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Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions

Zhang, David Yu (2011) Towards Domain-Based Sequence Design for DNA Strand Displacement Reactions. In: DNA computing and molecular programming. Lecture Notes in Computer Science . No.6518. Springer , Berlin, pp. 162-175. ISBN 978-3-642-18304-1.

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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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Additional Information:© 2011 Springer-Verlag Berlin Heidelberg. This research is supported in part by NSF grants 0832824 and 0728703. DYZ is supported by the Fannie and John Hertz Foundation. The author thanks Erik Winfree and David Soloveichik for testing the DD code. The author thanks Erik Winfree for suggestions regarding the manuscript.
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Fannie and John Hertz FoundationUNSPECIFIED
Series Name:Lecture Notes in Computer Science
Issue or Number:6518
Record Number:CaltechAUTHORS:20111006-082343451
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:27112
Deposited By: Tony Diaz
Deposited On:06 Oct 2011 15:42
Last Modified:03 Oct 2019 03:20

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