Could you provide more information about your PCR reaction? How much template did you add? Did you include a negative and/or positive control? How many PCR cycles did you run? Kamran Azmoodeh
Hi Kamran, The excessive smear might be the reason of too much concentration of template DNA. Use different concentrations such as 50x, 100x, 200x for initial trials. Hope it helps. Good luck!
Try running an unamplified dna sample against the size ladder in case you are using too much dna and the smear is template dna. I agree with Shubhra Singh that the amount of template dna could be the problem .Measure the od260 of a sample and amplify 25ng of dna or take one sample and dilute it 1:2, 1:4,1:8 and 1:16 and amplify all of these dilutions. How many cycles of pcr are you running