Bilayer-Spanning DNA Nanopores with Voltage-Switching between Open and Closed State

Abstract

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.

Stability and dynamics of membrane-spanning DNA nanopores

“…DNTs can be designed de novo with a wider range of architectures and functionalities than offered by protein nanopores. A number of DNT designs have been explored1819222324 and have been characterized functionally, both when reconstituted into artificial lipid bilayers22025 and when inserted into the membranes of cells26. Computational studies have been used to explore, for example, their conformational dynamics in relation to ion permeation2728.…”

Nanopore Sensing

“…248 A variety of DNA origami porin structures have been reported, and we have selectively included some representative designs herein. 84–88 …”

“…78–88 Moreover, integration of scanning probe techniques with nanopore platforms results in mobile nanopore sensors that can achieve localized analysis of a variety of surfaces and interfaces and, thus, provide numerous exciting opportunities in biophysics, cell biology, and material sciences.…”

Biomimetic Compartments Scaffolded by Nucleic Acid Nanostructures

“…A large‐diameter DNA nanopore, reported by the Simmel group, allowed the electrically driven translocation of ss‐ and dsDNA analytes . To regulate DNA nanopores, Göpfrich and co‐workers used voltage switch to open and close a DNA nanopore: a high voltage (≈100 mV) caused an electric‐field‐induced change of the DNA conformation and orientation thereby blocking the nanopore . A ligand‐controlled transporter was demonstrated by using DNA strand displacement to control the opening and closing of a DNA nanopore (Figure h).…”