Publication

Stability and dynamics of membrane-spanning DNA nanopores

Maingi, V., Burns, J. R., Uusitalo, J. J., Howorka, S., Marrink, S. J. & Sansom, M. S. P., 2017, In : Nature Communications. 8, p. 1-12 12 p., 14784.

Research output: Contribution to journalArticleAcademicpeer-review

  • Vishal Maingi
  • Jonathan R Burns
  • Jaakko J Uusitalo
  • Stefan Howorka
  • Siewert J Marrink
  • Mark S P Sansom

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.

Original languageEnglish
Article number14784
Pages (from-to)1-12
Number of pages12
JournalNature Communications
Volume8
Publication statusPublished - 2017

    Keywords

  • stability, molecular dynamics simulations, DNA nanopores, coarse-graine

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