Characterizing Slow Chemical Exchange in Nucleic Acids by Carbon CEST and Low Spin-Lock Field R1ρ NMR Spectroscopy

Quantitative characterization of dynamic exchange between various conformational states provides essential insights into the molecular basis of many regulatory RNA functions. Here, we present an application of nucleic-acid-optimized carbon chemical exchange saturation transfer (CEST) and low spin-lock field R-1 rho relaxation dispersion (RD) NMR experiments in characterizing slow chemical exchange in nucleic acids that is otherwise difficult if not impossible to be quantified by the ZZ-exchange NMR experiment. We demonstrated the application on a 47-nucleotide fluoride riboswitch in the ligand-free state, for which CEST and R-1 rho RD profiles of base and sugar carbons revealed slow exchange dynamics involving a sparsely populated (p similar to 10%) and shortly lived (tau similar to 10 ms) NMR invisible state. The utility of CEST and low spin-lock field R-1 rho RD experiments in studying slow exchange was further validated in characterizing an exchange as slow as similar to 60 s(-1).