RNAs form critical components of biological processes implicated in human diseases, making them attractive for small-molecule therapeutics. Expanding the sites accessible to nuclear magnetic resonance (NMR) spectroscopy will provide atomic-level insights into RNA interactions. Here, we present an efficient strategy to introduce 19F-13C spin pairs into RNA by using a 5-fluorouridine-5′-triphosphate and T7 RNA polymerase–based in vitro transcription. Incorporating the 19F-13C label in two model RNAs produces linewidths that are twice as sharp as the commonly used 1H-13C spin pair. Furthermore, the high sensitivity of the 19F nucleus allows for clear delineation of helical and nonhelical regions as well as GU wobble and Watson-Crick base pairs. Last, the 19F-13C label enables rapid identification of a small-molecule binding pocket within human hepatitis B virus encapsidation signal epsilon (hHBV ε) RNA. We anticipate that the methods described herein will expand the size limitations of RNA NMR and aid with RNA-drug discovery efforts.
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.
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.
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
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.