The Solution Structures of RNA Fragments Determined by Nuclear Overhauser Enhancement Measurements

Abstract

Over the last few years numerous NMR studies have appeared on the solution structure of small DNA oligonucleotides (see refs. 1–4 for reviews). In contrast, relatively few studies have appeared on RNA duplexes (5–10). This is probably due to two factors, both of which arise from the presence of the 2’-hydroxyl group in RNA. First, RNA is intrinsically more difficult to synthesize than DNA as an additional reactive group has to be protected during the course of the synthesis (11,12). Second, all the sugar resonances, with the exception of the H1’ resonances, are superimposed in a very narrow region of the 1H-NMR spectrum only 1 ppm in width, thereby considerably complicating the task of resonance assignment. As part of our continuing studies on the structure and dynamics of oligonucleotides in solution (see for examples refs. 4, 8, 13–17), we have embarked on a program to investigate the structures of small RNA fragments comprising specific portions of the yeast tRNAPhe molecule. This approach allows one to probe the details of the three dimensional solution structures of individual loops and double stranded stems as the spectral complexity exhibited by the whole tRNA molecule is greatly reduced, thereby enabling NOE measurements to be made on a large number of proton types, namely imino, aromatic, ribose and methyl protons.