High resolution proton NMR study of an isolated fragment of R17 bacteriophage mRNA

Abstract

HIGH resolution nuclear magnetic resonance (NMR) spectra of the hydrogen-bonded protons in helical regions of nucleic acids are an informative monitor of the base pairing¹. Studies of about 10 purified tRNAs and of model systems have shown that the ring NH protons of uracil and guanine, when involved in Watson-Crick base pairing, give resonances between −15 and −11 p.p.m. downfield from DSS^1,2. Since there is only one such proton in each base pair, the intensity in this spectral region is a direct measure of the number of base pairs. Simple rules have been derived to predict the NMR spectra originating from these protons on the basis of ring currents from the adjacent bases and for tRNA the comparison between predicted and observed spectra has strongly supported the clover leaf model of base pairing. In addition, ring current shifts from bases adjacent to the helical region provided information about the structure at the end of the helix. Here we apply this approach to the secondary structure of the R17 fragment discussed in the preceding paper³. We prepared 0.5 mg of the R17 fragment according to a somewhat modified method of Bernardi and Spahr⁴, and measured the NMR spectrum of a 25 µl sample.