Advances in Isotope Labeling for Solution Nucleic Acid NMR Spectroscopy.

Abstract

The availability of nucleic acid structural biology methods still lags behind that of proteins, as evidenced by the significantly smaller number of structures deposited in the PDB. The highly skewed ratio of nucleic acid structures, relative to their protein counterparts (~1:50), is inverted with respect to the cellular output of RNA and proteins in higher organisms (~50:1). While nuclear magnetic resonance (NMR) spectroscopy is an attractive biophysical tool to bridge this gap, the  conformational flexibility, line-broadening, and low chemical shift dispersion of nucleic acids have made the NMR method challenging, especially for nucleic acids larger than 35 nucleotides. The incorporation of NMR-active isotope labels is an effective strategy to combat these problems. Here, we review strides made to push the limits of nucleic acid structures solved by NMR using chemo-enzymatic DNA 13C-methyl and RNA aromatic 15N- and 19F-13C-labeling and evaluate some of the challenges and opportunities they present. We anticipate that the combination of these novel isotopic labeling patterns with superior NMR spectroscopic properties, with new emerging DNA/RNA synthesis methods (palindrome-nicking-dependent amplification and Segmental labeling and site-specific Modifications by Template-directed eXtension, may well stimulate advances in NMR studies of high-molecular-weight DNA/RNA and their complexes with important biological functions.