Hairpin structures in DNA words

  • Authors:

  • Lila Kari;Stavros Konstantinidis;Elena Losseva;Petr Sosík;Gabriel Thierrin

  • 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;Facultad de Informática, Universidad Politécnica de Madrid, Boadilla del Monte, Madrid, Spain;Department of Mathematics, The University of Western Ontario, London, ON, Canada

  • Venue:
  • DNA'05 Proceedings of the 11th international conference on DNA Computing
  • Year:
  • 2005

Quantified Score

Hi-index 0.00

Visualization

Abstract

We formalize the notion of a DNA hairpin secondary structure, examining its mathematical properties. Two related secondary structures are also investigated, taking into the account imperfect bonds (bulges, mismatches) and multiple hairpins. We characterize maximal sets of hairpin-forming DNA sequences, as well as hairpin-free ones. We study their algebraic properties and their computational complexity. Related polynomial-time algorithms deciding hairpin-freedom of regular sets are presented. Finally, effective methods for design of long hairpin-free DNA words are given.