Toward "wet" implementation of genetic algorithm for protein engineering

Abstract

We here propose an application of DNA computing to a practical problem, protein engineering, which is difficult to approach by using modern electronic computers. DNA molecules naturally carry the blueprints of proteins. DNA-based processing of this genetic information could give mutant proteins with desired properties. We conceived the use of genetic algorithm for this purpose, and designed an algorithm amenable to DNA-based implementation. The performance of this algorithm was examined on a model fitness landscape by computer experiments. Then, spontaneous DNA recombination during PCR was utilized to embody the crossover operation in the genetic algorithm, preparing for the "wet" implementation of the whole search process in the future. © Springer-Verlag Berlin Heidelberg 2005.