Towards domain-based sequence design for DNA strand displacement reactions

Authors:
David Yu Zhang
Affiliations:
California Institute of Technology, Pasadena, CA
Venue:
DNA'10 Proceedings of the 16th international conference on DNA computing and molecular programming
Year:
2010

Citing 3
Cited 3

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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.