Evolutionary Computation in Gene Regulatory Network Research

CHAPTER 9DESIGN AUTOMATION OF NUCLEIC ACID REACTION SYSTEM SIMULATED BY CHEMICAL KINETICS BASED ON GRAPH REWRITING MODEL

Ibuki Kawamata

Department of Bioengineering and Robotics, Graduate School of Engineering, Tohoku University, Miyagi, Japan

Masami Hagiya

Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo, Tokoyo, Japan

9.1 INTRODUCTION

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are used as a genetic information carrier and a functional module in nature. Gene regulatory network (GRN) focuses on the topology of how genes coded in DNA interact each other. In this chapter, we rather focus on direct interactions among nucleic acids than reactions through genes.

Specifically, we regard nucleic acids as a programmable material to directly implement artificial dynamic systems. Basic reactions employed in a system are simple base-pairing and enzymatic reactions. Functional systems, which we call nucleic acid reaction systems, can be programmed and driven by cascading such basic reactions.

Typical modules of nucleic acid reaction systems are combinatorial circuit [1, 2, 3], sensing switch [4, 5], and autonomous actuators [6, 7]. By combining such modules, applications such as molecular sensors [8, 9, 10], drug delivery system [11], cell diagnosis system [12], and implementation of neural network [13] have been demonstrated. Such systems are designed to contribute to subjects which can be categorized as follows: ...