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Sakowski S, Krasinski T, Waldmajer J, et al. Biomolecular computers with multiple restriction enzymes. Genet Mol Biol. 2017;40(4):860-870doi: 10.1590/1678-4685-GMB-2016-0132.
Sakowski, S., Krasinski, T., Waldmajer, J., Sarnik, J., Blasiak, J., & Poplawski, T. (2017). Biomolecular computers with multiple restriction enzymes. Genetics and molecular biology, 40(4), 860-870. https://doi.org/10.1590/1678-4685-GMB-2016-0132
Sakowski, Sebastian, et al. "Biomolecular computers with multiple restriction enzymes." Genetics and molecular biology vol. 40,4 (2017): 860-870. doi: https://doi.org/10.1590/1678-4685-GMB-2016-0132
Sakowski S, Krasinski T, Waldmajer J, Sarnik J, Blasiak J, Poplawski T. Biomolecular computers with multiple restriction enzymes. Genet Mol Biol. 2017 Oct-Dec;40(4):860-870. doi: 10.1590/1678-4685-GMB-2016-0132. Epub 2017 Oct 23. PMID: 29064510; PMCID: PMC5738618.
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Genet Mol Biol. 2017 Oct-Dec;40(4):860-870. doi: 10.1590/1678-4685-GMB-2016-0132. Epub 2017 Oct 23.

Biomolecular computers with multiple restriction enzymes.

Genetics and molecular biology

Sebastian Sakowski, Tadeusz Krasinski, Jacek Waldmajer, Joanna Sarnik, Janusz Blasiak, Tomasz Poplawski

Affiliations

  1. Faculty of Mathematics and Computer Science, University of Lodz, Lodz, Poland.
  2. Logic, Language and Information Group, Department of Philosophy, University of Opole, Opole, Poland.
  3. Department of Molecular Genetics, University of Lodz, Lodz, Poland.

PMID: 29064510 PMCID: PMC5738618 DOI: 10.1590/1678-4685-GMB-2016-0132

Abstract

The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann "bottleneck". Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro's group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals. This computer represented a two-state two-symbol finite automaton that was subsequently extended by using two restriction enzymes. In this paper, we propose the idea of a multistate biomolecular computer with multiple commercially available restriction enzymes as hardware. Additionally, an algorithmic method for the construction of transition molecules in the DNA computer based on the use of multiple restriction enzymes is presented. We use this method to construct multistate, biomolecular, nondeterministic finite automata with four commercially available restriction enzymes as hardware. We also describe an experimental applicaton of this theoretical model to a biomolecular finite automaton made of four endonucleases.

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