of nucleic acids. Here, we present an experiment for measuring off-resonance R_1ρ relaxation dispersion for guanine-C2, guanine-C6, thymine/uracil-C2, and thymine/uracil-C4 carbons in uniformly ¹³C/¹⁵N labeled nucleic acids. We demonstrate the utility of the experiment by characterizing chemical exchange in a G•T mismatch in duplex DNA between a dominant wobble conformation and two lowly-populated, short-lived, and rapidly interconverting Watson–Crick-like tautomeric states (G^enol•T ⇌ G•T^enol) implicated in DNA replicative errors. The population and exchange rate deduced from the guanine-C6, guanine-C2, and thymine-C4 off-resonance R_1ρ relaxation dispersion profiles were in excellent agreement with counterparts obtained from R_1ρ measurements on proton-bound carbon and nitrogen nuclei. The carbon chemical shifts of the minor state were downfield shifted relative to the wobble ground state, consistent with (G)C6 = O···HO-C4(T^enol) and (G^enol)C6-OH···O=C4(T) hydrogen bonding in the Watson-Crick-like tautomeric state. As a second application, we did not detect any exchange contribution to uracil-C2 and uracil-C4 R_1ρ profiles measured for a U·U mismatch in RNA, consistent with isomerization between two alternative wobble conformations occurring on the sub-microsecond timescale. These results establish carbonyl and guanidino carbons as valuable probes for chemical exchange measurements of micro-to-millisecond motions in nucleic acids.