Cross-correlated relaxation rates provide facile exchange signature in selectively labeled RNA

Abstract

Gerhard Wagner has made numerous contributions to NMR spectroscopy, particularly his developments in the field of spin-relaxation stand out in directly mapping the spectral density functions of proteins. He and his group developed experimental techniques to reveal the importance of dynamics to protein biological function and drug discovery. On his 75th birthday, we take this opportunity to highlight how some of those seminal ideas developed for proteins are being extended to RNAs.The role of dynamics in the structure and function of RNA has been a major interest in drug design and therapeutics. Here we present the use of cross-correlated relaxation rates (ηxy) from anti-TROSY (R2α) and TROSY (R2β) to rapidly obtain qualitative information about the chemical exchange taking place within the bacterial and human A-site RNA system while reducing the sets of relaxation experiments required to map dynamics. We show that ηxy correlates with the order parameter which gives information on how flexible or rigid a residue is. We further show R2β/ηxy can rapidly be used to probe chemical exchange as seen from its agreement with Rex. In addition, we report the ability of R2β/ηxy to determine chemical exchange taking place within the bacterial A-site RNA during structural transitions at pH 6.2 and 6.5. Finally, comparison of the R2β/ηxy ratios indicates bacterial A-site has greater R2β/ηxy values for G19 (1.34 s−1), A20 (1.38 s−1), U23 (1.63 s−1) and C24 (1.51 s−1) than human A-site [A19 (0.76 s−1), A20 (1.01 s−1), U23 (0.74 s−1) and C24 (0.71 s−1)]. Taken together, we have shown that the chemical exchange can quickly be analyzed for RNA systems from cross-correlated relaxation rates.