Patch clamp amplifiers do not have intrinsic bilayer capaciatance measurement capability. Therefore, this important measurement must be performed using a simple protocol.

In general, a calibrated triangular wave is applied to the membrane and then read the capacitance from the amplitude of the resulting square wave.

Begin by generating a triangle wave having a unit slope of 0.5 V/s. This can be done directly via a function generator, but many data acquisition programs have the ability to program the analog outputs.

One thing to note is that it is not particularly useful to have a waveform with a large period. Begin by setting the frequency of your triangular wave to 2 kHz. This sets the half-cycle duration to 1 ms. Next set the waveform amplitude to 0.5 mV (peak to peak). These settings should result in a half-cycle slope of 0.5 mV/ms.

Place the function generator output into the COMMAND IN of the patch clamp amplifier and re-program to the appropriate input scale factor. (For example, if the command in input is attenuated to x0.1 of the actual input signal, then the amplitude of the function generator will need to be increased 10 fold, or set it to 10 mV p-p.)

Next, the input/output waveforms should be calibrated. Attach a known capacitance (e.g., a model membrane) to the patch clamp headstage and apply the aformentioned triangular wave. A square wave output should be seen on the data acquisition system. This square wave is expected to return 1 pA of current per pF of membrane capacitance.

If a 100 pF capacitor is attached to the headstage, then the peak-to-peak amplitude of the square wave should be 100 pA on the data acquisition system. If it is not, then adjust either the frequency or amplitude (or both) of the function generator until the amplitude of the observed square wave is correct for your capacitor. The system is now calibrated.

Remove the known capacitor, form a bilayer membrane, and measure its capacitance.

Note that Warner's Bilayer Clamp amplifier has this and other useful, bilayer specific capabilities already built into it.