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An RNA pocket for an aliphatic hydrophobe


We have isolated an RNA with specific affinity for the L-valine side chain, using selection-amplification. The active RNA secondary structure, identified by repeated selection, is a highly conserved asymmetric (4:10) internal loop adjacent to required G-U pairs. The binding free-energy per methylene is up to 1.5 kcal mol−1 and very dependent on group position. Amino acid binding is L-stereoselective and distinguishes aliphatic sidechains by size and, given the same total size, by configuration. Though aliphatic-RNA interactions have frequently been neglected, their avidity and specificity seem sufficient for a biological role.

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Majerfeld, I., Yarus, M. An RNA pocket for an aliphatic hydrophobe. Nat Struct Mol Biol 1, 287–292 (1994).

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