Hi everyone, I am facing an issue with running the denaturing Urea-PAGE to visualize the digested fragment of the Oligos (the first labeled oligos are Cy2, and the second one is Cy5). First problem, I have been facing an issue with gel polymerization (size of gel 20*45 (W*H)); it forms air sacs during polymerization (image 1). The second issue, after running the gel (gel running apparatus from cleaver scientific (EV3330)), I got a very high-intensity background signal during the scan (using a Typhoon fluorescence gel scanner ) (Image 2). However, the background signal only appears during the Cy5 scan.

Please let me know the possible solutions.

Thank You