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1.D.46 The DNA Nanopore (DnaNP) Family

DNA Nanopores (DNPs) consist of biological channels embedded in cell membranes that regulate ionic transport by responding to external stimuli such as pH, voltage, and molecular binding and could theoretically be involved in biosensing, drug delivery and ionic circuit construction (Langecker et al. 2012; Langecker et al. 2014). Buchsbaum et al. 2014 described nanopores that can simultaneously respond to pH and transmembrane potential changes. DNA oligomers containing protonatable A and C bases are attached at the narrow opening of an asymmetric nanopore. Lowering the pH to 5.5 causes the positively charged DNA molecules to bind to other strands with negative backbones, thereby creating an electrostatic mesh that closes the pore to unprecedentedly high resistances of several tens of gigaohms. At neutral pH values, voltage switching causes the isolated DNA strands to undergo nanomechanical movement, as seen by a reversible current modulation. Buchsbaum et al. 2014 provided evidence that the pH-dependent reversible closing mechanism is robust and applicable to nanopores with inner pore diameters of up to 14 nm. The concept of creating an electrostatic mesh may be applied to other organic polymers. Some DNPs exhibit voltage switching between open (low voltage) and closed (high voltage) states (Seifert et al. 2014).  The main ion conducting path has been shown to run through the membrane-spanning channel lumen (Seifert et al. 2014).

Self-assembled DNA nanostructures have been used to create man-made transmembrane channels in lipid bilayers. A DNA-tile structure with a subnanometer channel and cholesterol-tags for membrane anchoring has an outer diameter of 5 nm and a molecular weight of 45 kDa, the dimensions of synthetic nanostructure comparable to biological ion channels (Göpfrich et al. 2015). Because of its simple design, the structure self-assembles within a minute, making its creation scalable for applications in biology. Ionic current recordings demonstrate that the tile structures enable ion conduction through lipid bilayers and show gating and voltage-switching behavior.  DNA-based membrane channels have openings much smaller than that of the archetypical six-helix bundle. 

The structures of DNA channels and their conductance mechanisms were studied by Yoo and Aksimentiev 2015. They reported the results of molecular dynamics simulations that characterized the biophysical properties with atomic precision. While remaining stable, the local structures of the channels undergo considerable fluctuations, departing from the idealized design. The transmembrane ionic current flows both through the central pore of the channel as well as along the DNA walls and through the gaps in the DNA structure. They found that conductance depends on the membrane tension, making them suitable for force sensing applications. Electro-osmosis governs drug-like molecule transport (Aksimentiev 2015). 

Ion conduction can be induced by a single DNA duplex that lacks a hollow central channel. Decorated with six porpyrin-tags, the duplex is designed to span lipid membranes. Combining electrophysiology measurements with all-atom molecular dynamics simulations, Göpfrich et al. 2016 elucidated the microscopic conductance pathway. Ions flow at the DNA-lipid interface as the lipid head groups tilt toward the amphiphilic duplex forming a toroidal pore filled with water and ions. Ionic current traces produced by the DNA-lipid channel show well-defined insertion steps, closures, and gating similar to those observed for traditional protein channels or synthetic pores. Ionic conductances obtained through simulations and experiments are in excellent quantitative agreement. The conductance mechanism with the smallest possible DNA-based ion channel offers a route to design a new class of synthetic ion channels with maximal simplicity. 

Göpfrich et al. 2016 used DNA to build the largest synthetic pore in a lipid membrane to date, approaching the dimensions of the nuclear pore complex and increasing the pore-area and the conductance tenfold compared to previous man-made channels. In their design, nineteen cholesterol-tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane. Confocal imaging and ionic current recordings revealed spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance. All-atom molecular dynamics simulations characterized the conductance mechanism at the atomic level and independently confirmed the DNA porins' large ionic conductance.  DNA nanopores are used as probes for sensing in addition to using substrates for sequencing (Liu and Wu 2016). 

DNA-based nanopores, synthetic biomolecular membrane pores whose geometry and chemical functionality can be tuned using the tools of DNA nanotechnology, make them promising molecular devices for applications in single-molecule biosensing and synthetic biology. Krishnan et al. 2016 introduced a large DNA membrane channel with an ≈4 nm diameter pore, which has stable electrical properties and spontaneously inserts into flat lipid bilayer membranes. Membrane incorporation is facilitated by a large number of hydrophobic functionalizations or, alternatively, streptavidin linkages between biotinylated channels and lipids. The channel displays an Ohmic conductance of ≈3 nS, consistent with its size, and allows electrically driven translocation of single-stranded and double-stranded DNA analytes. Using confocal microscopy and a dye influx assay, Krishnan et al. 2016 demonstrated the spontaneous formation of membrane pores in giant unilamellar vesicles. Pores can be created both in an outside-in and an inside-out configuration.

References associated with 1.D.46 family:

Buchsbaum, S.F., G. Nguyen, S. Howorka, and Z.S. Siwy. (2014). DNA-modified polymer pores allow pH- and voltage-gated control of channel flux. J. Am. Chem. Soc. 136: 9902-9905. 24992159
Gopfrich K., Zettl T., Meijering AE., Hernandez-Ainsa S., Kocabey S., Liedl T. and Keyser UF. (2015). DNA-Tile Structures Induce Ionic Currents through Lipid Membranes. Nano Lett. 15(5):3134-8. 25816075
Göpfrich, K., C.Y. Li, I. Mames, S.P. Bhamidimarri, M. Ricci, J. Yoo, A. Mames, A. Ohmann, M. Winterhalter, E. Stulz, A. Aksimentiev, and U.F. Keyser. (2016). Ion Channels Made from a Single Membrane-Spanning DNA Duplex. Nano Lett. [Epub: Ahead of Print] 27324157
Göpfrich, K., C.Y. Li, M. Ricci, S.P. Bhamidimarri, J. Yoo, B. Gyenes, A. Ohmann, M. Winterhalter, A. Aksimentiev, and U.F. Keyser. (2016). Large-Conductance Transmembrane Porin Made from DNA Origami. ACS Nano. [Epub: Ahead of Print] 27504755
Krishnan, S., D. Ziegler, V. Arnaut, T.G. Martin, K. Kapsner, K. Henneberg, A.R. Bausch, H. Dietz, and F.C. Simmel. (2016). Molecular transport through large-diameter DNA nanopores. Nat Commun 7: 12787. 27658960
Langecker, M., V. Arnaut, J. List, and F.C. Simmel. (2014). DNA nanostructures interacting with lipid bilayer membranes. Acc Chem Res 47: 1807-1815. 24828105
Langecker, M., V. Arnaut, T.G. Martin, J. List, S. Renner, M. Mayer, H. Dietz, and F.C. Simmel. (2012). Synthetic lipid membrane channels formed by designed DNA nanostructures. Science 338: 932-936. 23161995
Liu, L. and H.C. Wu. (2016). DNA-Based Nanopore Sensing. Angew Chem Int Ed Engl. [Epub: Ahead of Print] 27676313
Seifert A., Gopfrich K., Burns JR., Fertig N., Keyser UF. and Howorka S. (2015). Bilayer-spanning DNA nanopores with voltage-switching between open and closed state. ACS Nano. 9(2):1117-26. 25338165
Yoo J. and Aksimentiev A. (2015). Molecular Dynamics of Membrane-Spanning DNA Channels: Conductance Mechanism, Electro-Osmotic Transport, and Mechanical Gating. J Phys Chem Lett. 6(23):4680-7. 26551518