The Conformation of a Conserved Stem-Loop Structure in Ribosomal RNA

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Abstract
The RNA of small ribosomal subunits contains a conserved stem-loop structure near the 3′ end. Characteristics for the hairpins are: (a) a nine-basepairs stem; (b) a conserved A-U U-Gjunction in the stem; (c) a conserved sequence Gm6 2Am6 2A sequence in the loop (except yeast mitochondria and mutants from bacteria). We are using UV-optics, micro-calorimetry and 500 MHz-NMR to investigate fragments of about 50 nucleotides cleaved from the 3′ ends of small ribosomal subunit RNA's by bacteriocins. Our preliminary conclusions are: (1) Dimethylation of the adenines in the loop destabilizes the hairpin because of an increased stacking; (2) melting of the hairpin starts at the ends as well as in the middle at the 5-H junction; (3) basepair substitutions have an unexpectedly large effect on thermal stability.