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Published December 2, 2009 | Supplemental Material
Journal Article Open

Control of DNA Strand Displacement Kinetics Using Toehold Exchange

Abstract

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchange process was introduced as a method for designing fast and reversible strand displacement reactions. Here, we characterize the kinetics of DNA toehold exchange and model it as a three-step process. This model is simple and quantitatively predicts the kinetics of 85 different strand displacement reactions from the DNA sequences. Furthermore, we use toehold exchange to construct a simple catalytic reaction. This work improves the understanding of the kinetics of nucleic acid reactions and will be useful in the rational design of dynamic DNA and RNA circuits and nanodevices.

Additional Information

© 2009 American Chemical Society. Received: August 18, 2009. Publication Date (Web): November 6, 2009. We thank Xi Chen for a very careful reading of this paper and useful suggestions regarding the binding energy calculations. We thank Karthik Sarma for useful suggestions regarding rate constant fitting. We thank Niles Pierce, Justin Bois, and Joe Zadeh for discussion on the energetics parameters used by NUPACK. We thank Niles Pierce, Anne Condon, and Victor Beck for many helpful suggestions in the revision of the manuscript. We thank Bernard Yurke, Georg Seelig, and Joseph Schaeffer for insightful discussions. D.Y.Z. and E.W. were supported by NSF grants 0506468, 0622254, 0533064, 0728703, and 0832824. D.Y.Z. is supported by the Fannie and John Hertz Foundation.

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