Preventing undesirable bonds between DNA codewords

  • Authors:

  • Lila Kari;Stavros Konstantinidis;Petr Sosík

  • Affiliations:

  • Department of Computer Science, The University of Western Ontario, London, ON, Canada;Dept. of Mathematics and Computing Science, Saint Mary's University, Halifax, Nova Scotia, Canada;Department of Computer Science, The University of Western Ontario, London, ON, Canada

  • Venue:
  • DNA'04 Proceedings of the 10th international conference on DNA computing
  • Year:
  • 2004

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Abstract

The input data for DNA computing must be encoded into the form of single or double DNA strands. As complementary parts of single strands can bind together forming a double-stranded DNA sequence, one has to impose restrictions on these sets of DNA words (=languages) to prevent them from interacting in undesirable ways. We recall a list of known properties of DNA languages which are free of certain types of undesirable bonds. Then we introduce a general framework in which we can characterize each of these properties by a solution of a uniform formal language inequation. This characterization allows us among others to construct (i) a uniform algorithm deciding in polynomial time whether a given DNA language possesses any of the studied properties, and (ii) in many cases also an algorithm deciding whether a given DNA language is maximal with respect to the desired property.