ECodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments.

ABSTRACT: We present a systematic computational framework, eCodonOpt, for designing parental DNA sequences for directed evolution experiments through codon usage optimization. Given a set of homologous parental proteins to be recombined at the DNA level, the optimal DNA sequences encoding these proteins are sought for a given diversity objective. We find that the free energy of annealing between the recombining DNA sequences is a much better descriptor of the extent of crossover formation than sequence identity. Three different diversity targets are investigated for the DNA shuffling protocol to showcase the utility of the eCodonOpt framework: (i) maximizing the average number of crossovers per recombined sequence; (ii) minimizing bias in family DNA shuffling so that each of the parental sequence pa

SUBMITTER: Moore GL 

PROVIDER: S-EPMC117206 | biostudies-literature | 2002 Jun

REPOSITORIES: biostudies-literature