Detection of annealed oligos - (Jan/05/2009 )
I am currently trying to insert/clone my annealed oligos (shRNA) into pSUPERIOR.neo vector (from Oligoengine). I was just wondering if you can detect or check if the oligos are annealed. Any suggestions? My oligos are 60-mer each with sticky ends.
Many thanks and have a nice day.
1. Are your oligos phosphorylated?
2. What is your annealing and ligation protocol?
Yes you can by agarose gel electrophoresis. After annealing, run the annealed oligos along side equal amount of single stranded oligos, you will be able to see the ds-oligos migrate differently from ss-oligos.
I am thinking if you have more time and want to demonstrate convincingly to your supervisor, you should run non-denaturing acrylamide gel. Stain with etbr.