I am doing a diversity analysis of sugarcane germplasm using SSR technique. When I am running PCR products in PAGE the ladder and samples are not open properly. I apply 40w and run 2 1/2 hrs in 6% PAGE gel with 1x TBE (height of gel 6'). Next time, I run same set of samples in PAGE with urea. In this gel samples and ladder open properly but handling of gel is difficult. Bands are not clear as previous. In some papers they mention PAGE with urea. But in some references mention PAGE without urea. please advice me which one is the most suitable for me.
I have used High Resolution Agarose Gels or Methapor agarose gels to separate SSR fragments. Results were very good and I wonder if this could be an additional option for you.
What kind of SSR markers do you have? Locus specific? If yes, look to my article there is using of 6 % denaturated PAGE gels (with urea) stained with silver.
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