I did a gel electrophoresis with my SYBR Green qPCR products (starting material is miRNAs) on agarose gel. First I tried 4% agarose gel with TBE buffer, but I wasn't able to observe anything on the gel. In addition, the blue shade of the loading dye on the gel disappeared during the electrophoresis after some point. Then, I tried to decrease the agarose concentration and prepared 2.5% agarose gel. The same thing happened. No visible bands. I do not observe anything even for the DNA ladder. (I did not forget to add EtBr). Any recommendations?
What method are you using to isolate the miRNA? What is the expected size of your amplification? How many cycles do you use in your amplification and what amount of the total reaction do you load in the gel (everything, half,...)? I suppose you are using an additional anchoring molecule to amplify your miRNA
Before commenting on your gel I have a quick question: what is the product you are running on gel... is that a ssDNA/ds DNA/RNA? and how many bases long? Generally single stranded RNA or DNA can be resolved on denaturing gels (Urea-PAGE) and short double stranded DNA on native PAGE gels.
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