Nuclear magnetic resonance studies on structure and breathing dynamics of transfer RNA

The hydrogen-bonded ring NH protons of the complementary base pairs in Escherichia coli isoleucine tRNA have been studied by 500 MHz nuclear magnetic resonance. These protons generate a set of about 30 well-resolved resonances in the -10p.p.m. to-15 p.p.m. region of the spectrum and can be observed in H2O solutions by Fourier transform NMR using the Redfield 214 observation pulse. Each of these low field protons has been assigned to its respective base pair in the tRNA by sequential nuclear Overhauser effect connectivity to its nearest neighbours. The helix-coil opening rates for several individual base pairs have been determined by monitoring the solvent-exchange contribution to the inversion recovery rate or the saturation recovery rate of the assigned ring NH peaks. Contrary to current theory, the two most rapidly opening base pairs in the molecule are located not at the helix termini but in the interior of helices.