Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions

  • David Yu Zhang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6518)

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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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • David Yu Zhang
    • 1
  1. 1.California Institute of TechnologyPasadenaUSA

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