Intensive in vitro experiments of implementing and executing finite automata in test tube

Junna Kuramochi, Yasubumi Sakakibara

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

5 Citations (Scopus)

Abstract

We report our intensive in vitro experiments in which we have implemented and executed several finite-state automata in test tube. First, we employ the length-encoding technique proposed and presented in [4, 3] 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 design and develop 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. To our knowledge, this is the first in vitro experiments that have succeeded to execute 6-states automaton in test tube.

Original languageEnglish
Title of host publicationLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages193-202
Number of pages10
Volume3892 LNCS
DOIs
Publication statusPublished - 2006
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)03029743
ISSN (Electronic)16113349

Other

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

Fingerprint

Finite Automata
Finite automata
Tube
Encoding
Experiment
Experiments
Strings
Streptavidin
DNA
Biotin
Finite State Automata
Self-assembly
Ligation
State Transition
Annealing
Complementary DNA
DNA Sequence
DNA sequences
Automata
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

Kuramochi, J., & Sakakibara, Y. (2006). Intensive in vitro experiments of implementing and executing finite automata in test tube. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 3892 LNCS, pp. 193-202). (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_15

Intensive in vitro experiments of implementing and executing finite automata in test tube. / Kuramochi, Junna; Sakakibara, Yasubumi.

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3892 LNCS 2006. p. 193-202 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 3892 LNCS).

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

Kuramochi, J & Sakakibara, Y 2006, Intensive in vitro experiments of implementing and executing finite automata in test tube. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 3892 LNCS, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 3892 LNCS, pp. 193-202, 11th International Workshop on DNA Computing, DNA11, London, ON, Canada, 05/6/6. https://doi.org/10.1007/11753681_15
Kuramochi J, Sakakibara Y. Intensive in vitro experiments of implementing and executing finite automata in test tube. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3892 LNCS. 2006. p. 193-202. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/11753681_15
Kuramochi, Junna ; Sakakibara, Yasubumi. / Intensive in vitro experiments of implementing and executing finite automata in test tube. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3892 LNCS 2006. pp. 193-202 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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