ISOLEUCINE - RNA SITES WITH ASSOCIATED CODING SEQUENCES

An RNA family that binds isoleucine with K-d = 200-500 mu M was repeti tively isolated from a ribonucleotide transcript pool containing 50 ra ndomized positions. The RNA site is specific, discriminating against b ranched side chains of different size (valine-one methylene smaller th an isoleucine) by at least 1.3 kcal/mol and against the shape (linear) of norleucine by 0.6 kcal/mol. The binding site was localized by sequ ence comparison, by synthesis of mutant and truncated active derivativ es, and by chemical modification-interference. The binding site is sma ll, no more than 10-12 nt, containing an asymmetric internal loop (6 o ver 2 nt) that includes the isoleucine codon AUU and a sequence of fou r G's, two of which are involved in G.U and G.C base pairs. Areas of U /G concentration like these may signal a hydrophobic RNA site.