Automatic Design of DNA Logic Gates Based on Kinetic Simulation

Authors:
Ibuki Kawamata;Fumiaki Tanaka;Masami Hagiya
Affiliations:
Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan 113-8656;Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan 113-8656;Graduate School of Information Science and Technology, University of Tokyo, Tokyo, Japan 113-8656
Venue:
DNA Computing and Molecular Programming
Year:
2009

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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.