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• W2162592907 abstract "Translation elongation is an accurate and rapid process, dependent upon efficient juxtaposition of tRNAs in the ribosomal A- and P-sites. Here, we sought evidence of A- and P-site tRNA interaction by examining bias in codon pair choice within open reading frames from a range of genomes. Three distinct and marked effects were revealed once codon and dipeptide biases had been subtracted. First, in the majority of genomes, codon pair preference is primarily determined by a tetranucleotide combination of the third nucleotide of the P-site codon, and all 3 nt of the A-site codon. Second, pairs of rare codons are generally under-used in eukaryotes, but over-used in prokaryotes. Third, the analysis revealed a highly significant effect of tRNA-mediated selection on codon pairing in unicellular eukaryotes, Bacillus subtilis, and the gamma proteobacteria. This was evident because in these organisms, synonymous codons decoded in the A-site by the same tRNA exhibit significantly similar P-site pairing preferences. Codon pair preference is thus influenced by the identity of A-site tRNAs, in combination with the P-site codon third nucleotide. Multivariate analysis identified conserved nucleotide positions within A-site tRNA sequences that modulate codon pair preferences. Structural features that regulate tRNA geometry within the ribosome may govern genomic codon pair patterns, driving enhanced translational fidelity and/or rate." @default.
• W2162592907 created "2016-06-24" @default.
• W2162592907 creator A5021452315 @default.
• W2162592907 creator A5042003887 @default.
• W2162592907 creator A5051384943 @default.
• W2162592907 date "2006-02-06" @default.
• W2162592907 modified "2023-10-14" @default.
• W2162592907 title "tRNA properties help shape codon pair preferences in open reading frames" @default.
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• W2162592907 doi "https://doi.org/10.1093/nar/gkj488" @default.
• W2162592907 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/1363775" @default.
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• W2162592907 hasPublicationYear "2006" @default.
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