State transitions by molecules

Kensaku Sakamoto, Daisuke Kiga, Ken Komiya, Hidetaka Gouzu, Shigeyuki Yokoyama, Shuji Ikeda, Hiroshi Sugiyama, Masami Hagiya

Research output: Contribution to journalArticle

68 Citations (Scopus)

Abstract

In our previous paper, we described a method by which a state machine is implemented by a single-stranded DNA molecule whose 3'-end sequence encodes the current state of the machine. Successive state transitions are performed in such a way that the current state is annealed onto an appropriate portion of DNA encoding the transition table of the state machine and the next state is copied to the 3'-end by extension with polymerase. In this paper, we first show that combined with parallel overlap assembly, a single series of successive transitions can solve NP-complete problems. This means that the number of necessary laboratory steps is independent from the problem size. We then report the results of two experiments concerning the implementation of our method. One is on isothermal reactions which greatly increase the efficiency of state transitions compared with reactions controlled by thermal cycles. The other is on the use of unnatural bases for avoiding out-of-frame annealing. The latter result can also be applied to many DNA-based computing paradigms.

Original languageEnglish
Pages (from-to)81-91
Number of pages11
JournalBioSystems
Volume52
Issue number1-3
DOIs
Publication statusPublished - 1999 Oct
Externally publishedYes

Fingerprint

State Transition
State Machine
DNA
Molecules
Single-Stranded DNA
Annealing
Overlap
Computational complexity
Table
single-stranded DNA
Encoding
NP-complete problem
annealing
Hot Temperature
Paradigm
Cycle
Necessary
Series
Computing
Experiment

Keywords

  • DNA-Based computing
  • Hairpin structure
  • Isothermal reaction and reaction with thermal cycles
  • Successive state transition
  • Whiplash PCR

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Biotechnology
  • Drug Discovery

Cite this

Sakamoto, K., Kiga, D., Komiya, K., Gouzu, H., Yokoyama, S., Ikeda, S., ... Hagiya, M. (1999). State transitions by molecules. BioSystems, 52(1-3), 81-91. https://doi.org/10.1016/S0303-2647(99)00035-0

State transitions by molecules. / Sakamoto, Kensaku; Kiga, Daisuke; Komiya, Ken; Gouzu, Hidetaka; Yokoyama, Shigeyuki; Ikeda, Shuji; Sugiyama, Hiroshi; Hagiya, Masami.

In: BioSystems, Vol. 52, No. 1-3, 10.1999, p. 81-91.

Research output: Contribution to journalArticle

Sakamoto, K, Kiga, D, Komiya, K, Gouzu, H, Yokoyama, S, Ikeda, S, Sugiyama, H & Hagiya, M 1999, 'State transitions by molecules', BioSystems, vol. 52, no. 1-3, pp. 81-91. https://doi.org/10.1016/S0303-2647(99)00035-0
Sakamoto K, Kiga D, Komiya K, Gouzu H, Yokoyama S, Ikeda S et al. State transitions by molecules. BioSystems. 1999 Oct;52(1-3):81-91. https://doi.org/10.1016/S0303-2647(99)00035-0
Sakamoto, Kensaku ; Kiga, Daisuke ; Komiya, Ken ; Gouzu, Hidetaka ; Yokoyama, Shigeyuki ; Ikeda, Shuji ; Sugiyama, Hiroshi ; Hagiya, Masami. / State transitions by molecules. In: BioSystems. 1999 ; Vol. 52, No. 1-3. pp. 81-91.
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