Presence of bubbles in the lower fluid cell can affect the level of background noise, baseline current, as well as baseline stability.
As the nanopore is semi-transparent, bubbles in the lower fluid cell can be seen with a simple visual inspection when the upper fluid cell is removed. Very small bubbles that cannot be seen may still disrupt the fluid bridge to the upper fluid cell. Their presence causes instability or blocking of the baseline ionic current.
Air is trapped in the porous electrode paste (in the lower fluid cell) and can come out when fluid is loaded. Pre-wetting the lower fluid cell with electrolyte containing surfactant helps to alleviate bubble formation in the bottom well during the course of a measurement.It is a good idea to keep electrolyte in the lower fluid cell after taking the nanopore off for cleaning or to change nanopores. This will stop the electrode paste drying out and creating a new set of air bubbles.
Bubbles can also be introduced through incorrect pipetting. Always use reverse pipetting when adding sample to fluid cells.