Unravel four hairpins!

Authors:
Atsushi Kameda;Masahito Yamamoto;Azuma Ohuchi;Satsuki Yaegashi;Masami Hagiya
Affiliations:
Japan Science and Technology Corporation, Kawaguchi City, Saitama, Japan 332-0012;Japan Science and Technology Corporation, Kawaguchi City, Saitama, Japan 332-0012 and Graduate School of Information Science and Technology, Hokkaido University, Kita-ku, Sapporo, Japan 060-8628;Japan Science and Technology Corporation, Kawaguchi City, Saitama, Japan 332-0012 and Graduate School of Information Science and Technology, Hokkaido University, Kita-ku, Sapporo, Japan 060-8628;Japan Science and Technology Corporation, Kawaguchi City, Saitama, Japan 332-0012;Japan Science and Technology Corporation, Kawaguchi City, Saitama, Japan 332-0012 and Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, To ...
Venue:
Natural Computing: an international journal
Year:
2008

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Abstract

DNA machines consisting of consecutive hairpins, which we have previously described, have various potential applications in DNA computation. In the present study, a 288-base DNA machine containing four consecutive hairpins was successfully constructed by ligation and PCR. PAGE and fluorescence spectroscopy experiments verified that all four hairpins were successfully opened by four opener oligomers, and that hairpin opening was dependent on the proper openers added in the correct order. Quantitative analysis of the final results by fluorescence spectroscopy indicated that all four hairpins were open in about 1/4 to 1/3 of the DNA machines.