I am getting 10000 panned molecules on plaque, But when doing Mini prep getting low amount of DNA, While cutting with required restriction enzymes getting unwanted smears and bands but not required one. This is common for almost 6 different molecules against which we are trying to get binding affinity using our phage display. Interesting part is that we have 10000 plaques for all six different antigens in this study. Not yet done PCR for phage material and only 1 round of panning has been applied. Can someone help to figure out what could be possible problem. As it is common for all six molecules against which panning is done using Iron beads, TG1 cells used.

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