Abstract
Recently, DNA logic gates and DNA machines have been developed using only a simple complementary base pairing of DNA, that is, hybridization and branch migration. Because such reaction systems have been designed by trial and error, it has been difficult to design a complex system and to correctly verify the reaction. The purpose of this research is to develop a method for automatically searching and designing DNA logic gates based on a kinetic simulation. Since the solution space that should be searched is quite large, a simulated-annealing method is used to search for a highly evaluated system from many candidates and find a semi-optimal one. A simulator based on a kinetic model is developed, which calculates the time change of concentrations of abstracted DNA molecules. An evaluation function, in which the evaluation value rises when the logic gate works correctly, is also designed. The effectiveness of the proposed method is evaluated experimentally with an AND gate, which is designed automatically.
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Seelig, G., Soloveichik, D., Zhang, D.Y., Winfree, E.: Enzyme-free nucleic acid logic circuits. Science 314(5805), 1585–1588 (2006)
Zhang, D.Y., Turberfield, A.J., Yurke, B., Winfree, E.: Engineering entropy-driven reactions and networks catalyzed by DNA. Science 318(5853), 1121–1125 (2007)
Yin, P., Choi, H.M.T., Calvert, C.R., Pierce, N.A.: Programming biomolecular self-assembly pathways. Nature 451(7176), 318–322 (2008)
Qian, L., Winfree, E.: A simple dna gate motif for synthesizing large-scale circuits. In: Proceedings of 14th International Meeting on DNA Computing (DNA14), pp. 139–151 (2008)
Seelig, G., Yurke, B., Winfree, E.: Catalyzed relaxation of a metastable DNA fuel. Journal of the American Chemical Society 128(37), 12211–12220 (2006)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Kawamata, I., Tanaka, F., Hagiya, M. (2009). Automatic Design of DNA Logic Gates Based on Kinetic Simulation. In: Deaton, R., Suyama, A. (eds) DNA Computing and Molecular Programming. DNA 2009. Lecture Notes in Computer Science, vol 5877. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-10604-0_9
Download citation
DOI: https://doi.org/10.1007/978-3-642-10604-0_9
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-10603-3
Online ISBN: 978-3-642-10604-0
eBook Packages: Computer ScienceComputer Science (R0)