Development of an In Vivo Computer Based on Escherichia coli

  • Hirotaka Nakagawa
  • Kensaku Sakamoto
  • Yasubumi Sakakibara
Conference paper

DOI: 10.1007/11753681_16

Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)
Cite this paper as:
Nakagawa H., Sakamoto K., Sakakibara Y. (2006) Development of an In Vivo Computer Based on Escherichia coli. In: Carbone A., Pierce N.A. (eds) DNA Computing. DNA 2005. Lecture Notes in Computer Science, vol 3892. Springer, Berlin, Heidelberg

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.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Hirotaka Nakagawa
    • 1
  • Kensaku Sakamoto
    • 2
  • Yasubumi Sakakibara
    • 1
  1. 1.Department of Biosciences and InformaticsKeio UniversityYokohamaJapan
  2. 2.RIKEN Genomic Sciences CenterYokohamaJapan

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