Efficient Codon Optimization with Motif Engineering

摘要

It is now common to add protein coding genes into cloning vectors for expression within non-native host organisms. Codon opti mization supports translational efficiency of the desired protein product, by exchanging codons which are rarely found in the host organism with more frequently observed codons. Motif engineering, such as removal of restriction enzyme recognition sites or addition of immuno-stimulatory elements, is also often necessary. We present an algorithm for optimiz ing codon bias of a gene with respect to a well motivated measure of bias, while simultaneously performing motif engineering. The measure is the previously studied codon adaptation index, which favors the use, in the gene to be optimized, of the most abundant codons found in the host genome. We demonstrate the efficiency and effectiveness of our al gorithm on the GENCODE dataset and provide a guarantee that the solution found is always optimal.