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The present special issue contains a selection of extended versions of papers presented in the 12th International Meeting on DNA Computing, held on June 5–9 in 2006, in Seoul, Korea. Since the first meeting held in Princeton in 1995, this international meeting has been providing a unique forum for scientists from multidisciplinary backgrounds to assemble and exchange their ideas and latest results, toward the final common goal of developing DNA based computing devices. The 12th meeting resulted in a great success, and we enjoyed all programs within an excellent organization and pleasant atmosphere supported by the organizing committee. We would specially like to thank Prof. Byoung-Tak Zhang, the committee chair.