Dabby MPP 2011

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The Kinetics of Toehold-Mediated Four-Way Branch Migration

  • Nadine Dabby, Ho-Lin Chen, Erik Winfree, Caltech

Abstract

Many developments in DNA nanotechnology rely on three-way branch migration as a mechanism to implement switches, circuits, motors, assembly and amplification. Four-way branch migration, the process by which two double-stranded oligonucleotides that share the same stem sequence simultaneously exchange strands has been used to perform directional motion via insertion, but the applications of the four-way branch migration mechanism have not been fully explored. While three-way branch migration reaction rates can be controlled over six orders of magnitude, four-way branch migration may give us a greater range and finer resolution control over this rate. We have found that by designing the toeholds involved in a four-way branch migration reaction, we can control the effective reaction rate over seven orders of magnitude. We characterize the kinetics of DNA toehold-mediated four-way branch migration and model it as a two-step process. The ability to control the kinetics of these reactions will greatly facilitate the programming of dynamic behaviors mediated by four-way branch migration.

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