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

*この研究の対応する著者

研究成果: Article査読

21 被引用数 (Scopus)

抄録

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.

本文言語English
ページ(範囲)18-25
ページ数8
ジャーナルBioSystems
83
1
DOI
出版ステータスPublished - 2006 1月
外部発表はい

ASJC Scopus subject areas

  • 統計学および確率
  • モデリングとシミュレーション
  • 生化学、遺伝学、分子生物学(全般)
  • 応用数学

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