DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing

Ken Komiya, Kensaku Sakamoto, Atsushi Kameda, Masahito Yamamoto, Azuma Ohuchi, Daisuke Kiga, Shigeyuki Yokoyama, Masami Hagiya

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

Parallelism is one of the major advantages of molecular computation. A large number of data encoded in DNA molecules can be processed simultaneously by molecular biology techniques, although only a single set of instructions has been implemented in a solution. We have developed a computing machine, called the "whiplash" machine, which is made of DNA polymerase and a hairpin DNA. This machine simulates a finite state machine, executing its own instructions encoded in the DNA moiety, and would thus be applicable to multiple-instruction operation in a solution. In the present study, we explored the feasibility of this novel type of parallelism by applying the whiplash machine in a computation of the directed Hamiltonian path problem. The possible paths in a given graph were represented with different instruction sets, which were then implemented separately by whiplash machines in a test tube. After an autonomous operation of the machines, only the machine that implemented the instruction set corresponding to the Hamiltonian path was recovered from the tube. On the basis of the efficiency of machine operation, which was experimentally determined, 1010 different instruction sets could be implemented simultaneously in a 1-ml solution.

Original languageEnglish
Pages (from-to)18-25
Number of pages8
JournalBioSystems
Volume83
Issue number1
DOIs
Publication statusPublished - 2006 Jan
Externally publishedYes

Fingerprint

Molecular Computing
DNA-directed DNA polymerase
DNA-Directed DNA Polymerase
Hamiltonians
DNA
Hamiltonian path
Molecular Computers
Parallelism
Tube
Molecular biology
Finite automata
Molecular Biology
State Machine
Molecules
Path
Architecture
Computing
Graph in graph theory
molecular biology

Keywords

  • Directed Hamiltonian path problem
  • DNA-based computing
  • Molecular state machine
  • Whiplash machine

ASJC Scopus subject areas

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

Cite this

DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing. / Komiya, Ken; Sakamoto, Kensaku; Kameda, Atsushi; Yamamoto, Masahito; Ohuchi, Azuma; Kiga, Daisuke; Yokoyama, Shigeyuki; Hagiya, Masami.

In: BioSystems, Vol. 83, No. 1, 01.2006, p. 18-25.

Research output: Contribution to journalArticle

Komiya, Ken ; Sakamoto, Kensaku ; Kameda, Atsushi ; Yamamoto, Masahito ; Ohuchi, Azuma ; Kiga, Daisuke ; Yokoyama, Shigeyuki ; Hagiya, Masami. / DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing. In: BioSystems. 2006 ; Vol. 83, No. 1. pp. 18-25.
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