Stability and dynamics of membrane-spanning DNA nanopores

Vishal Maingi, Jonathan R. Burns, Jaakko J. Uusitalo, Stefan Howorka (), Siewert J. Marrink and Mark S. P. Sansom ()
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Vishal Maingi: University of Oxford
Jonathan R. Burns: Institute of Structural Molecular Biology, University College London
Jaakko J. Uusitalo: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen
Stefan Howorka: Institute of Structural Molecular Biology, University College London
Siewert J. Marrink: Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen
Mark S. P. Sansom: University of Oxford

Nature Communications, 2017, vol. 8, issue 1, 1-12

Abstract: Abstract Recently developed DNA-based analogues of membrane proteins have advanced synthetic biology. A fundamental question is how hydrophilic nanostructures reside in the hydrophobic environment of the membrane. Here, we use multiscale molecular dynamics (MD) simulations to explore the structure, stability and dynamics of an archetypical DNA nanotube inserted via a ring of membrane anchors into a phospholipid bilayer. Coarse-grained MD reveals that the lipids reorganize locally to interact closely with the membrane-spanning section of the DNA tube. Steered simulations along the bilayer normal establish the metastable nature of the inserted pore, yielding a force profile with barriers for membrane exit due to the membrane anchors. Atomistic, equilibrium simulations at two salt concentrations confirm the close packing of lipid around of the stably inserted DNA pore and its cation selectivity, while revealing localized structural fluctuations. The wide-ranging and detailed insight informs the design of next-generation DNA pores for synthetic biology or biomedicine.

Date: 2017
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DOI: 10.1038/ncomms14784

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