Structural analysis of the A and B conformers of escherichia coli 5 S ribosomal RNA by infrared spectroscopy

Abstract

1. Introduction Rapid progress is being made in elucidating the structure of pro- and eukaryotic 5 S RNAs using dif- ferent physical, biochemical and sequence analysis approaches (reviewed in [ 11). It seems to be evident from comparative sequence studies [l-5] that a general base pairing scheme of the type first proposed in [2] is valid for eukaryotic 5 S RNAs and that a general secondary structure of the type first proposed in [3] extended by few base pairs is the structural basis for prokaryotic 5 S RNAs. Experimental evi- dence supporting these basic secondary structures is now manifold and derives, e.g., from such powerful specific techniques as high-resolution ‘H NMR spec- troscopy [6,7] and slow tritium exchange studies [8]. Summarizing data from optical ([6,9] and references within), infrared [lo], Raman [l l-131, and ‘H NMR spectroscopy [6,7] it became obvious that both for prokaryotic and eukaryotic 5 S RNA molecules in solution a highly ordered secondary/tertiary structure exists with an amount of about 35-42 base pairs (58-70% of all nucleotides are base-paired) in the presence of stabilizing ions. and the infrared thermal melting curves reveal partic- ular differences between both conformers at 570°C which may be useful with respect to the analysis of the intricate problem of the A-to-B conformational transition(s). 2. Materials and methods Here, we report the results of infrared spectro- scopic studies of the A and B conformers of