Development of an in vivo computer based on Escherichia coli

Hirotaka Nakagawa, Kensaku Sakamoto, Yasubumi Sakakibara

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

12 Citations (Scopus)

Abstract

We present a novel framework to develop a programmable and autonomous in vivo computer using 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. Second, 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 [8]. 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 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.

Original languageEnglish
Title of host publicationDNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers
Pages203-212
Number of pages10
DOIs
Publication statusPublished - 2006 Jul 13
Event11th International Workshop on DNA Computing, DNA11 - London, ON, Canada
Duration: 2005 Jun 62005 Jun 9

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume3892 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other11th International Workshop on DNA Computing, DNA11
CountryCanada
CityLondon, ON
Period05/6/605/6/9

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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    Nakagawa, H., Sakamoto, K., & Sakakibara, Y. (2006). Development of an in vivo computer based on Escherichia coli. In DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers (pp. 203-212). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3892 LNCS). https://doi.org/10.1007/11753681_16