Ionic Conductivity, Structural Deformation and Programmable Anisotropy of DNA Origami in Electric Field
Li, Chen Yu
Hemmig, Elisa A
American Chemical Society
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Li, C. Y., Hemmig, E. A., Kong, J., Yoo, J., Hernández-Ainsa, S., Keyser, U., & Aksimentiev, A. (2015). Ionic Conductivity, Structural Deformation and Programmable Anisotropy of DNA Origami in Electric Field. ACS Nano, 9 1420-1433. https://doi.org/10.1021/nn505825z
The DNA origami technique can enable functionalization of inorganic structures for singlemolecule electric current recordings. Experiments have shown that several layers of DNA molecules—a DNA origami plate— placed on top of a solid-state nanopore is permeable to ions. Here, we report a comprehensive characterization of the ionic conductivity of DNA origami plates by means of all-atom molecular dynamics (MD) simulations and nanocapillary electric current recordings. Using the MD method, we characterize the ionic conductivity of several origami constructs, revealing the local distribution of ions, the distribution of the electrostatic potential and contribution of different molecular species to the current. The simulations determine the dependence of the ionic conductivity on the applied voltage, the number of DNA layers, the nucleotide content and the lattice type of the plates. We demonstrate that increasing the concentration of Mg2+ ions makes the origami plates more compact, reducing their conductivity. The conductance of a DNA origami plate on top of a solid-state nanopore is determined by the two competing effects: bending of the DNA origami plate that reduces the current and separation of the DNA origami layers that increases the current. The latter is produced by the electro-osmotic flow and is reversible at the time scale of a hundred nanoseconds. The conductance of a DNA origami object is found to depend on its orientation, reaching maximum when the electric field aligns with the direction of the DNA helices. Our work demonstrates feasibility of programming the electrical properties of a self-assembled nanoscale object using DNA.
DNA nanotechnology, nanopore, molecular dynamics, FRET, DNA sequencing, anisotropic conductivity, self-assembly
C.Y.L., J.Y. and A.A. were supported in part by the grants from the National Science Foundation (DMR-0955959, PHY-1430124 and ECC-1227034), and the National Institutes of Health (R01- HG007406). E.A.H. acknowledges support from Schweizerische Studienstiftung (Swiss Study Foundation) and Gonville & Caius College. S.H.A. acknowledges support from a Herchel Smith postdoctoral fellowship. J.K. acknowledges support from Chinese Scholarship Council and Cambridge Overseas Trust. UFK was supported by an ERC starting grant (PassMembrane, 261101). The authors gladly acknowledge supercomputer time provided through XSEDE Allocation Grant MCA05S028 and the Blue Waters Sustained Petascale Computer System (UIUC).
European Research Council (261101)
External DOI: https://doi.org/10.1021/nn505825z
This record's URL: https://www.repository.cam.ac.uk/handle/1810/247442