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.