Recognizing DNA splicing

  • Authors:

  • Matteo Cavaliere;Nataša Jonoska;Peter Leupold

  • Affiliations:

  • Department of Computer Science and Artificial Intelligence, University of Sevilla, Sevilla, Spain;Department of Mathematics, University of South Florida, Tampa, FL;Research Group on Mathematical Linguistics, Rovira i Virgili University, Tarragona, Spain

  • Venue:
  • DNA'05 Proceedings of the 11th international conference on DNA Computing
  • Year:
  • 2005

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Abstract

Motivated by recent techniques developed for observing evolutionary dynamics of a single DNA molecule, we introduce a formal model for accepting an observed behavior of a splicing system. The main idea is to input a marked DNA strand into a test tube together with certain restriction enzymes and, possibly, with other DNA strands. Under the action of the enzymes, the marked DNA strand starts to evolve by splicing with other DNA strands. The evolution of the marked DNA strand is “observed” by an outside observer and the input DNA strand is “accepted” if its (observed) evolution follows a certain expected pattern. We prove that using finite splicing system (finite set of rules and finite set of axioms), universal computation is attainable with simple observing and accepting devices made of finite state automata.