Chemo-enzymatic synthesis of [2-13C, 7-15 N]-ATP for facile NMR analysis of RNA

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

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 (η_xy) from anti-TROSY (R_2α) and TROSY (R_2β) 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 η_xy correlates with the order parameter which gives information on how flexible or rigid a residue is. We further show R_2β/η_xy can rapidly be used to probe chemical exchange as seen from its agreement with R_ex. In addition, we report the ability of R_2β/η_xy 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 R_2β/η_xy ratios indicates bacterial A-site has greater R_2β/η_xy 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.

Isotope Labels Combined with Solution NMR Spectroscopy Make Visible the Invisible Conformations of Small-to-Large RNAs

RNA is central to the proper function of cellular processes important for life on earth and implicated in various medical dysfunctions. Yet, RNA structural biology lags significantly behind that of proteins, limiting mechanistic understanding of RNA chemical biology. Fortunately, solution NMR spectroscopy can probe the structural dynamics of RNA in solution at atomic resolution, opening the door to their functional understanding. However, NMR analysis of RNA, with only four unique ribonucleotide building blocks, suffers from spectral crowding and broad linewidths, especially as RNAs grow in size. One effective strategy to overcome these challenges is to introduce NMR-active stable isotopes into RNA. However, traditional uniform labeling methods introduce scalar and dipolar couplings that complicate the implementation and analysis of NMR measurements. This challenge can be circumvented with selective isotope labeling. In this review, we outline the development of labeling technologies and their application to study biologically relevant RNAs and their complexes ranging in size from 5 to 300 kDa by NMR spectroscopy.

Synthesis of [7-15N]-GTPs for RNA structure and dynamics by NMR spectroscopy

Several isotope-labeling strategies have been developed for the study of RNA by nuclear magnetic resonance (NMR) spectroscopy. Here, we report a combined chemical and enzymatic synthesis of [7-15N]-guanosine-5'-triphosphates for incorporation into RNA via T7 RNA polymerase-based in vitro transcription. We showcase the utility of these labels to probe both structure and dynamics in two biologically important RNAs.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s00706-022-02892-1.

Isotope-Labeled RNA Building Blocks for NMR Structure and Dynamics Studies

RNA structural research lags behind that of proteins, preventing a robust understanding of RNA functions. NMR spectroscopy is an apt technique for probing the structures and dynamics of RNA molecules in solution at atomic resolution. Still, RNA analysis by NMR suffers from spectral overlap and line broadening, both of which worsen for larger RNAs. Incorporation of stable isotope labels into RNA has provided several solutions to these challenges. In this review, we summarize the benefits and limitations of various methods used to obtain isotope-labeled RNA building blocks and how they are used to prepare isotope-labeled RNA for NMR structure and dynamics studies.

Quantifying the effects of long-range 13C-13C dipolar coupling on measured relaxation rates in RNA

Selective stable isotope labeling has transformed structural and dynamics analysis of RNA by NMR spectroscopy. These methods can remove ¹³C-¹³C dipolar couplings that complicate ¹³C relaxation analyses. While these phenomena are well documented for sites with adjacent ¹³C nuclei (e.g. ribose C1'), less is known about so-called isolated sites (e.g. adenosine C2). To investigate and quantify the effects of long-range (> 2 Å) ¹³C-¹³C dipolar interactions on RNA dynamics, we simulated adenosine C2 relaxation rates in uniformly [U-¹³C/¹⁵N]-ATP or selectively [2-¹³C]-ATP labeled RNAs. Our simulations predict non-negligible ¹³C-¹³C dipolar contributions from adenosine C4, C5, and C6 to C2 longitudinal (R₁) relaxation rates in [U-¹³C/¹⁵N]-ATP labeled RNAs. Moreover, these contributions increase at higher magnetic fields and molecular weights to introduce discrepancies that exceed 50%. This will become increasingly important at GHz fields. Experimental R₁ measurements in the 61 nucleotide human hepatitis B virus encapsidation signal ε RNA labeled with [U-¹³C/¹⁵N]-ATP or [2-¹³C]-ATP corroborate these simulations. Thus, in the absence of selectively labeled samples, long-range ¹³C-¹³C dipolar contributions must be explicitly taken into account when interpreting adenosine C2 R₁ rates in terms of motional models for large RNAs.