Codon optimization and in silico cloning

A codon optimization approach was used to improve recombinant protein expression. Codon optimization is essential because the genetic code's degeneracy permits most of the amino acids to be encoded by multiple codons. Java Codon Adaptation Tool (JCat) server (http://www.prodoric.de/JCat) was used in the codon system of E. coli (strain K12) to obtain the codon adaptation index (CAI) values and GC contents to determine the levels of protein expression. The best CAI value is 1.0, while > 0.8 is regard a good score, and the GC content range from 30 to 70%. There are unfavorable effects on translation and transcriptional efficiencies beyond this range⁶³. The multi-epitope vaccine's optimized gene sequence was cloned in E. coli plasmid vector pET-30a (+), NdeI and HindIII restriction sites were added to the N and C-terminals of the sequence, respectively. Finally, the optimized sequence of the final vaccine construct (with restriction sites) was inserted into the plasmid vector pET-30a (+) using the SnapGene software (https://www.snapgene.com/free-trial/) to confirm the expression of the vaccine.