Towards the Sequence Design Preventing Pseudoknot Formation

  • Lila Kari
  • Shinnosuke Seki
Conference paper
Part of the Proceedings in Information and Communications Technology book series (PICT, volume 1)


This paper addresses a pseudoknot-freeness problem of DNA and RNA sequences, motivated by biomolecular computing. Watson-Crick (WK) complementarity forces DNA strands to fold into themselves and form so-called secondary structures, which are usually undesirable for biomolecular computational purposes. This paper studies pseudoknot-bordered words, a mathematical formalization of a common secondary structure, the pseudoknot. We obtain several properties of WK-pseudoknot-bordered and -unbordered words. One of the main results of the paper is that a sufficient condition for a WK-pseudoknot-unbordered word u to result in all words in u  +  being WK-pseudoknot-unbordered is for u not to be a primitive word.


Cyclic Permutation Pseudoknots Structure Primitive Word Equilibrium Partition Function Nonempty Word 
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Copyright information

© Springer Tokyo 2009

Authors and Affiliations

  • Lila Kari
    • 1
  • Shinnosuke Seki
    • 1
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondonCanada

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