Abstract
Optical computing promises spatially parallel information processing, but the diffraction phenomenon prevents us from performing computations at a nanometer scale. To overcome the problem, the idea of DNA computing is useful because it offers methods for manipulating information at that scale. We have been studying on photonic DNA automaton, which is an implementation of automaton using light and DNA as information carriers. The internal state of the automaton is represented by the position of a specific DNA in a DNA nano-structure, and the state transition is executed by changing the position in the structure in accordance with photonic signals. In this paper, we describe a photonic switch of the position of a DNA strand in a DNA nano-structure by photonic control of other DNAs. The position is controlled through conformation-change of a pair of hairpin-DNAs that are responsive to visible and UV light irradiation. Experimental results show that the position of the DNA switches to the two position in response to visible and UV light. The method is applicable to state-transition of the photonic DNA automaton.
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References
Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z., Shapiro, E.: Programmable and autonomous computing machine made of biomolecules. Nature 414, 430–434 (2001)
Benenson, Y., Gil, B., Ben-Dor, U., Adar, R., Shapiro, E.: An autonomous molecular computer for logical control of gene expression. Nature 429, 1–6 (2004)
Head, T.: Photocomputing: explorations with transparency and opacity. Parallel Processing Letters 17(4), 339–347 (2004)
Aldaye, F.A., Palmer, A.L., Sleiman, H.F.: Assembling Materials with DNA as the Guide. Science 321, 1794–1799 (2008)
Rinker, S., Ke, Y., Liu, Y., Chhabra, R., Yan, H.: Self-assembled DNA nanostructures for distance dependent multivalent ligand-protein binding. Nature nanotechnology 3, 418–422 (2008)
Ogura, Y., Horiguchi, Y., Tanida, J.: Stepwise State-Transition of DNA Structures Controlled Through Sequential Photonic Signals. In: Preliminary proceedings of the 14th international meeting on DNA computing, p. 197 (2008)
Sakai, H., Ogura, Y., Tanida, J.: An Implementation of a Nanoscale Automaton Using DNA Conformation Controlled by Optics Signals. In: International Topical Meeting on Information Photonics 2008, pp. 172–173 (2008)
Sakai, H., Ogura, Y., Tanida, J.: Positional state representation and its transition control for photonic DNA automaton. In: 15th International Meeting on DNA Computing and Molecular Programming, pp. 60–71 (2009)
Sakai, H., Ogura, Y., Tanida, J.: An Implementation of a Nanoscale Automaton Using DNA Conformation Controlled by Optical Signals. Japanese Journal of Applied Physics 48, 09LA01 (2009)
Asanuma, H.: Synthesis of azobenzene-tethered DNA for reversible photo-regulation of DNA functions: hybridization and transcription. Nature Protocols 2, 203–213 (2007)
Kallenbach, N.R., Ma, R., Seeman, N.C.: An immobile nucleic acid junction constructed from oligonucleotides. Nature 305, 829–831 (1983)
Ma, R., Kallenbach, N.R., Sheardy, R.D., Petrillo, M.L., Seeman, N.C.: Three-arm acid junctions are flexible. Nucleic Acids Research 14, 9745–9753 (1986)
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Sakai, H., Ogura, Y., Tanida, J. (2010). Photonic Switching of DNA’s Position That Represents the Internal State in Photonic DNA Automaton. In: Peper, F., Umeo, H., Matsui, N., Isokawa, T. (eds) Natural Computing. Proceedings in Information and Communications Technology, vol 2. Springer, Tokyo. https://doi.org/10.1007/978-4-431-53868-4_32
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DOI: https://doi.org/10.1007/978-4-431-53868-4_32
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-53867-7
Online ISBN: 978-4-431-53868-4
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