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Matt Lewis Department of Pathology
University of Liverpool

Colony screening by PCR


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 5 µl 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 37°C.

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 Component 25 x pre-mix
11.5 µl
2 µl
0.6 µl
0.5 µl
0.1 µl
0.1 µl
5 µl
0.2 µl
10 x PCR buffer
MgCl2 (50 mM)
10mM dNTPs (i.e. a mixture of all four at 10 mM each)
primer 1 (100 µM)
primer 2 (100 µM)
cheap Taq
287.5 µl
50 µl
15 µl
12.5 µl
2.5 µl
2.5 µl
0 µl
5 µl

Add 15 µl of pre-mix to each PCR tube.

PCR program

Cycles Temperature Duration
1 94°C 60 seconds
25 94°C 30 seconds
55°C 30 seconds
72°C 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.

No responsibility is assumed by for any injury and/or damage to persons or property as a matter of products liability, negligence or otherwise, or from any use or operation of any methods, products, instructions or ideas contained in the material herein. It is the users responsibility to ensure that all procedures are carried out according to appropriate Health and Safety requirements.