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Initial Amino Acid:Codon Assignments and Strength of Codon:Anticodon Binding

Published version
Peer-reviewed

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Authors

paragon-plus: 5579267  ORCID logo  https://orcid.org/0000-0001-6558-8712
paragon-plus: 5897191 
paragon-plus: 1774950  ORCID logo  https://orcid.org/0000-0001-7099-4731

Abstract

The ribosome brings 3′-aminoacyl-tRNA and 3′-peptidyl-tRNAs together to enable peptidyl transfer by binding them in two major ways. First, their anticodon loops are bound to mRNA, itself anchored at the ribosomal subunit interface, by contiguous anticodon:codon pairing augmented by interactions with the decoding center of the small ribosomal subunit. Second, their acceptor stems are bound by the peptidyl transferase center, which aligns the 3′-aminoacyl- and 3′-peptidyl-termini for optimal interaction of the nucleophilic amino group and electrophilic ester carbonyl group. Reasoning that intrinsic codon:anticodon binding might have been a major contributor to bringing tRNA 3′-termini into proximity at an early stage of ribosomal peptide synthesis, we wondered if primordial amino acids might have been assigned to those codons that bind the corresponding anticodon loops most tightly. By measuring the binding of anticodon stem loops to short oligonucleotides, we determined that family-box codon:anticodon pairings are typically tighter than split-box codon:anticodon pairings. Furthermore, we find that two family-box anticodon stem loops can tightly bind a pair of contiguous codons simultaneously, whereas two split-box anticodon stem loops cannot. The amino acids assigned to family boxes correspond to those accessible by what has been termed cyanosulfidic chemistry, supporting the contention that these limited amino acids might have been the first used in primordial coded peptide synthesis.

Description

Publication status: Published

Keywords

Journal Title

Journal of the American Chemical Society

Conference Name

Journal ISSN

0002-7863
1520-5126

Volume Title

146

Publisher

American Chemical Society
Sponsorship
Simons Foundation (290362)
Medical Research Council (MC_UP_A024_1009)