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Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications

Oxford University Press
Publication Date
  • Nar Methods Online
  • Engineering
  • Mathematics
  • Physics


OP-NARE130802 10641..10658 On the biophysics and kinetics of toehold-mediated DNA strand displacement Niranjan Srinivas1,*, Thomas E. Ouldridge2,*, Petr Sˇulc2, Joseph M. Schaeffer3, Bernard Yurke4, Ard A. Louis2, Jonathan P. K. Doye5 and Erik Winfree1,3,6,* 1Computation and Neural Systems, California Institute of Technology, Pasadena, CA 91125, USA, 2Rudolph Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, Oxford OX1 3NP, UK, 3Computer Science, California Institute of Technology, Pasadena, CA 91125, USA, 4Departments of Electrical and Computer Engineering, Materials Science and Engineering, Boise State University, ID83725, USA, 5Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK and 6Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA Received March 29, 2013; Revised July 18, 2013; Accepted August 14, 2013 ABSTRACT Dynamic DNA nanotechnology often uses toehold- mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomeno- logically modeled, detailed biophysical understand- ing has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally inves- tigate the thermodynamics of three-way branch mi- gration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower 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 addit

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