An RNA family that binds isoleucine with Kd
= 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.