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Hairpin Structures Defined by DNA Trajectories

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DNA Computing (DNA 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4287))

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Abstract

We examine scattered hairpins, which are structures formed when a single strand folds into a partially hybridized stem and a loop. To specify different classes of hairpins, we use the concept of DNA trajectories, which allows precise descriptions of valid bonding patterns on the stem of the hairpin. DNA trajectories have previously been used to describe bonding between separate strands.

We are interested in the mathematical properties of scattered hairpins described by DNA trajectories. We examine the complexity of set of hairpin-free words described by a set of DNA trajectories. In particular, we consider the closure properties of language classes under sets of DNA trajectories of differing complexity. We address decidability of recognition problems for hairpin structures.

For a full version, see [1]. Research supported in part by a grant from NSERC. Research conducted at the Jodrey School of Computer Science, Acadia University.

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Author information

Authors and Affiliations

  1. Department of Computer Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada

    Michael Domaratzki

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  1. Michael Domaratzki
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Editors and Affiliations

  1. Department of Chemistry, Purdue University, 560 Oval Drive, 47907-2084, West Lafayette, IN, USA

    Chengde Mao

  2. Faculty of Education and Integrated Arts and Sciences, Department of Mathematics, Waseda University, 1-6-1 Nishiwaseda, Shinjuku-ku, 169-8050, Tokyo, Japan

    Takashi Yokomori

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Domaratzki, M. (2006). Hairpin Structures Defined by DNA Trajectories. In: Mao, C., Yokomori, T. (eds) DNA Computing. DNA 2006. Lecture Notes in Computer Science, vol 4287. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11925903_14

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  • DOI: https://doi.org/10.1007/11925903_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-49024-1

  • Online ISBN: 978-3-540-68423-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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