I'm culturing cells on PDMS microchannel. However, the PDMS loses its transparency due to cell media. I saw PDMS lose transparency in water, too. I want to prevent it because it hinders microscopy.
PDMS was prepared at a mixing ratio of 10:1 (base to curing agent). Baking time is around 10h. And I didn't treat with n-pentane and IPA. In fact, I don't know how the treat works. What is it for?
Based on your explanations, I think your PDMS is not in fact polymer and is an oligomer. I believe, there should be some problems with the cross-link of your PDMS pre-polymer with its curing agent.
There should be no problem with the long cure time. I often leave fluidics in the oven over the weekend and they never have problems. Our lab even does a 200OC anneal for 4 hours with no noticeable degradation in optical quality. If the PDMS is mixed well before curing and not tacky when it comes out of the oven, then it is cured.
I would suggest that you may have some structure in the surface of the PDMS that gives you a poor interface between the aqueous phase and the solid phase. This structure could be the cells adhered to the PDMS channels, or may be structure from your casting master that results in a hydrophobic surface that traps small air bubbles that are behaving like an array of disorganized lenses.
You should post some images of the channels with and without the aqueous phase and with and without cells.
Maybe you did not mix properly the PDMS with the curing agent. You have to mix very dynamically and have a lot of bubbles before putting the mix into degasing chamber !