小中大
Hi, there,
Here are something about rare codon that I know. Hopefully the following is usefulSmile
1 There are mainly five rare codons for E. Coli:
AGG, AGA for Arg (codon usage: 0.003 and 0.006, respectively);
ATA for Ile (0.006);
CCC for Pro (0.016);
CTA for Leu (0.008).
2 Usually, the clusters of rare codon in N-terminus, especially near the start codon can dramatically impact the expression level.
As SmallDonkey said, Rosetta is designed to solve the problem. The sequence should be checked before cloning and expression. I mean, it a part of project for recombinant expression.
A strain from Strategen, named BL21 DE3 codonplus RIPL (where RIPL are the one-letter for the four amino acids), a well known strain, is also competent for express heterogenous protein with rare codons. As in a paper published in Nature, 2007, the authors express three protein successfully using this strain. Note that there are 24-32 rare codons in each protein, which contain 240-320 residues.
