Surface charge (nanopore)
The surface charge of a nanopore is the electric charge carried by its walls when they are in water. Silica and silicon nitride, the usual materials of solid-state nanopores, are negatively charged at neutral pH. The charge attracts a cloud of positive ions to the wall, and in a pore a few nanometers wide that cloud is a large part of everything inside. It changes how much current the pore carries, which way the water inside it flows, whether the current is the same in both directions, how noisy it is, and what a molecule meets on its way in.
Origin
In water the surface of silica is covered with silanol groups, SiOH, which can lose a proton and become SiO−. Silicon nitride has the same groups at its oxidized surface and amine groups besides, which can gain a proton, so its charge changes sign with pH. The pH at which the positive and negative groups balance is the point of zero charge. Hoogerheide, Garaj and Golovchenko found it for a silicon nitride pore about 3.3 nm in radius from the conductance, which was lowest at pH 4.1 in a solution of 110 mM ionic strength.[1] Above that pH the wall is negative, and more so as the pH rises.
The size of the charge is usually given per area. A density of −0.02 C/m2, a value often used in models, is one elementary charge for every 8 nm2, so the wall of a pore 5 nm wide and 10 nm long, which has an area of 157 nm2, holds about 20 of them. The pore that Hoogerheide's group modeled had about 150 sites that could gain or lose a proton, few enough that the behavior of individual sites shows up in the current.
Effects
Surface conduction
The counterions at the wall conduct current along it, in parallel with the bulk solution. The wall matters when the pore is narrower than about four times the ratio of the surface conductance to the conductivity of the solution, a length that grows as the salt gets dilute. In 1 M potassium chloride the wall adds about 8 percent to a 5 nm pore, and at 10 mM it carries most of the current (see Pore conductance). The conductance then stops following the salt concentration. Stein, Kruithof and Dekker found such a plateau in 2004 in silica channels as thin as 70 nm and fitted it with a model whose one free parameter was the surface charge.[2] How far the charge reaches into the liquid is the Debye length, 0.3 nm at 1 M and 10 nm at 1 mM; the layer of screening ions is the electric double layer.
Flow
When a voltage is applied, the screening ions move and drag the water with them. At neutral pH in a silicon nitride pore the positive ions flow toward the negative electrode, opposite to the motion of DNA, and the water goes with them. This is electroosmotic flow. It can slow DNA on its way in or push neutral molecules through, and it is one of the forces to be counted when calculating the capture rate.
Rectification
In a pore that is wider at one end, charged walls make the current larger in one direction than the other (see Ion current rectification). Wei, Bard and Feldberg described the effect in 1997 for quartz nanopipettes, whose walls are charged in the same way.[3]
Noise
The charge is not fixed. Each group is a small acid or base that gains and loses protons at random. Hoogerheide and colleagues found an excess current noise that exceeded all other sources between 0.1 and 10 kHz, traced it to those fluctuations, and noted that it varies with pH and could be reduced by working at a chosen pH. Their noise peaked at pH 7.5, nowhere near the pH of the lowest conductance.[1] This is the reason that a sample buffer is not a free choice. See Nanopore noise.
Changing it
The wall can be coated. A lipid bilayer on the inside of a pore screens the charge of the underlying wall and was the basis of the single-protein measurements of Yusko and colleagues.[4] The particles that pass through carry charge too. Polystyrene beads are sold with sulfate, carboxyl or amine groups on their surfaces, and DNA carries two negative charges for each base pair, of which about 0.5 remain effective in 1 M salt after counterions condense on the strand.
At Molecular Reality
The company's interactive pore simulators handle the wall differently. Nanopore Studio gives each of its five membrane materials a surface charge and computes electroosmotic flow from it, and Nanopore Physics Studio gives its membrane none, so that it has no double layer and no flow along the walls.[5] The company's plans for the virology game SARS Invaders named the surfaces of its analytes as the thing to vary, in the phrase "polystyrene beads with different surface functionalities".[6]
See also
References
- ^ a b Hoogerheide, D. P.; Garaj, S.; Golovchenko, J. A. (2009). "Probing surface charge fluctuations with solid-state nanopores". Physical Review Letters 102 (25): 256804. doi:10.1103/PhysRevLett.102.256804.
- ^ Stein, D.; Kruithof, M.; Dekker, C. (2004). "Surface-charge-governed ion transport in nanofluidic channels". Physical Review Letters 93 (3): 035901. doi:10.1103/PhysRevLett.93.035901.
- ^ Wei, C.; Bard, A. J.; Feldberg, S. W. (1997). "Current rectification at quartz nanopipet electrodes". Analytical Chemistry 69 (22): 4627-4633. doi:10.1021/ac970551g.
- ^ Yusko, E. C.; et al. (2017). "Real-time shape approximation and fingerprinting of single proteins using a nanopore". Nature Nanotechnology 12 (4): 360-367. doi:10.1038/nnano.2016.267.
- ^ "Company records". Molecular Reality Corporation. October 2026.
- ^ "Early Releases on Maxine's Quest". Molecular Reality Corporation. 2022.