I am working with SSR polymorphism.The fragment size is around 200 bp. There could be 2-4 base differences among the samples. What percentage of agarose gel I should use? What are the ideal running conditions to obtain maximum resolution?
I agree with Tom Masi. Agarose gels do not have enough resolution to distinguish 1% difference in DNA length, whatever the conditions are.
6% acrylamide gel will certainly separate 2-base difference, but you may need relatively long gel like 40-60 cm to ensure the separation of 202 bp from 200 bp.
You need to be careful that the migration of DNA on acrylamide gels is affected by base composition.
You can please refer to the links below to obtain certain valuable informations:-
1. https://www.neb.com/tools-and-resources/usage-guidelines/agarose-gel-resolution
2. http://www.sigmaaldrich.com/catalog/product/sial/a4718?lang=en®ion=IN
3. http://download.bioon.com/view/upload/month_1006/20100628_da87f42a6df4ff5a5730LAY9zaKjAr0e.attach.pdf
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