Colony screening by PCR Notes This is the fastest way to screen bacterial colonies. Our PCR machine takes 24 tubes so I routinely screen 22 colonies + 1 negative + 1 positive control. Choosing the primers Ideally you want a primer pair that can only work if the correct construct is present eg. a vector flanking primer and a gene specific primer. However, this may not allow you a positive control (essential) so you might have to use both vector flanking primers instead. If you have enough space in your PCR machine you could do both. Typical Protocol Set up 24 PCR tubes each containing 5ml H2O. Touch a fresh toothpick (or yellow tip) onto a colony, dip it into a PCR tube, then streak it onto a fresh replicate agar plate using a numbered template (that is, all 24 colonies on a single agar plate). I don't label the PCR tubes. I can tell what number they are and also whether they have been 'dipped' by their position in the rack/block. Repeat this for the 22 (or whatever) colonies for tube 23 (negative control) use a colony that is negative (or use nothing). for tube 24 (positive control) use a colony that will yield a product with your primers. If you don't have a +ve colony then use a tiny amount of plasmid DNA Incubate the replicate agar plate at 37C. These streaked colonies will be visible within 6-8 hours so you can set up overnight miniprep cultures on the same day. Set up a 25 x PCR pre-mix as follows; 1 x pre-mix _ 25 x pre-mix 2ml 0.6ml 0.1ml 0.1ml 5ml 12ml 0.2ml 10 x PCR buffer MgCl2 (50mM) primer 1 (100mM) primer 2 (100mM) Template H2O cheap Taq 50ml 15ml 2.5ml 2.5ml - ml 300ml 5ml Add 15ml of pre-mix to each PCR tube. PCR program Cycles Temperature Duration 1 94C 60 seconds 25 94C 30 seconds 55C 30 seconds 72C 1 minute This PCR should take less than 2 hours. While the PCR is running prepare the agarose gel ready to analyze the PCR products. When you have the result you can go to the replica agar plate on the same day and set up miniprep cultures of the likely candidate colonies.

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