High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides

Structural information at atomic resolution of biomolecular assemblies, such as RNA and RNA protein complexes, is fundamental to comprehend biological function. Modern spectroscopic methods offer exceptional opportunities in this direction. Here we present the capability of pulse EPR to report highresolution long-range distances in RNAs by means of a recently developed spin labeled nucleotide, which carries the TEMPO group directly attached to the nucleobase and preserves Watson-Crick base-pairing. In a representative RNA duplex with spin-label separations up to 28 base pairs (approximate to 8 nm) we demonstrate that the label allows for a model-free conversion of inter-spin distances into base-pair separation (Delta bp) if broad-band pulse excitation at Q band frequencies (34 GHz) is applied. The observed distance distribution increases from +/- 0.2 nm for Delta bp = 10 to only +/- 0.5 nm for Delta bp = 28, consistent with only small deviations from the ideal A-form RNA structure. Molecular dynamics (MD) simulations conducted at 20 degrees C show restricted conformational freedom of the label. MD-generated structural deviations from an ideal A-RNA geometry help disentangle the contributions of local flexibility of the label and its neighboring nucleobases and global deformations of the RNA double helix to the experimental distance distributions. The study demonstrates that our simple but strategic spin labeling procedure can access detailed structural information on RNAs at atomic resolution over distances that match the size of macromolecular RNA complexes.