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On the biophysics and kinetics of toehold-mediated DNA strand displacement

Niranjan Srinivas, Thomas E. Ouldridge, Petr Sulc, Bernard Yurke, Ard A. Louis, Jonathan P.K. Doye and Erik Winfree

Nucl. Acids Res. 41, 10641-10658 (2013)


Dynamic DNA nanotechnology often employs toehold-mediated strand displacement for controlling reaction kinetics. While the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding remains elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model which represents each nucleotide as a 3-dimensional rigid body in continuous space. Further, we experimentally investigate the thermodynamics of 3-way branch migration. We argue that (i) the physical process by which a single step of branch migration occurs is significantly more displacementcult than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would in turn facilitate the simulation and construction of more complex molecular devices.

The full paper is available from Nucleic Acids Research