Codon pairs

Apparently there is nonrandom codon pair utilization in many species. Codon pairs may affect translational elongation rates and therefore protein production. (There can be translational pause sites that are species-specific.)

CODA genomics checks and optimizes for such things.

(Note: I haven't read the papers to evaluate this claim. Just posting the info here so that I remember it.)

References

1. Gutman GA and Hatfield GW. Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci U S A. 1989 May;86(10):3699-703. DOI:10.1073/pnas.86.10.3699 |
2. Irwin B, Heck JD, and Hatfield GW. Codon pair utilization biases influence translational elongation step times. J Biol Chem. 1995 Sep 29;270(39):22801-6. DOI:10.1074/jbc.270.39.22801 |
3. Trinh R, Gurbaxani B, Morrison SL, and Seyfzadeh M. Optimization of codon pair use within the (GGGGS)3 linker sequence results in enhanced protein expression. Mol Immunol. 2004 Jan;40(10):717-22. DOI:10.1016/j.molimm.2003.08.006 |