SingletubeconfirmationPCRprotocol

The following colony PCR protocol has been designed to be performed in individual reaction tubes. We usually test three colonies from each transformation along with a wild-type control. A series of five different PCR tests are performed on each colony to confirm both of the novel recombination junctions .

1. Clonal purification

- Pick three colonies from a transformation plate and streak each one out to single colonies on separate G418 containing plates (200mg/l).

- Incubate at 30°C for two to three days.

*This step reduces background by eliminating aborted transformants.

2. Zymolyase treatment

- Transfer a small portion of a well-isolated colony (~1 mm) into 50 μl solution containing 60 U/ml of Zymolyase (This solution is generated by resuspending 6 mg of 100T Zymolyase in 10 mls of water. Ordering information: Seikagaku Corp., #120493-1).

- Sterile yellow tips work great for this task.

- Repeat this step for each of the 3 isolates and the wild-type control.

- Incubate the Zymolyase solutions at 37 ° C for 30 minutes followed by 10 minutes at 95 ° C.

*It is not necessary to remove the Zymolyase solution by pelleting the cells before the PCR.

*The Zymolyase treated cells can be stored at 4 ° C for several days before being used as template for the colony PCR. However, fresher is probably better.

*The amount of cells that gets picked into the Zymolyase does not seem to be too critical - similar PCR results were obtained when 1 μl, 5 μl or 10 μl of the Zymo treated cells were used as template. 

3. PCR reactions

- The lyophilized confirmation primers (~5-10 nmoles of each oligonuleotide) should be resuspended in 750 μl of TE (final concentration of ~10 μM). We use 5 μl of each primer in 50 μl PCR reactions (~ 1 μM final primer concentration).

- Label 20 thin-wall PCR tubes (5 for each isolate) and add the following primer pairs: A-B, A-kanB, C-D, kanC-D, and A-D. Tubes 1-5 are for isolate #1, 6-10 are for isolate #2, ..., and tubes 16-20 are for the wild-type control. Each of the 20 tubes should contain 10 μl of the primer mix (5 μl of each primer).

- Add the 5 μl of the Zymo treated cells to each of the 20 PCR reactions. For example, add 5 μl of the Zymo solution from isolate #1 to PCR tubes 1-5, 5 μl of the Zymo solution from isolate #2 to PCR tubes 6-10 and so on.

- Make a PCR master mix by combining: 638 μl water, 110 μl 10 x Taq Buffer, 11 μl NTP's, and 11 μl Taq Polymerase.

- Add 35 μl of the PCR mix to each of the 20 PCR tubes that already contain the 15 μl of primers and template.

110 μl           5 μl   10 x Taq buffer(see below) 
 11 μl         0.5 μl   20 mM dNTP's (0.2 mM)
 11 μl         0.5 μl   Taq Polymerase (2.5 units)
638 μl   22 X   29 μl   water
                 5 μl   10 μM upstream primer: A,C,or kanC (1 μM)
                 5 μl   10 μM downstream primer:B,kanB,or D(1 μM)
					5 μl   Zymolyase treated cells
                50 μl total volume

*10 x Taq buffer contains: 100 mM Tris-HCl (pH 8.4), 500 mM KCl, 15 mM MgCl2.

*The final concentrations are shown in parentheses.

*The Taq Polymerase should be added last and PCR mixture should be kept on ice until the PCR is started. Alternatively, a "hot start" can be performed by adding the Taq polymerase to the individual tubes after the PCR mixtures have been heated to 94°C. Hot start improves the PCR results but this step is labor intensive and we have not found it to be necessary.

4. PCR conditions:

                     3 min, 94 °C (initial denaturation)

              --->   15 sec, 94 °C
   35 cycles: --->   15 sec, 57 °C
              --->   60 sec, 72 °C

                     3 min, 72 °C (final elongation)

5. Agarose gel electrophoresis

- Add 10 μl 6x loading buffer (30% glycerol, 50mM EDTA, 0.25% bromophenol blue) to the 50 μl PCR reaction.

- Load 10 μl on a 1.5% agarose gel.