Maingi, V;
Burns, JR;
Uusitalo, JJ;
Howorka, S;
Marrink, SJ;
Sansom, MSP;
(2017)
Stability and dynamics of membrane-spanning DNA nanopores.
NATURE COMMUNICATIONS
, 8
, Article 14784. 10.1038/ncomms14784.
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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.
| Type: | Article |
|---|---|
| Title: | Stability and dynamics of membrane-spanning DNA nanopores |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1038/ncomms14784 |
| Publisher version: | http://dx.doi.org/10.1038/ncomms14784 |
| Additional information: | This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
| Keywords: | Science & Technology, Multidisciplinary Sciences, Science & Technology - Other Topics, MOLECULAR-DYNAMICS, ION CHANNELS, FORCE-FIELD, CARBON NANOTUBES, WATER PERMEATION, LIPID-BILAYER, SIMULATIONS, PROTEINS, CONDUCTANCE, TRANSPORT |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > UCL BEAMS UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences UCL > Provost and Vice Provost Offices > UCL BEAMS > Faculty of Maths and Physical Sciences > Dept of Chemistry |
| URI: | https://discovery.ucl.ac.uk/id/eprint/1549793 |
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