Watson-Crick conjugate and commutative words

  • Authors:

  • Lila Kari;Kalpana Mahalingam

  • Affiliations:

  • University of Western Ontario, Department of Computer Science, London, ON, Canada;University of Western Ontario, Department of Computer Science, London, ON, Canada

  • Venue:
  • DNA13'07 Proceedings of the 13th international conference on DNA computing
  • Year:
  • 2007

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Abstract

This paper is a theoretical study of notions in combinatorics of words motivated by information being encoded as DNA strands in DNA computing. We generalize the classical notions of conjugacy and commutativity of words to incorporate the notion of an involution function, a formalization of the Watson-Crick complementarity of DNA single-strands. We define and study properties of Watson-Crick conjugate and commutative words, as well as Watson-Crick palindromes. We obtain, for example, a complete characterization of the set of all words that are notWatson-Crick palindromes. Our results hold for more general functions, such as arbitrary morphic and antimorphic involutions. They generalize classical results in combinatorics of words, while formalizing concepts meaningful for DNA computing experiments.