An RNA pocket for an aliphatic hydrophobe

Abstract

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.

RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code

“…This new interpretation is supported by data emphasized in the original discussion (Table 2, (Majerfeld and Yarus 1994)), showing that the 1.6 kcal/mol distinction only occurred when a methylene group was moved or removed on Lvaline itself. The distinction made between smaller side chains differing by a methylene was considerably smaller.…”

“…Its derivation did not permit deduction of RNA site nucleotides, so we have not used it below for coding triplet calculations. Interest in its original detection (Majerfeld and Yarus 1994) was instead focused on data suggesting that it preferred L-valine and could distinguish amino acid side chains that differed from valine by one methylene group by up to 1.6 kcal/mol. This raised the unexpected possibility that RNA sites could distinguish aliphatic hydrophobic structures by interacting with them productively.…”

RNA–ligand chemistry: A testable source for the genetic code

“…In Figure 2 are all the presently informative amino acid sites, meaning those for which chemical data are available (L-valine is excluded for this reason; Majerfeld & Yarus, 1994)+ In particular, these include the recent tyrosine-binding RNAs (Mannironi et al+, 2000) whose description provoked this re-analysis+ These tyrosine sites are derived from an initial set of dopamine-binding RNAs (Mannironi et al+, 1997)+ In Figure 2, sites arising from separate selections appear in separate panels+ The initially randomized nucleotides that are the basis of the analysis are capitalized, and lower case is used for initially fixed sequences, appended for experimental convenience during amplification+ Because fixed sequences are not results of selection, they are not included in the analysis+ However, they are shown where their explicit presence clarifies the structure of the binding site+ Coding triplets in initially randomized regions are in colored bold face+ Chemical data (such as protections and interferences) that may identify the subset of binding-site nucleotides are summarized as symbols above or below the implicated nucleotide or internucleotide linkage+…”

Molecular recognition of amino acids by RNA aptamers: The evolution into an L-tyrosine binder of a dopamine-binding RNA motif

“…The ability of RNA to form specific binding sites for free amino acids is now well established and RNA sites for various amino acids have been recently isolated from random RNA pools by selection-amplification techniques (for a review, see Yarus, 1998)+ To date, the best characterized RNA site for a free amino acid is the arginine-binding site+ Eight independent arginine RNA aptamers were isolated by in vitro selection (Connell et al+, 1993;Connell & Yarus, 1994;Famulok, 1994;Geiger et al+, 1996;Tao & Frankel, 1996), which indicates that there are several different motifs that can generate specific RNA sites for arginine+ Moreover, natural examples of arginine RNA sites are the highly conserved group I intron's guanosine cosubstrate sites, where the arginine site lies inside the guanosine site (Yarus, 1988;Hicke et al+, 1989)+ The capability of RNA to form amino acid-binding pockets, not only for the intensively polar side chain of arginine but also for aliphatic hydrophobic side chains, has been shown by the isolation of valine and isoleucine RNA aptamers (Majerfeld & Yarus, 1994, 1998)+ The well-characterized isoleucine-binding sites are highly specific, distinguish side chains of different shapes and polarity, and show affinities for the cognate amino acid not dissimilar to those of many proteins that bind hydrophobic ligands+ In spite of the varied specificities featured by the RNA aptamers, conferred by definite functional groups, the overall structure of the described amino acid-binding sites is quite simple, and asymmetric internal loops are their most prominent structures+…”