I've recently started using an Edinburgh Systems FS5 fluorometer with no experience or training other than the instructional videos they provide on a memory pen.
I'd like to know what the best type of 96 well plates are to use for fluorescence emission readings, as I am currently using opaque black plates with a curved opaque bottom. I believe the Fluorometer is top-reading.
I'm using Alizarin Red S which is a dye that will become fluorescent when binding to a boronic acid and emit at 572 nm (excitation 468 nm). However the values and trends I am seeing do not seem to reflect what is expected, and this is shown even more so when I analyse completely blank well plates. I tried completely clear well plates previous to this but got similar results and also read that you should not use this as it reflects the light away from the wells.
I've also tried to use a rhodamine sample to get better results but the emission is similar to that shown for an empty well. Is there a better way to calibrate the laser rather than manually turning the mirrors for the detector etc as suggested in the instructional manual for this specific type of instrument?