Open-pore current
The open-pore current is the ionic current through a pore with nothing in it, at a fixed applied voltage. It is written I0 and equals the pore conductance G times the voltage V. It is the first number measured on a new pore and the level to which every event is compared: a molecule in the pore shows up as a dip below I0, and the depth of the dip is usually quoted as a fraction of it (see current blockade). A pore that cannot hold a steady open-pore current cannot be used for anything else.
What sets the level
At a few hundred millivolts and in 1 M potassium chloride, a protein pore such as alpha-hemolysin passes about 120 pA at 120 mV, and solid-state pores a few nanometers wide pass about 0.3 to 6 nA at 200 mV. The table in Ionic current runs from 2 nm to 100 µm. Within a single pore the current should follow the voltage in a straight line, and a plot of current against voltage, the IV curve, is the usual first test. A straight line through the origin is what a simple, symmetric pore gives. A curve that bends, passes more current in one direction than the other, or fails to cross at zero points to an asymmetric and charged pore, to a bubble, or to an offset in the electrodes (see Ion current rectification and Surface charge (nanopore)).
Checking a new pore
The conductance of a pore gives its size when its length is known, so the first reading of I0 is also a measurement of the pore. The ruler is rough: Frament and Dwyer showed that for a pore of unknown shape the dependence of conductance on salt does not fix the geometry, and that simplified models can mislead by more than 40 percent in key dimensions.[1] A diameter inferred from I0 is the diameter of the model.
The more common use is as a pass-or-fail test. A pore that carries no current is not wet, or is blocked. A pore that carries much less than the formula predicts often has a gas bubble in it. In 2006 Smeets and colleagues measured the same solid-state pore repeatedly and found that its conductance and its low-frequency noise changed greatly from run to run, with noise power differing by up to five orders of magnitude, and concluded that nanobubbles were the dominant source of noise (see Nanobubble).[2]
Drift
A baseline that moves is the commonest complaint about solid-state pores. Several things move it, and each can be put in the same units.
- Temperature: the conductivity of the electrolyte rises about 2 percent for each degree. A shift of 0.1 °C changes a 3.1 nA baseline by 6 pA.
- Electrode offset: the baseline follows G times any change in the voltage the pore really sees. A drift of 1 mV in a silver chloride electrode changes the current of a 15.5 nS pore by 15.5 pA. When the two chambers hold different salt concentrations the electrodes produce a voltage on their own, 75 mV for a 20-fold ratio, and the current does not cross zero at zero applied voltage until the offset is nulled.[3] See Ag/AgCl electrode.
- Concentration: evaporation from a small chamber raises the salt, and a rise of 1 percent raises the current by 31 pA.
- The pore itself: debris that lodges in it lowers the current in steps, and the walls can change with pH and time (see Clogging (nanopore)).
Against a DNA blockade of several hundred picoamperes these are small. Against the events of a small protein, which can be tens of picoamperes, they are not.
Noise also scales with the level. The low-frequency noise of a pore rises with the square of the current (Hooge's relation), so a pore passing more current is also a noisier one, and the choice of voltage is a trade, as set out in Nanopore noise.
Using the baseline
Analysis software treats I0 as a moving quantity. A common method estimates the baseline by a running average of the points that are not part of an event, and recomputes the average and its standard deviation until both stop changing; events are then the stretches that fall more than a set number of standard deviations below it.[4] Depths are then divided by the local baseline, which lets events from different pores, or from one pore on different days, be put on the same scale. See Event detection (nanopore).
At Molecular Reality
The MR1 Nanopore Reader has two descriptions of the level it must hold. The repository's acquisition specification lists a full scale of ±2.048 nA with a 1 GΩ feedback resistor, which would clip the 5.9 nA that a 10 nm pore in a 20 nm membrane passes in 1 M potassium chloride at 200 mV. The amplifier as drawn, with a gain of about 10 MΩ, spans roughly ±240 to ±510 nA and would not.[5] In the simulated trace of the Clay TV of Maxine's Quest the open pore is one of three current levels, the others being partial and deep blockades at 68 and 35 percent of it.[5]
See also
References
- ^ Frament, C. M.; Dwyer, J. R. (2012). "Conductance-based determination of solid-state nanopore size and shape: an exploration of performance limits". Journal of Physical Chemistry C 116 (44): 23315-23321. doi:10.1021/jp305381j.
- ^ Smeets, R. M. M.; Keyser, U. F.; Wu, M.-Y.; Dekker, N. H.; Dekker, C. (2006). "Nanobubbles in solid-state nanopores". Physical Review Letters 97 (8): 088101. doi:10.1103/PhysRevLett.97.088101.
- ^ Wanunu, M.; et al. (2010). "Electrostatic focusing of unlabelled DNA into nanoscale pores using a salt gradient". Nature Nanotechnology 5 (2): 160-165. doi:10.1038/nnano.2009.379.
- ^ Plesa, C.; Dekker, C. (2015). "Data analysis methods for solid-state nanopores". Nanotechnology 26 (8): 084003. doi:10.1088/0957-4484/26/8/084003.
- ^ a b "Company records". Molecular Reality Corporation. October 2026.