Hairpin-based state machine and conformational addressing: Design and experiment |
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| Authors: | Kameda Atsushi Yamamoto Masahito Uejima Hiroki Hagiya Masami Sakamoto Kensaku Ohuchi Azuma |
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| Affiliation: | (1) Japan Science and Technology Corporation (JST-CREST), Kawaguchi Center Building, 4-1-8 Honcho, Kawaguchi City Saitama, 332-0012, Japan;(2) Division of Systems and Information Engineering, Graduate School of Engineering Hokkaido University, North 13, West 8, Kita-ku, Sapporo 060-8628, Japan;(3) JAPAN PATENT OFFICE, 3-4-3 Kasumigaseki, Chiyoda-ku Tokyo, 100-8915, Japan;(4) JST-CREST and Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Japan;(5) Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku Tokyo, 113-0032, Japan |
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| Abstract: | In this paper, we propose a new architecture for a multi-state DNA machine whose conformation of repeated hairpin structures changes sequentially in response to input oligomers. As an application of the machine, we also propose molecular memory in which the machine is used as a memory unit. Addressing in the memory is realized through state transitions of the machine. We then describe a method for designing DNA sequences of the machine, which exhaustively checks conformational changes of the machine by dividing its secondary structure into hairpin units. The method is based on the minimum free energy of the structure, the structure transition paths, and the total frequency of optimal and suboptimal structures. DNA sequences designed by the method were tested in a chemical experiment in which a machine consisting of two hairpins was actually constructed. As a result, we verified that the multi-state DNA machine realized the expected changes in its secondary structure. |
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| Keywords: | DNA computing molecular computing molecluar machine molecular memory |
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