Probing the three-dimensional structures of DNA and RNA oligonucleotides in solution by nuclear Overhauser enhancement measurements

Abstract

DNA and RNA oligonucleotides are ideally suited for high-resolution X-ray crystallographic and 1H-NMR studies. The solution structures of such oligonucleotides can potentially be solved using proton-proton nuclear Overhauser enhancement measurements to demonstrate the proximity of protons in space and to determine their separation, thereby enabling a comparison of the structure in the crystalline and solution states to be made. In this review we describe the general strategy for the sequential resonance assignments of oligonucleotide 1H-NMR spectra, the essential prerequisite for further structural work, the approach to obtaining interproton distances from pre-steady state nuclear Overhauser enhancement measurements, and the use of interproton distances in structure determination. This is illustrated by several examples including double- and single-stranded DNA oligonucleotides as well as RNA stem and loop structures.