By a News Reporter-Staff News Editor at Life Science Weekly -- Investigators publish new report on DNA Research. According to news reporting out of Oxford, United Kingdom, by NewsRx editors, research stated, "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 phenomenologically modeled, detailed biophysical understanding has remained elusive."
Our news journalists obtained a quote from the research from the University of Oxford, "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 investigate the thermodynamics of three-way branch migration. 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 additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics."
According to the news editors, the research concluded: "Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems."
For more information on this research see: On the biophysics and kinetics of toehold-mediated DNA strand displacement. Nucleic Acids Research, 2013;41(22):10641-10658. Nucleic Acids Research can be contacted at: Oxford Univ Press, Great Clarendon St, Oxford OX2 6DP, England. (Oxford University Press - www.oup.com/; Nucleic Acids Research - nar.oxfordjournals.org)
Our news journalists report that additional information may be obtained by contacting N. Srinivas, University of Oxford, Dept. of Chem, Phys & Theoret Chem Lab, Oxford OX1 3QZ, United Kingdom. Additional authors for this research include T.E. Ouldridge, P. Sulc, J.M. Schaeffer, B. Yurke, A.A. Louis, J.P.K. Doye and E. Winfree (see also DNA Research).
Keywords for this news article include: Oxford, Europe, Biophysics, DNA Research, United Kingdom
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