Question regarding immobilization of a Gram - bacteria: is it necessary to use a CM3 chip? I've read some articles (albeit 7-8 years old) in which the author(s) utilized CM5 chips for this procedure. The data looks pretty good, but I'm new to SPR technology and thought I'd ask those who have more experience.
Also, we will be using DNA aptamers (70- to 80-mers) in various concentrations as analyte. Given the interaction, what would you all recommend for regeneration buffer/cocktail?
I don't have experience in immobilizing bacteria.
The CM3 sensor chip has a short dextran matrix so your bacteria will be closer to the surface. This can be beneficial to the response. If you don't have a CM3, use a CM5 first to find out if your setup works.
About the regeneration. You have to determine the best regeneration solution emperically. There is no single best regeneration solution. In the past when I used DNA-probes I washed with high salt (NaCl) solutions.
We tried a CM5 chip and attempted to isolate the bacteria with not much luck at all. The author whose protocol I'm following did a manual immobilization with a 1 ul/min flow rate. Using the X100, the lowest flow rate I've got available to me is 5 ul/min. I don't see how that one factor (everything else in her protocol is being followed to the letter!) could keep the bacteria from being immobilized. Frustrating!
We'll keep trying and will order CM3 chips in the meantime. I'll keep the board posted regarding any success.