DNA splicing: computing by observing

  • Authors:

  • Matteo Cavaliere;Nataša Jonoska;Peter Leupold

  • Affiliations:

  • Centre for Computational and Systems Biology, Microsoft Research --- University of Trento, Trento, Italy;Department of Mathematics, University of South Florida, Tampa, USA 33620;Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain 43005

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2009

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Abstract

Motivated by several techniques for observing molecular processes in real-time we introduce a computing device that stresses the role of the observer in biological computations and that is based on the observed behavior of a splicing system. The basic idea is to introduce a marked DNA strand into a test tube with other DNA strands and restriction enzymes. Under the action of these enzymes the DNA starts to splice. An external observer monitors and registers the evolution of the marked DNA strand. The input marked DNA strand is then accepted if its observed evolution follows a certain expected pattern. We prove that using simple observers (finite automata), applied on finite splicing systems (finite set of rules and finite set of axioms), the class of recursively enumerable languages can be recognized.