Programmable and autonomous computing machine made of biomolecules View Full Text


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Article Info

DATE

2001-11

AUTHORS

Yaakov Benenson, Tamar Paz-Elizur, Rivka Adar, Ehud Keinan, Zvi Livneh, Ehud Shapiro

ABSTRACT

Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine, which stimulated work leading to the development of modern computers. The Turing machine and its special cases, including finite automata, operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers. Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated, but the realization of computing devices operating autonomously on the molecular scale remains rare. Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton's hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton's final state, and thus the computational result. In our implementation 1012 automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 microl solution at room temperature at a combined rate of 109 transitions per second with a transition fidelity greater than 99.8%, consuming less than 10-10 W. More... »

PAGES

430

References to SciGraph publications

  • 2000-09. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules in NATURE
  • 2005-06-29. In vitro implementation of finite-state machines in AUTOMATA IMPLEMENTATION
  • 1943-12. A logical calculus of the ideas immanent in nervous activity in BULLETIN OF MATHEMATICAL BIOLOGY
  • 1990-01. A logical calculus of the ideas immanent in nervous activity in BULLETIN OF MATHEMATICAL BIOLOGY
  • 1998-08. Design and self-assembly of two-dimensional DNA crystals in NATURE
  • 1982-12. The thermodynamics of computation—a review in INTERNATIONAL JOURNAL OF THEORETICAL PHYSICS
  • 2000-01. DNA computing on surfaces in NATURE
  • 2000-10. The past, present and future of molecular computing in NATURE REVIEWS MOLECULAR CELL BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/35106533

    DOI

    http://dx.doi.org/10.1038/35106533

    DIMENSIONS

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    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/11719800


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