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

Advances in Isotope Labeling for Solution Nucleic Acid Nuclear Magnetic Resonance Spectroscopy

The availability of structural biology methods for nucleic acid still lags behind that of proteins, as evidenced by the smaller number of structures (DNA: 2513, RNA: 1899, nucleic acid-protein complexes: 13 842, protein: 196 887) deposited in the protein database. The skewed ratio of nucleic acid structures, relative to proteins (≈1:50), is inverted with respect to the cellular output of RNA and proteins in higher organisms (≈50:1). While nuclear magnetic resonance (NMR) is an attractive biophysical tool capable of bridging this gap at the molecular level, the conformational flexibility, line broadening, and low chemical shift dispersion of nucleic acids have made the NMR method challenging, especially for structures larger than 35 nucleotides. The incorporation of NMR-active isotopes is a f strategy to combat these problems. Significant strides made to push the size limits of nucleic acid structures solved by NMR using chemoenzymatic 13C- methyl and aromatic 15N- and 19F-13C-labeling are reviewed and challenges and opportunities are evaluated. Combining these isotopic labeling patterns with superior NMR spectroscopic properties, and new DNA/RNA synthesis methods (palindrome-nicking-dependent amplification and segmental labeling and site-specific modifications by template-directed tension), may stimulate advances in NMR studies of large DNA/RNA and their complexes with important biological functions.

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.