Isoleucine:RNA sites with associated coding sequences

Abstract

An RNA family that binds isoleucine with K_d = 200–500 μM was repetitively isolated from a ribonucleotide transcript pool containing 50 randomized positions. The RNA site is specific, discriminating against branched side chains of different size (valine—one methylene smaller than 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 sequence comparison, by synthesis of mutant and truncated active derivatives, and by chemical modification–interference. The binding site is small, no more than 10–12 nt, containing an asymmetric internal loop (6 over 2 nt) that includes the isoleucine codon AUU and a sequence of four 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.