Characterizing micro-to-millisecond chemical exchange in nucleic acids using off-resonance R1ρ relaxation dispersion

Abstract

This review describes off-resonance R_1ρ relaxation dispersion NMR methods for characterizing microsecond-to-millisecond chemical exchange in uniformly ¹³C/¹⁵N labeled nucleic acids in solution. The review opens with a historical account of key developments that formed the basis for modern R_1ρ techniques used to study chemical exchange in biomolecules. A vector model is then used to describe the R_1ρ relaxation dispersion experiment, and how the exchange contribution to relaxation varies with the amplitude and frequency offset of an applied spin-locking field, as well as the population, exchange rate, and differences in chemical shifts of two exchanging species. Mathematical treatment of chemical exchange based on the Bloch-McConnell equations is then presented and used to examine relaxation dispersion profiles for more complex exchange scenarios including three-state exchange. Pulse sequences that employ selective Hartmann-Hahn cross-polarization transfers to excite individual ¹³C or ¹⁵N spins are then described for measuring off-resonance R_1ρ(¹³C) and R_1ρ(¹⁵N) in uniformly ¹³C/¹⁵N labeled DNA and RNA samples prepared using commercially available ¹³C/¹⁵N labeled nucleotide triphosphates. Approaches for analyzing R_1ρ data measured at a single static magnetic field to extract a full set of exchange parameters are then presented that rely on numerical integration of the Bloch-McConnell equations or the use of algebraic expressions. Methods for determining structures of nucleic acid excited states are then reviewed that rely on mutations and chemical modifications to bias conformational equilibria, as well as structure-based approaches to calculate chemical shifts. Applications of the methodology to the study of DNA and RNA conformational dynamics are reviewed and the biological significance of the exchange processes is briefly discussed.