Development of a bacteria computer: From in silico finite automata to in vitro and in vivo

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

We overview a series of our research on implementing finite automata in vitro and in vivo in the framework of DNA-based computing [1,2]. First, we employ the length-encoding technique proposed and presented in [3,4] 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 double-strand 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 with 2 up 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. We show some successful experiments to run an in vivo finite-state automaton on E. coli.

Original languageEnglish
Title of host publicationPrograms, Proofs, Processes - 6th Conference on Computability in Europe, CiE 2010, Proceedings
Pages362-371
Number of pages10
DOIs
Publication statusPublished - 2010 Jul 29
Event6th Conference on Computability in Europe, CiE 2010 - Ponta Delgada, Azores, Portugal
Duration: 2010 Jun 302010 Jul 4

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume6158 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other6th Conference on Computability in Europe, CiE 2010
CountryPortugal
CityPonta Delgada, Azores
Period10/6/3010/7/4

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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