IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v8y2017i1d10.1038_ncomms14784.html
   My bibliography  Save this article

Stability and dynamics of membrane-spanning DNA nanopores

Author

Listed:
  • 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)

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.

Suggested Citation

  • Vishal Maingi & Jonathan R. Burns & Jaakko J. Uusitalo & Stefan Howorka & Siewert J. Marrink & Mark S. P. Sansom, 2017. "Stability and dynamics of membrane-spanning DNA nanopores," Nature Communications, Nature, vol. 8(1), pages 1-12, April.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14784
    DOI: 10.1038/ncomms14784
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms14784
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms14784?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Le Luo & Swathi Manda & Yunjeong Park & Busra Demir & Jesse Sanchez & M. P. Anantram & Ersin Emre Oren & Ashwin Gopinath & Marco Rolandi, 2023. "DNA nanopores as artificial membrane channels for bioprotonics," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    2. Katya Ahmad & Abid Javed & Conor Lanphere & Peter V. Coveney & Elena V. Orlova & Stefan Howorka, 2023. "Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_ncomms14784. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.