The re-engineering of biological protein pore scaffolds is a successful approach 12, 13 which has led, for example, to components for label-free biosensing [14][15][16][17] and portable genome sequencing 18, 19 . Creating completely new architectures with synthetic materials can offer greater design freedom and translate into more functions and applications [20][21][22][23][24][25][26] . A key challenge in the de-novo design of membrane channels is, however, to achieve an atomistically defined structure of predictable nanomechanical properties 3 because the traditional building blocks of polypeptides and organic polymers are highly flexible 2, 4 . DNA, by contrast, is known to fold into predetermined structures and is able to meet most the criteria required for creating synthetic channels [27][28][29][30][31][32][33] . Indeed, membrane-spanning DNA nanopores have been very 3" "recently built to feature a central hollow barrel which is open at both ends [5][6][7][8][9] . The barrel is composed of six hexagonally arranged, interconnected DNA duplexes that enclose a 2 nm-wide lumen with a length ranging from 17 to 42 nm. The innovative step was the inclusion of hydrophobic anchors 5, 7, 9 to insert the negatively charged pores into the hydrophobic bilayer membrane. While of novelty and considerable interest 34, 35 , the barrels do not exploit the full design flexibility offered by DNA nanotechnology and do not exhibit the higher-order functions of ion channels which can bind ligands, respond by nanomechanical opening, and select cargo for transport.We used the simple geometric shape of an open barrel as a starting point to rationally design a nanodevice that can regulate the flux of matter across a bilayer membrane.The aim of the first design step was reduce the pore height to approximate the bilayer thickness 36 and thereby avoid structural flexibility and potential leakiness 37 . A pore height of 7 nm (Fig. 1a, NP) was achieved using a six-helix-bundle architecture with six concatenated DNA strands, each of which connects two neighboring duplexes at their termini (Fig. 1b). This connectivity is drastically simpler than classical origami 38 based on cadnano software where oligonucleotides run through multiple duplexes and cause a minimum height of approx. 15 nm 5, 38 . Our design with connections at the duplex ends also avoids traditional internal cross-overs that cause structural deviations from parallel aligned duplexes 39 .The second step was to design a molecular gate that closes one barrel entrance but reopens the channel upon binding of a ligand. A origami plate has been previously used as a controllable lid for a DNA origami box 32 . But our molecular models supported by biophysical studies 37 suggest that the plate might be structurally too flexible and leaky 4" "to form a tight seal. As a solution, we designed a nanodevice that features in its closed state, NP-C (Fig. 1c), a simple "lock" strand which is bound closely to the entrance by hybridization to two docking sites. The sites are formed by th...

DNA nanotechnology excels at rationally designing bottom-up structures that can functionally replicate naturally occurring proteins. Here we describe the design and generation of a stable DNA-based nanopore that structurally mimics the amphiphilic nature of protein pores and inserts into bilayers to support a steady transmembrane flow of ions. The pore carries an outer hydrophobic belt comprised of small chemical alkyl groups which mask the negatively charged oligonucleotide backbone. This modification overcomes the otherwise inherent energetic mismatch to the hydrophobic environment of the membrane. By merging the fields of nanopores and DNA nanotechnology, we expect that the small membrane-spanning DNA pore will help open up the design of entirely new molecular devices for a broad range of applications including sensing, electric circuits, catalysis, and research into nanofluidics and controlled transmembrane transport.

Holding tight: An artificial membrane nanopore assembled from DNA oligonucleotides carries porphyrin tags (red), which anchor the nanostructure into the lipid bilayer. The porphyrin moieties also act as fluorescent dyes to aid the microscopic visualization of the DNA nanopore.

Membrane-spanning nanopores from folded DNA are a recent example of biomimetic man-made nanostructures that can open up applications in biosensing, drug delivery, and nanofluidics. In this report, we generate a DNA nanopore based on the archetypal six-helix-bundle architecture and systematically characterize it via single-channel current recordings to address several fundamental scientific questions in this emerging field. We establish that the DNA pores exhibit two voltage-dependent conductance states. Low transmembrane voltages favor a stable high-conductance level, which corresponds to an unobstructed DNA pore. The expected inner width of the open channel is confirmed by measuring the conductance change as a function of poly(ethylene glycol) (PEG) size, whereby smaller PEGs are assumed to enter the pore. PEG sizing also clarifies that the main ion-conducting path runs through the membrane-spanning channel lumen as opposed to any proposed gap between the outer pore wall and the lipid bilayer. At higher voltages, the channel shows a main low-conductance state probably caused by electric-field-induced changes of the DNA pore in its conformation or orientation. This voltage-dependent switching between the open and closed states is observed with planar lipid bilayers as well as bilayers mounted on glass nanopipettes. These findings settle a discrepancy between two previously published conductances. By systematically exploring a large space of parameters and answering key questions, our report supports the development of DNA nanopores for nanobiotechnology.

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.

Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

Chemistry plays a crucial role in creating synthetic analogues of biomacromolecular structures. Of particular scientific and technological interest are biomimetic vesicles that are inspired by natural membrane compartments and organelles but avoid their drawbacks, such as membrane instability and limited control over cargo transport across the boundaries. In this study, completely synthetic vesicles were developed from stable polymeric walls and easy‐to‐engineer membrane DNA nanopores. The hybrid nanocontainers feature selective permeability and permit the transport of organic molecules of 1.5 nm size. Larger enzymes (ca. 5 nm) can be encapsulated and retained within the vesicles yet remain catalytically active. The hybrid structures constitute a new type of enzymatic nanoreactor. The high tunability of the polymeric vesicles and DNA pores will be key in tailoring the nanocontainers for applications in drug delivery, bioimaging, biocatalysis, and cell mimicry.

Synthetically replicating key biological processes requires the ability to puncture lipid bilayer membranes and to remodel their shape. Recently developed artificial DNA nanopores are one possible synthetic route due to their ease of fabrication. However, an unresolved fundamental question is how DNA nanopores bind to and dynamically interact with lipid bilayers. Here we use single-molecule fluorescence microscopy to establish that DNA nanopores carrying cholesterol anchors insert via a two-step mechanism into membranes. Nanopores are furthermore shown to locally cluster and remodel membranes into nanoscale protrusions. Most strikingly, the DNA pores can function as cytoskeletal components by stabilizing autonomously formed lipid nanotubes. The combination of membrane puncturing and remodeling activity can be attributed to the DNA pores’ tunable transition between two orientations to either span or co-align with the lipid bilayer. This insight is expected to catalyze the development of future functional nanodevices relevant in synthetic biology and nanobiotechnology.