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Erschienen in:
2006 | OriginalPaper | Buchkapitel
Hairpin Structures in DNA Words
verfasst von : Lila Kari, Stavros Konstantinidis, Elena Losseva, Petr Sosík, Gabriel Thierrin
Erschienen in: DNA Computing
Verlag: Springer Berlin Heidelberg
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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.