HYDROGEN EXCHANGE STUDIES OF sRNA

Abstract

Measurements of the hydrogen exchange behavior of mixed yeast sRNA are reported. Only hydrogens involved in hydrogen bonds exchange slowly enough to be measured. The mechanism of the exchange is discussed in terms of two possible pathways, one dependent on local opening or "breathing" of structure, and one involving direct exchange without "breathing." The response of the kinetic exchange curves to varying salt conditions rules out the latter pathway. The rates of exchange of various hydrogens, then, reflect the relative stabilities of various segments of the molecule. Observation of changes in rates may allow measurement of the contribution of various factors to the thermodynamic stability of nuclei acids. We find about 77 hydrogen bonds per average 70 nucleotide sRNA molecule indicating the involvement of about 82 per cent of the nucleotides in helix. (Compare the recent estimates of 76% helix and 71 H bonds/molecule by Felsenfeld and collaborators.) The non-hydrogen-bonded bases must "loop out" from the largely helical structure (except terminal (C) CA). The estimated number of "looped out" bases is consistent with the model of Cantoni et al. but also with a model containing two small loops. Some possible implications of the "breathing" of sRNA for errors in recognition functions and for the design and function of loops and the odd bases are discussed.