Self-Assembled DNA Nanopores That Span Lipid Bilayers

Burns, Jonathan R.; Stulz, Eugen; Howorka, Stefan

doi:10.1021/nl304147f

Cited by 277 publications

(396 citation statements)

References 74 publications

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“…[22] The AFM-derived length and width of 13.0 AE 2.7 nm and 6.9 AE 1.5 nm (fullwidth-at-half-maximum), respectively, were in good agreement with the theoretical dimensions (14 nm and 5.5 nm). The experimental dimensions reported here are smaller than of similarly sized pores of previous studies [18,19] because the present AFM read-out examined densely packed barrels (Figure 2 c) which is different to the isolated structures of the preceding reports. We investigated whether NP-EP interacts with lipid bilayers by monitoring the UV-melting profiles of the DNA.…”

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confidence: 81%

Back Cover: Membrane‐Spanning DNA Nanopores with Cytotoxic Effect (Angew. Chem. Int. Ed. 46/2014)

Burns¹,

Al‐Juffali²,

Janes³

et al. 2014

Angew Chem Int Ed

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Self-assembled DNA nanostructures with chemistry-enabled functionality are of great interest in nanobiotechnology. Herein, chemically modified DNA nanopores are designed to puncture cellular membranes and cause cytotoxicity. The nanopores are assembled from DNA oligonucleotides to form a 2 nm-high hydrophobic belt at one terminus. The belt is composed of charge-neutralized ethyl phosphorothioate (EP) groups which are required to decrease cell viability. The mode by which the pores achieve cell killing is elucidated with confocal microscopy. This study is the first to describe the interaction of DNA nanopores with cells. The work lays the foundation for the future development of cytotoxic agents with cancer type-specificity.Chemistry can play an important role in expanding the functional repertoire of DNA nanostructures. [1,2] Designed nanomaterials have been developed by equipping DNA scaffolds [2,3] with chemical linkages to spatially arrange nanoparticles, [4] fluorophores, [5] or proteins.[6] These DNA nanostructures have been mostly applied for cell-free applications but not for cell biology even though the latter field benefits from nanomaterials as demonstrated with canonical nucleic acids. [7,8] One class of chemically modified DNA nanostructures of potential in cell biology are membrane-spanning DNA nanopores. In general, engineered nanopores that facilitate transmembrane flux [9] can be used for cell permeabilization, drug delivery, [10] but also biosensing. [11][12][13] In the latter, label-free analytical strategy, individual molecules passing or binding inside a nanoscale pore are detected based on the associated changes in the ionic pore current. A wide range of analytes can be sensed, [11,14] and DNA can be sequenced by threading individual strands through the pore. [12,15] Nanopores have traditionally been constructed with re-engineered or de-novo protein scaffolds, or organic synthetic building blocks.[16]Nanopores composed of folded DNA are the most recent category. [17][18][19][20] Formed either by scaffold and staple strands [17] or short oligonucleotides, [18,19] the highly negatively charged DNA nanopores insert into hydrophobic bilayer membranes by chemical lipid anchors, whereby cholesterol, [17] porphyrin, [19] and a belt of EP tags [18] were successfully tested. In light of their established ability to span reconstituted membranes, we postulated that the pores could be adapted and exploited to puncture biological cell membranes. Our interest was spiked by the prospect of rationally designing DNA nanostructures for cell biological applications, such as gene transfection, drug permeabilization or targeted killing of diseased cells.Here we examine whether a membrane-spanning DNA nanopore can interact with cancer cells and potentially trigger cell death (Figure 1 a and b). Our nanopore was composed of a bundle of six DNA duplexes folded from six DNA strands (see Figure S1 in the Supporting Information). The hollow nanobarrel has a channel width of approximately 2 nm, an Figure 1. A membrane-...

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confidence: 81%

Back Cover: Membrane‐Spanning DNA Nanopores with Cytotoxic Effect (Angew. Chem. Int. Ed. 46/2014)

Burns¹,

Al‐Juffali²,

Janes³

et al. 2014

Angew Chem Int Ed

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“…11) [136,137]. Langecker and co-workers designed a DNA origami membrane plug with a central channel that penetrates through the membrane [137].…”

Section: B Trans-membrane Channelsmentioning

confidence: 99%

“…11 E,F) [136]. On this occasion, targeted chemical modification of the DNA backbones is used to insert a ring of hydrophobic ethyl groups that match the hydrophobic thickness of the lipid bilayer.…”

Section: B Trans-membrane Channelsmentioning

confidence: 99%

Application of nucleic acid–lipid conjugates for the programmable organisation of liposomal modules

Beales

Vanderlick

2014

Advances in Colloid and Interface Science

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“…DNA has been used to build a variety of nanoscale structures including rotaxanes, [1][2][3] catenenes, 4 reconfigurable three-dimensional objects, 5 biomimetic systems [6][7][8] and chemically fuelled molecular motors. [9][10][11] Proteins possess larger chemical diversity than nucleic acids and are, therefore, attractive building elements in nanotechnology.…”

Section: Introductionmentioning

confidence: 99%

A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore

2015

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Rotaxanes, pseudorotaxanes and catenanes are supramolecular complexes with potential use in nanomachinery, molecular computing and single-molecule studies. Here we constructed a protein rotaxane in which a polypeptide thread is encircled by a Cytolysin A (ClyA) nanopore and capped by two proteins stoppers. The rotaxane could be switched between two states. At low negative applied potentials (<−50 mV) one of the protein stoppers resided inside the nanopore indefinitely. Under this configuration the rotaxane prevents the diffusion of protein molecules across the lipid bilayer and provides a useful platform for single-molecule analysis. High negative applied potentials (−100 mV) dismantled the interlocked rotaxane system by the forceful translocation of the protein stopper, allowing new proteins to be trapped inside or transported across the nanopore. The observed voltage threshold for the translocation of the protein stopper through the nanopore related well to the biphasic voltage dependence of the residence time measured for the freely diffusing protein stopper. We propose a model in which molecules translocate through a nanopore when the average dwell time decreases with the applied potential.

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Self-Assembled DNA Nanopores That Span Lipid Bilayers

Cited by 277 publications

References 74 publications

Back Cover: Membrane‐Spanning DNA Nanopores with Cytotoxic Effect (Angew. Chem. Int. Ed. 46/2014)

Back Cover: Membrane‐Spanning DNA Nanopores with Cytotoxic Effect (Angew. Chem. Int. Ed. 46/2014)

Application of nucleic acid–lipid conjugates for the programmable organisation of liposomal modules

A Protein Rotaxane Controls the Translocation of Proteins Across a ClyA Nanopore

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