Efficient Codon Optimization with Motif Engineering
It is now common to add protein coding genes into cloning vectors for expression within non-native host organisms. Codon optimization 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 optimizing 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 algorithm on the GENCODE dataset and provide a guarantee that the solution found is always optimal.
KeywordsCodon Usage Codon Bias Codon Optimization Nucleic Acid Research Codon Adaption Index
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- 13.Satya, R.V., Mukherjee, A., Ranga, U.: A pattern matching algorithm for codon optimization and cpg motif-engineering in dna expression vectors. In: CSB 2003: Proceedings of the IEEE Computer Society Conference on Bioinformatics, pp. 294–305. IEEE Computer Society, Washington, DC, USA (2003)Google Scholar
- 15.The ENCODE Consortium: The ENCODE (ENCyclopedia of DNA elements) project. Science 306(5696), 636–640 (2004)Google Scholar