NIH MBI Laboratory for Structural Genomics and Proteomics

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Rare Codon Calculator (RaCC) Rare Codon Calculator (RaCC)

Over-expression of recombinant protein in E. coli may be severely diminished (to the point of being undetectable) if the ORF that codes for the protein uses "rare" codons that are infrequently used by E. coli. In particular, codons for arginine (AGG, AGA, CGA), leucine (CTA), isoleucine (ATA), and proline (CCC) may be a problem. For instance, the presence of more than ~ 8-9 of the two rarest Arg codons (AGG and AGA), particularly back-to-back as a tandem repeat, has prevented over-expression of Pyrobaculum aerophilum proteins in our lab. RaCC will determine the number of rare E. coli codons in a DNA sequence.

The following references may be useful:

"Cloning of the gene for inorganic pyrophosphatase from a thermoacidophilic archaeon, Sulfolobus sp. strain 7, and overproduction of the enzyme by coexpression of tRNA for arginine rare codon" by Wakagi T, Oshima T, Imamura H, Matsuzawa H
Biosci Biotechnol Biochem 1998 Dec; 62(12):2408-14
"Improved High-Level Expression System for Eukaryotic Genes in Escherichia coli Using T7 RNA Polymerase and Rare ^ArgtRNAs" by Schenk, P.M., Baumann, S., Mattes, R., Steinbib, H.-H.
BioTechniques 1995 v.19 no.2 196-198
"Codon Bias-Adjusted BL21 Derivatives for Protein Expression" by Carsten-Peter Carstens \& Anna Waesche
Strategies Newsletters (Stratagene) May 1999; vol. 12 #2 pg. 49-51

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