Single-ion channel recordings on quartz substrates

Measuring trapped DNA at the liquid-air interface for enhanced single molecule sensing

Nanopore sensing is a promising tool with widespread application in single-molecule detection. Borosilicate glass nanopores are a viable alternative to other solid-state nanopores due to low noise and cost-efficient fabrication. For dielectric materials, including borosilicate glass, the capacitive noise is one of the major contributors to noise, which depends on the wall thickness and the surface area submerged in an ionic solution. Here, we investigated the root mean square (I_RMS) noise and ionic conductance for borosilicate nanopores in different depths (i.e., tip submersion depth) ranging from the solution surface (assumed to be zero) to 5000 μm. Our findings demonstrate a decrease in I_RMS noise as the pipette moves toward the surface. We further demonstrate that borosilicate nanopores can detect single lambda DNA (λ-DNA) molecules with a high signal-to noise ratio close to the liquid-air interface. Specifically, our results indicate a higher signal to noise ratio as the submersion depth is reduced owing to the reduced surface area and thus capacitive noise. Further, our experimental results show higher DNA capture frequency at the air-water interface due to a combined effect of evaporation and an evaporation-induced thermal gradient at the surface. Therefore, our findings demonstrate that borosilicate glass nanopores are suitable for studying interfacial concentration gradients of molecules, specifically DNA, with a higher signal to noise.

A low-noise silicon nitride nanopore device on a polymer substrate

We report a novel low-noise nanopore device employing a polymer substrate. The Si substrate of a fabricated Si-substrate-based silicon nitride (Si3N4) membrane was replaced with a polymer substrate. As such, laser machining was used to make a micro-size hole through the polyimide (PI) substrate, and a thin Si3N4 membrane was then transferred onto the PI substrate. Finally, a nanopore was formed in the membrane using a transmission electron microscope for detection of biomolecules. Compared to the Si-substrate-based device, the dielectric noise was greatly reduced and the root-mean-square noise level was decreased from 146.7 to 5.4 pA. Using this device, the translocation of double-strand deoxyribonucleic acid (DNA) was detected with a high signal/noise (S/N) ratio. This type of device is anticipated to be available for future versatile sequencing technologies.

A low-noise solid-state nanopore platform based on a highly insulating substrate

A solid-state nanopore platform with a low noise level and sufficient sensitivity to discriminate single-strand DNA (ssDNA) homopolymers of poly-A40 and poly-T40 using ionic current blockade sensing is proposed and demonstrated. The key features of this platform are (a) highly insulating dielectric substrates that are used to mitigate the effect of parasitic capacitance elements, which decrease the ionic current RMS noise level to sub-10 pA and (b) ultra-thin silicon nitride membranes with a physical thickness of 5 nm (an effective thickness of 2.4 nm estimated from the ionic current) are used to maximize the signal-to-noise ratio and the spatial depth resolution. The utilization of an ultra-thin membrane and a nanopore diameter as small as 1.5 nm allow the successful discrimination of 40 nucleotide ssDNA poly-A40 and poly-T40. Overall, we demonstrate that this platform overcomes several critical limitations of solid-state nanopores and opens the door to a wide range of applications in single-molecule-based detection and analysis.

Dual-pore glass chips for cell-attached single-channel recordings

While high-throughput planar patch-clamp instruments are now established to perform whole-cell recordings for drug screening, the conventional micropipette-based approach remains the gold standard for performing cell-attached single-channel recordings. Generally, planar platforms are not well-suited for such studies due to excess noise resulting from low seal resistances and the use of substrates with poor dielectric properties. Since these platforms tend to use the same pore to position a cell by suction and establish a seal, biological debris from the cell suspension can contaminate the pore surface prior to seal formation, reducing the seal resistance. Here, femtosecond laser ablation was used to fabricate dual-pore glass chips optimized for use in cell-attached single-channel recordings that circumvent this problem by using different pores to position a cell and to establish a seal. This dual-pore design also permitted the use of a relatively small patch aperture (D ~ 150 to 300 nm) that is better-suited for establishing high-resistance seals than the micropores used typically in planar patch-clamp setups (D ~ 1 to 2 μm) without compromising the ability of the device to position a cell. Taking advantage of the high seal resistances and low capacitive and dielectric noise realized using glass substrates, patch-clamp experiments with these dual-pore chips consistently achieved high seal resistances (rate of gigaseal formation = 61%, mean seal resistance = 53 GΩ), maintained gigaseals for prolonged durations (up to 6 hours), achieved RMS noise values as low as 0.46 pA at 5 kHz bandwidth, and enabled single-channel recordings in the cell-attached configuration that are comparable to those obtained by conventional patch-clamp.

Ultra-stable glass microcraters for on-chip patch clamping

Dual-sided laser ablation is used to form glass microcraters commensurate with the size of a cell. These microcraters allow for ultra-stable, low noise recordings of planar patch-clamped cells.

Rapid fabrication and piezoelectric tuning of micro- and nanopores in single crystal quartz

We outline the fabrication of piezoelectric through-pores in crystalline quartz using a rapid micromachining process, and demonstrate piezoelectric deformation of the pore. The single-step fabrication technique combines ultraviolet (UV) laser irradiation with a thin layer of absorbing liquid in contact with the UV-transparent quartz chip. The effects of different liquid media are shown. We demonstrate that small exit pores, with diameters nearing the 193 nm laser wavelength and with a smooth periphery, can be achieved in 350 μm thick quartz wafers. Special crater features centring on the exit pores are also fabricated, and the depth of these craters are tuned. Moreover, by applying a voltage bias across the thickness of this piezoelectric wafer, we controllably contract and expand the pore diameter. We also provide a sample application of this device by piezoelectrically actuating alamethicin ion channels suspended over the deformable pore.

Mechanical actuation of ion channels using a piezoelectric planar patch clamp system

High-throughput screening of ion channels is now possible with the advent of the planar patch clamp system. This system drastically increases the number of ion channels that can be studied, as multiple ion channel experiments can now be conducted in parallel. However, due to tedious, usually pressure-driven mechanotransduction techniques, there has been a slow integration of this technology into the field of mechanosensitive ion channels. By implementing a piezoelectric quartz substrate into a planar patch clamp system, we show that the patch clamp substrate itself can be used to mechanically actuate ion channels. The piezoelectric substrate transduces an external, applied electric field into a mechanical tension, so precise actuation of the membrane can be accomplished. By applying this electric field only to the outer edges of the substrate, no ulterior electric field is created in the vicinity of the membrane during actuation. Further, with resonant frequencies ranging from 1 kHz to 200 MHz, quartz substrates can be used to apply a wide range of time-varying tensions to cell membranes. This will allow for new and instructive investigations into the dynamic mechanotransductive properties of ion channels.