Wafer-scale fabrication of fused silica chips for low-noise recording of resistive pulses through nanopores

Abstract

This paper presents a maskless method to manufacture fused silica chips for low-noise resistivepulse sensing. The fabrication includes wafer-scale density modification of fused silica with a femtosecond-pulsed laser, low-pressure chemical vapor deposition (LPVCD) of silicon nitride (SiN x ) and accelerated chemical wet etching of the laser-exposed regions. This procedure leads to a freestanding SiN x window, which is permanently attached to a fused silica support chip and the resulting chips are robust towards Piranha cleaning at ∼80°C. After parallel chip manufacturing, we created a single nanopore in each chip by focused helium-ion beam or by controlled breakdown. Compared to silicon chips, the resulting fused silica nanopore chips resulted in a four-fold improvement of both the signal-to-noise ratio and the capture rate for signals from the translocation of IgG 1 proteins at a recording bandwidth of 50 kHz. At a bandwidth of ∼1 MHz, the noise from the fused silica nanopore chips was three-to six-fold reduced compared to silicon chips. In contrast to silicon chips, fused silica chips showed no laser-induced current noise-a significant benefit for experiments that strive to combine nanopore-based electrical and optical measurements.

Estimation of Shape, Volume, and Dipole Moment of Individual Proteins Freely Transiting a Synthetic Nanopore

“…In addition, dipole moment is an excellent protein descriptor that is orthogonal to protein volume and shape, such that simultaneous quantification of these three parameters in sub-millisecond time frames of unmodified proteins in solution may enable plug-and-play benchtop protein analysis systems that characterize and count single proteins. The approach introduced here can likely be optimized: ongoing improvements in SNR will reduce the spread in parameter estimates, − and further increases in recording bandwidth through improved CMOS current amplifiers will increase event capture rates, resolve larger fractions of t d distributions, and monitor information about protein rotation and shape at smaller time steps. Each of these improvements will further reduce the uncertainty of nanopore-based characterization of single proteins.…”

Devices for Nanoscale Guiding of DNA through a 2D Nanopore

“…Specifically, identical nucleotides will produce a range of current fluctuations during a given measurement. Some of this is due to system noise (from the pore, chip, and amplifier), − which can be solved by increasing SNR. However, molecular dynamics simulations indicate that different orientations of nucleotides within a nanopore can produce a distribution of current modulations greater than those produced by the steric differences between different nucleotides .…”

From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena

“…If the membrane resistance is lower than the pore resistance, it will cause the current to preferentially flow through the substrate material bypassing the nanopore. Therefore, as discussed in Section 2, the pore for transport measurements must be built from high-resistance materials such as intrinsic silicon, fused glass chips, [133,134] or conical shaped glass nano-capillaires. [48] Besides preparing the sample, further difficulties arise with accurate measurements of conductivity due to the high resistivity of measurement techniques and nanopore membranes with low leakage.…”