I don't think you would really need a 30 % PAG to resolve 20 nt. Are you attempting Maxam-Gilbert sequencing or dideoxy? There will always be an issue with small fragments, but higher up it should be OK. It might help if you upload your current result so we could see where the problem might be.

Marko is correct . The first few bases of sequencing are always difficult. Using more sequencing primer improves this but does not fully solve the problem. Some tries are pyrosequencing, cloning the shortmer into a vector and sequencing from further away or possibly amplifying with a long tail on one primer and sequencing off the end of the tail to move the region of interest further from the sequencing primer

thank all for your answers. our lab doesnt have 40 cm long gel. we only have 15 cm gel. so i am figuring out a way to run a gel in it by making higher percentage gel.

hey all. Thanks for your answers. Our professor is agreed to purchase 40 cm length sequencing gel electrophorosis apparatus. But the problem is that biorad sequencing apparatus is not available here. Can you name some other company who sells this type of apparatus other than biorad and biometra

You can check Thermo Scientific. They sell Owl aluminium-backed sequencers (I am not sure I am allowed to post links to commercial sites here, but you can find it easily on the web). There are two models that are 45 cm long by 20 or 35 cm wide.

hi dr. david.thanks for your suggestion. I am wondering that why gel casting stand is expensive. the thermofisher owl is 2000 dollar for appratus and 800 dollar for gel casting stand. is there any other company that can give casting stand with appratus