Toward “wet” implementation of genetic algorithm for protein engineering

Authors:
Kensaku Sakamoto;Masayuki Yamamura;Hiroshi Someya
Affiliations:
Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo;Department of Computational Intelligence and Systems Science, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Yokohama, Japan;Department of Prediction and Control, The Institute of Statistical Mathematics, Tokyo, Japan
Venue:
DNA'04 Proceedings of the 10th international conference on DNA computing
Year:
2004

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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.