Probing Surface Charge Fluctuations with Solid-State Nanopores

Abstract

We identify a contribution to the ionic current noise spectrum in solid-state nanopores that exceeds all other noise sources in the frequency band 0.1-10 kHz. Experimental studies of the dependence of this excess noise on pH and electrolyte concentration indicate that the noise arises from surface charge fluctuations. A quantitative model based on surface functional group protonization predicts the observed behaviors and allows us to locally measure protonization reaction rates. This noise can be minimized by operating the nanopore at a deliberately chosen pH.As nanodevices are increasingly used for single-molecule detection and manipulation in the time domain, their noise characteristics at kHz frequencies gain additional significance. In the case of protein nanopores, noise has elucidated both pore and analyte dynamics [1][2][3]; in solidstate nanopores to date, noise has simply interfered with detection of DNA and proteins [4][5][6][7][8][9]. Previous work has described a variety of noise sources in solid-state nanopores and typical measuring apparatus [10][11][12].In this Letter, we identify a new source of current noise in solid-state nanopores that is dominant in the frequency range from 0.1-10 kHz. A simple analysis of the noise dependence on pH and the electrolyte ionic strength, based on a few general assumptions, suggests that the noise originates from surface charge fluctuations. Finally, we develop a quantitative model based on protonization of surface functional groups [1] and compare it to the experimental results. Our technique is sensitive to a few tens of active surface groups in the nanopore, allowing us to observe variations in local surface properties from nanopore to nanopore and to guide optimization of single-molecule detectors.Nanopores were fabricated with a transmission electron microscope [13] in a thin film of lowstress, amorphous silicon nitride, resulting in single, roughly hourglass-shaped [14] channels 55 nm long and ~4 nm in diameter at the smallest point. The silicon nitride film containing the nanopore separates two reservoirs of potassium chloride electrolyte in a sealed fluidic cell; current measurements were made between Ag/AgCl electrodes in each reservoir (Fig. 1). Noise measurements on different nanopores show the same general features and pH spectral shapes, while the sensitivity and local nature of the technique reveals sample-to-sample variability [15]. The noise sources we observe appear to be intrinsic to the silicon nitride nanopore surface and are not as variable as 1/f noise [12].The power spectral densities (PSDs) of typical current recordings (Fig. 1, inset) demonstrate various expected noise sources: with no applied voltage bias (lower spectrum), only thermal (Johnson) noise (thick dashed line) and high-frequency capacitive noise driven by the preamplifier input are present. With applied voltage bias across the nanopore device (upper spectrum), conductance fluctuations such as 1/f noise (dotted line) become apparent. We also observe the appearance of an...

Synchronized Optical and Electronic Detection of Biomolecules Using a Low Noise Nanopore Platform

“…23,24 However, the frequency dependence of this noise source is inconsistent with that of surface charge protonation noise or temperature dependant thermal and dielectric noise. 22,25 Furthermore, this peaks absence within the Py-SiN x platforms power spectrum suggests the source of noise is related to the Si substrate. The optical transparency of the SiN x membrane and photon energy (2.54 eV) is sufficient for electron-hole pair generation in the Si substrate (band gap ~1.1 eV), reported to promote photoreduction of H + at p-type Si interfaces.…”

Probing surface hydrophobicity of individual protein at single-molecule resolution using solid-state nanopores

“…At pH 4, the protein is positively charged (Fig. 6a) and EO flow can be negligible since the SiN nanopore is nearly electro neutral on the wall at this pH [51]. So translocation can only be observed when the negative potential is applied to trans side as the electrophoretic force drives the protein to pass through.…”

Solid-State Nanopore Sensors for Nucleic Acid Analysis

“…Two dominant sources of noise have been documented in the literature: a low frequency current fluctuation with 1/f characteristics (flicker noise) and a high-frequency background noise component associated with the capacitance of the Si support chip (dielectric noise). [86][87][88][89][90][91] Minimizing these respective noise components is integral to improving the sensitivity and signal-to-noise ratio of nanopore sensors.…”

“…[87] The model presented was based on protonization of surface functional groups and was sensitive to a few tens of active surface groups in the nanopore. In contrast, Smeets et al concluded that low frequency noise was predominantly due to the total number of charge carriers in the nanopore thereby following Hooge's phenomenological relation, rather than on surface charge characteristics.…”

“…[119] The strong electrostatic binding observed in our experiments was not reported in SiO 2 and Si 3 N 4 , likely as these systems exhibit a net negatively charged surface at pH 7.5 resulting from the deprotonation of surface silanol groups. [87] Furthermore, a comparison of the surface charge ) systems. [73,150] Thus, polymer-pore interactions involving electrostatic binding events are expected to be more prominent in Al 2 O 3 nanopores.…”