title: DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing.
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, 10(10) different instruction sets could be implemented simultaneously in a 1-ml solution.
authors.affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
authors.forename: Ken
authors.initials: K
authors.lastname: Komiya
authors.forename: Kensaku
authors.initials: K
authors.lastname: Sakamoto
authors.forename: Atsushi
authors.initials: A
authors.lastname: Kameda
authors.forename: Masahito
authors.initials: M
authors.lastname: Yamamoto
authors.forename: Azuma
authors.initials: A
authors.lastname: Ohuchi
authors.forename: Daisuke
authors.initials: D
authors.lastname: Kiga
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
authors.forename: Masami
authors.initials: M
authors.lastname: Hagiya
mesh_terms: D039301:Computers, Molecular; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D009690:Nucleic Acid Conformation
chemical_list: D004247:DNA; D004259:DNA-Directed DNA Polymerase