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| University of California Irvine professors G. Wesley Hatfield (CODA co-founder) and George Gutman first published the discovery of a unique, translational pausing phenomenon linked to the over-representation of specific, adjacent codon pairs or di-codons. This phenomenon is independent of codon usage related to tRNA level variation among organisms.
As described in the original paper, a series of clever expression tests correlated a translational slowdown or “pause” at the ribosomal level. |
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The ECO label signifies 124 over-represented di-codons as compared to random (RAND) distribution. By moving 1, 2 and 3 codons away, data was conclusive this is a nearest neighbor or di-codon phenomenon. Select pairs are highly over-represented. G A Gutman and G W Hatfield,Nonrandom utilization of codon pairs in Escherichia coli, P.N.A.S., USA. 1989, 86: 3699–3703 (view/download PDF) |
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| The presence of these translational pause signals is universal. Living organisms from bacteria to animals all contain over-represented, di-codons which appear to have been conserved through evolution, and may regulate the amount and quality of protein translated from a given transcript.
The actual di-codons vary widely from organism to organism, so moving an open reading frame (ORF) into a heterologous host can scramble these signals. |
 Comparison of the amino acid homology of Triose Isomerase against the presence of respective over-represented di-codons. While many di-codon locations are preserved, many species have unique over-representation in a particular protein. |
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| Di-Codons and Translational Pauses The work of Irwin, et al* have demonstrated that certain over-represented di-codons (incompatible tRNAs) are translated slower than under-represented pairs and that they define translation pause signals. A massive computation design removes all or part of these di-codons, along with codon optimization, mRNA secondary structure reduction, calculation of oligonucleotide melting temperatures (TM) that creates self-assembling genes, and multiple other parameters. This flexible proprietary, global gene computation can be tailored to individual design needs. |
 Over represented di-codons have been shown to result in translational step “slow downs” at the A & P ribosomal sites. This slow down is due to a steric hindrance in the ribosome during translation. *Becky Irwin, J. Denis Heck, G. Wesley Hatfield. Codon Pair Utilization Biases Influence Translational Elongation Step Times J. Biol. Chem. 1995 270: 22801-22806 (view/download PDF) |
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| Many of the implications of this phenomenon are still not understood and require further testing. Explanations for evolutionary preservation range from facilitation of post translational modification to down regulation of protein expression which resulted in species differentiation. CODA’s current use of this discovery is a component of the optimization process to achieve maximum expression in E. coli. Research programs with industry and academia will continue to explore this phenomenon and its impact on successful protein expression. | ||