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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)

Abstract

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.

Keywords

Cyclic Permutation Pseudoknots Structure Primitive Word Equilibrium Partition Function Nonempty Word 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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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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