Graph-theoretic formalization of hybridization in DNA sticker complexes

  • Authors:

  • Robert Brijder;Joris J. M. Gillis;Jan Van Den Bussche

  • Affiliations:

  • Hasselt University and Transnational University of Limburg;Hasselt University and Transnational University of Limburg;Hasselt University and Transnational University of Limburg

  • Venue:
  • DNA'11 Proceedings of the 17th international conference on DNA computing and molecular programming
  • Year:
  • 2011

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Abstract

Sticker complexes are a formal graph-based data model for a restricted class of DNA complexes, motivated by potential applications to databases. This data model allows for a purely declarative definition of hybridization. We introduce the notion of terminating hybridization, and characterize this notion in purely graph-theoretic terms. Terminating hybridization can still produce results of exponential size. We indicate a class of complexes where hybridization is guaranteed to be polynomially bounded.