Stability and dynamics of membrane-spanning DNA nanopores

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

doi:10.1038/ncomms14784

Cited by 71 publications

(83 citation statements)

References 80 publications

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“…1c). In analogy to small DNA pores 44–46 , the mechanism and energetics for membrane insertion of the large pore most likely involves a first step that tethers the pore to the bilayer without puncturing, possibly in a non-perpendicular orientation to the membrane. In a second step, the pore reorients itself to span the lipid bilayer.…”

Section: Resultsmentioning

confidence: 99%

Synthetic protein-conductive membrane nanopores built with DNA

et al. 2019

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Nanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.

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Section: Resultsmentioning

confidence: 99%

Synthetic protein-conductive membrane nanopores built with DNA

et al. 2019

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“…For example, DNA-based artificial cytoskeletons can be used to shape membrane vesicles. 9–12 Similarly, DNA-based pores can be anchored to puncture the membrane 13–18 for applications such as bio-sensing 19–21 or controlled drug release. 17 Membrane-anchored DNA nanostructures can also probe membrane interaction forces 22 or alter the composition of a lipid bilayer membrane.…”

Section: Introductionmentioning

confidence: 99%

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes

et al. 2018

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Lipid-anchored DNA can attach functional cargo to bilayer membranes in DNA nanotechnology, synthetic biology, and cell biology research. To optimize DNA anchoring, an understanding of DNA-membrane interaction in terms of binding strength, extent, and structural dynamics is required. Here we use experiments and molecular dynamics (MD) simulations to determine how membrane binding of cholesterol-modified DNA depends on electrostatic and steric factors involving lipid head-group charge, duplexed or single stranded DNA, and buffer composition. The experiments distinguish between free and membrane vesicle-bound DNA, and thereby reveal the surface density of anchored DNA and its binding affinity, something which had previously not been known. The Kd values range from 8.5 ± 4.9 to 466 ± 134 uM whereby negatively charged head-groups led to weak binding due to the electrostatic repulsion to the negatively charged DNA. Atomistic molecular dynamics simulations explain the findings and elucidate the dynamic nature of anchored DNA such as the mushroom-like conformation of single stranded DNA hovering over the bilayer surface in contrast to a straight-up conformation of double stranded DNA. The biophysical insight into binding strength to membranes as well as the molecular accessibility of DNA for hybridization to molecular cargo is expected to facilitate creating biomimetic DNA versions of natural membrane nanopores and cytoskeletons for research and nanobiotechnology.

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“…Naturally occurring ion transporters are proteins, whereas artificial ones can be made in different ways, usually from peptides, 9 macrocyclic organic compounds, 10 , 11 or appropriately functionalized polymers including DNA. 12 − 15 Substances that affect ion transport or its regulation play important roles in both basic research and drug development. Carborane-capped gold nanoparticles 16 in the 1–4 nm size range are known for their ability to store and release cationic charge that is counterbalanced by excess electrons in the metal core.…”

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confidence: 99%

Ion Transport across Biological Membranes by Carborane-Capped Gold Nanoparticles

et al. 2017

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Carborane-capped gold nanoparticles (Au/carborane NPs, 2–3 nm) can act as artificial ion transporters across biological membranes. The particles themselves are large hydrophobic anions that have the ability to disperse in aqueous media and to partition over both sides of a phospholipid bilayer membrane. Their presence therefore causes a membrane potential that is determined by the relative concentrations of particles on each side of the membrane according to the Nernst equation. The particles tend to adsorb to both sides of the membrane and can flip across if changes in membrane potential require their repartitioning. Such changes can be made either with a potentiostat in an electrochemical cell or by competition with another partitioning ion, for example, potassium in the presence of its specific transporter valinomycin. Carborane-capped gold nanoparticles have a ligand shell full of voids, which stem from the packing of near spherical ligands on a near spherical metal core. These voids are normally filled with sodium or potassium ions, and the charge is overcompensated by excess electrons in the metal core. The anionic particles are therefore able to take up and release a certain payload of cations and to adjust their net charge accordingly. It is demonstrated by potential-dependent fluorescence spectroscopy that polarized phospholipid membranes of vesicles can be depolarized by ion transport mediated by the particles. It is also shown that the particles act as alkali-ion-specific transporters across free-standing membranes under potentiostatic control. Magnesium ions are not transported.

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Stability and dynamics of membrane-spanning DNA nanopores

Cited by 71 publications

References 80 publications

Synthetic protein-conductive membrane nanopores built with DNA

Synthetic protein-conductive membrane nanopores built with DNA

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes

Ion Transport across Biological Membranes by Carborane-Capped Gold Nanoparticles

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