A separation method for DNA computing based on concentration control

A separation method for DNA computing based on concentration control is presented. The concentration control method was earlier developed and has enabled us to use DNA concentrations as input data and as filters to extract target DNA. We have also applied the method to the shortest path problems, and have shown the potential of concentration control to solve large-scale combinatorial optimization problems. However, it is still quite difficult to separate different DNA with the same length and to quantify individual DNA concentrations. To overcome these difficulties, we use DGGE and CDGE in this paper. We demonstrate that the proposed method enables us to separate different DNA with the same length efficiently, and we actually solve an instance of the shortest path problems. Masahito Yamamoto, Ph.D.: He is associate professor of information engineering at Hokkaido University. He received Ph.D. from the Graduate School of Engineering, Hokkaido University in 1996. His current research interests include DNA computing based the laboratory experiments. He is a member of Operations Research Society of Japan, Japanese Society for Artificial Intelligence, Information Processing Society of Japan etc. Atsushi Kameda, Ph.D.: He is the research staff of Japan Science and Technology Corporation, and has participated in research of DNA computing in Hokkaido University. He received his Ph.D. from Hokkaido University in 2001. For each degree he majored in molecular biology. His research theme is about the role of polyphosphate in the living body. As one of the researches relevant to it, he constructed the ATP regeneration system using two enzyme which makes polyphosphate the phosphagen. Nobuo Matsuura: He is a master course student of Division of Systems and Information Engineering of Hokkaido University. His research interests relate to DNA computing with concentration control for shortest path problems, as a means of solution of optimization problems with bimolecular. Toshikazu Shiba, Ph.D.: He is associate, professor of biochemical engineering at Hokkaido University. He received his Ph.D. from Osaka University in 1991. He majored in molecular genetics and biochemistry. His research has progressed from bacterial molecular biology (regulation of gene expression of bacterial cells) to tissue engineering (bone regeneration). Recently, he is very interested in molecular computation and trying to apply his biochemical idea to information technology. Yumi Kawazoe: She is a master course student of Division of Molecular Chemistry of Hokkaido University. Although her major is molecular biology, she is very interested in molecular computation and bioinformatics. Azuma Ohuchi, Ph.D.: He is professor of Information Engineering at the University of Hokkaido, Sapporo, Japan. He has been developing a new field of complex systems engineering, i.e., Harmonious Systems Engineering since 1995. He has published numerous papers on systems engineering, operations research, and computer science. In addition, he is currently supervising projects on DNA computing, multi-agents based artificial market systems, medical informatics, and autonomous flying objects. He was awarded “The 30th Anniversary Award for Excellent Papers” by the Information Processing Society of Japan. He is a member of Operations Research Society of Japan, Japanese Society for Artificial Intelligence, Information Processing Society of Japan, Japan Association for Medical Informatics, IEEE Computer Society, IEEE System, Man and Cybernetics Society etc. He received PhD from Hokkaido University in 1976.