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Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions

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DNA Computing and Molecular Programming (DNA 2010)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 6518))

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Abstract

DNA strand displacement has been used to construct a variety of components, devices, and circuits. The sequences of involved nucleic acid molecules can greatly influence the kinetics and function of strand displacement reactions. To facilitate consideration of spurious reactions during the design process, one common strategy is to subdivide DNA strands into domains, continuous nucleic acid bases that can be abstracted to act as a unit in hybridization and dissociation. Here, considerations for domain-based sequence design are discussed, and heuristics are presented for the sequence design of domains. Based on these heuristics, a randomized algorithm is implemented for sequence design.

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Author information

Authors and Affiliations

  1. California Institute of Technology, Pasadena, CA, USA

    David Yu Zhang

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  1. David Yu Zhang
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Editors and Affiliations

  1. Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, 223-8522, Yokohama, Japan

    Yasubumi Sakakibara

  2. Department of Chemical Engineering, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China

    Yongli Mi

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Zhang, D.Y. (2011). Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions. In: Sakakibara, Y., Mi, Y. (eds) DNA Computing and Molecular Programming. DNA 2010. Lecture Notes in Computer Science, vol 6518. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18305-8_15

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  • DOI: https://doi.org/10.1007/978-3-642-18305-8_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-18304-1

  • Online ISBN: 978-3-642-18305-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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