A separation method for DNA computing based on concentration control

Authors:
Masahito Yamamoto;Atsushi Kameda;Nobuo Matsuura;Toshikazu Shiba;Yumi Kawazoe;Azuma Ohuchi
Affiliations:
Japan Science and Technology Corporation (JST) Honmachi 4-1-8, Kawaguchi 332-0012, Japan and Hokkaido University North 13, West 8, Kita-ku, Sapporo 060-8628, JAPAN;Japan Science and Technology Corporation (JST) Honmachi 4-1-8, Kawaguchi 332-0012, JAPAN;Hokkaido University North 13, West 8, Kita-ku, Sapporo 060-8628, JAPAN;Hokkaido University North 13, West 8, Kita-ku, Sapporo 060-8628, JAPAN;Hokkaido University North 13, West 8, Kita-ku, Sapporo 060-8628, JAPAN;Hokkaido University North 13, West 8, Kita-ku, Sapporo 060-8628, JAPAN
Venue:
New Generation Computing
Year:
2002

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Abstract

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.