Isoleucine:RNA sites with associated coding sequences.

An RNA family that binds isoleucine with Kd = 200-500 microM 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.