A More Complex Isoleucine Aptamer with a Cognate Triplet

Michal Legiewicz,Michael Yarus

doi:10.1074/jbc.m502329200

Abstract

The simplest RNA that can meet a column affinity selection for isoleucine was previously defined using selection amplification with decreasing numbers of randomized nucleotides. This simplest UAUU motif was a small asymmetric internal loop. Conserved positions of the loop include isoleucine codon and anticodon triplets (Lozupone C., Changayil, S., Majerfeld, I., and Yarus, M. (2003) RNA (N. Y.) 9, 1315-1322). Using new primer sequences, we now select a somewhat more complex isoleucine binding RNA, requiring 4.7 more bits of information to describe. The newly selected structure is a terminal or hairpin loop of 20 nucleotides, 15 being invariant. An information profile shows that the new binding site contains five short functional loop regions joined by less significant single nucleotide positions. Among the important nucleotides is a conserved isoleucine anticodon, supporting the escaped triplet theory, which posits a stereochemical genetic code originating in RNA amino acid binding sites.

Highlights

Among important functions is amino acid binding, which was arguably a crucial activity during the era when encoded polypeptide synthesis first appeared
Among the important nucleotides is a conserved isoleucine anticodon, supporting the escaped triplet theory, which posits a stereochemical genetic code originating in RNA amino acid binding sites
The new motif likely poises loop nucleotides to create a site for the ligand

Summary

Introduction

Among important functions is amino acid binding, which was arguably a crucial activity during the era when encoded polypeptide synthesis (translation) first appeared. Using in vitro selection or SELEX (6 – 8) many artificial amino acid binding RNAs have been recovered including tryptophan [9], arginine (10 –14), valine [15], isoleucine [16], tyrosine [17], phenylalanine [18], histidine, tryptophan, and leucine.3 In these binding sites, cognate codons and anticodons appear improbably concentrated; a probability of 5.4*10Ϫ11 on the assumption that affinity and coding sequences are unrelated (19 –21). Aptamer selections can be constructed to favor the simplest molecular solutions that answer a particular selection regime Such a “simplest” isoleucine-binding RNA has been selected [16, 22] using two different sets of primers. We report a novel isoleucine-binding RNA selected using different conditions It is more complex than the simplest motif, 37.9 compared with 33.2 bits of information. Like the UAUU motif, which contains an isoleucine anticodon and codon, the new simplest motif has an isoleucine anticodon triplet among the functional nucleotides of the amino acid binding site

Methods

Results

Conclusion