I've been trying to purifiy my electrophoresis bands but they are very closed to each other, I've tried 2% agarose gels, ran at 90V for 2 hours and this is as far as I can get them to separate. My advisor suggested me to use acrilamide gels, but I need to find a percentage to separate long PCR products and a protocol, anyone has one that can share?, also some advice on how to separate them, we need to sequence them.
How much is the size difference in both fragments? And what sequencing you wanted to perform ?
Anyway, increasing agarose percentage would be primary option. Ofcourse, PAGE is better in separating dna fragments with small differences in size.
Hi
I have this problem sometime a go. The best thing helped me well was by making agarose gel denser. So, try to make your agarose gel like 3%.
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