Bio-Molecular Computing of Finite-State Machine

We overview a series of our research on implementing finite automata in vitro and in vivo in the framework of DNA-based computing [2, 3]. First, we employ the lengthencoding technique proposed and presented in [5, 4] to implement finite automata in test tube. In the length-encoding method, the states and state transition functions of a target finite automaton are effectively encoded into DNA sequences, a computation (accepting) process of finite automata is accomplished by self-assembly of encoded complementary DNA strands, and the acceptance of an input string is determined by the detection of a completely hybridized doublestrand DNA. Second, We report our intensive in vitro experiments in which we have implemented and executed several finite-state automata in test tube. We have designed and developed practical laboratory protocols which combine several in vitro operations such as annealing, ligation, PCR, and streptavidin-biotin bonding to execute in vitro finite automata based on the length-encoding technique. We have carried laboratory experiments on various finite automata of from 2 states to 6 states for several input strings. Third, we present a novel framework to develop a programmable and autonomous in vivo computer using Escherichia coli (E. coli), and implement in vivo finite-state automata based on the framework by employing the protein-synthesis mechanism of E. coli. Our fundamental idea to develop a programmable and autonomous finite-state automata on E. coli is that we first encode an input string into one plasmid, encode state-transition functions into the other plasmid, and introduce those two plasmids into an E. coli cell by electroporation. Fourth, we execute a protein-synthesis process in E. coli combined with four-base codon techniques to simulate a computation (accepting) process of finite automata, which has been proposed for in vitro translation-based computations in [4]. This approach enables us to develop a programmable in vivo computer by simply replacing a plasmid encoding a state-transition function with others. Further, our in vivo finite automata are autonomous because the Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Bionetics ’08, November 25-28, 2008, Hyogo, Japan Copyright 2008 ICST 978-963-9799-35-6 protein-synthesis process is autonomously executed in the living E. coli cell. We show some successful experiments to run an in vivo finite-state automaton on E. coli.