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Bioinform Biol Insights. 2010 Jun 28;4:55-60.

A plausible role for the presence of internal shine-dalgarno sites.

Author information

  • 1Computational Biology Service Unit, Cornell University, Ithaca NY USA.

Abstract

The presence of nucleotide hybridization between the 3' end of 16S rRNA and mRNA sequence upstream of the start codon is well known in bacteria. In this paper, we detect the presence of such hybridization sites inside the coding regions of E. coli genes, and analyze their proximity to clusters of slow-translating codons. We study this phenomenon in genes of high and low expression separately. Based on our findings, we propose an explanation for the presence of RNA hybridization within the translated regions of bacterial genes.

KEYWORDS:

Shine-Dalgarno; codon; gene expression; hybridization; translation

PMID:
20634982
[PubMed]
PMCID:
PMC2901628
Free PMC Article
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