Colony Screening PCR

Colony PCR

We should have assembled Gene 68 and the vector together into one DNA construct which was transformed into bacterial cells to produce colonies. While each colony ought to have the correct DNA construct, both the assembly process and the process of Assembly PCR (templateless and finish PCR) that we used to create Gene 68 are not perfect and do, in fact, produce many smaller DNA fragments. We therefore always need to screen the bacterial colonies to verify that they contain a correct DNA construct. Colonies are checked first by colony PCR, which verifies the size of the gene, and then by DNA sequencing, which verifies that there are no mutations in the DNA sequence. When screening, we want to start with several clones to maximize the likelihood that we have at least one clone that is correct. We will therefore be setting up 8 PCR reactions (6 different DNA clones (bacterial colonies) plus positive and negative controls. Colony PCR is a commonly used method to quickly and directly screen bacterial colonies without first extracting the DNA from the cells for use as a template for PCR.

Reaction Setup:

1. In a large microcentrifuge tube on ice, combine the following components:

    •125 ul of 2X master mix (2X MM)
    •25 ul of primer mix 
    •93 ul of sterile water 
    •7 ul of DMSO

2. Pipet up and down 10X to completely mix the contents of the tube.

3. Aliquot (distribute) 25 ul per tube of the mix into 8 PCR tubes (the very small ones).

4. Obtain one LB+Amp plate and label the back side of the plate with the numbers 1-6, your initials, and the date.

5. Use a sterile toothpick to pick up one individual colony from your bacterial plate from last week. Dip the sterile toothpick into one of the PCR tubes. As soon as the solution looks cloudy, remove the toothpick. Using the same toothpick, streak the toothpick onto the new labeled LB+Amp plate at position #1.

6. Repeat step #5 for colonies #2-6.

7. Into PCR tube #7, add 1 ul from tube PC.

8. Into PCR tube #8, add 1 ul of sterile water.

9. Put your 8 PCR tubes into one column of the PCR machine and begin the PCR reaction.

Reaction Conditions:

1 cycle:

       	98°C, 30 seconds

35 cycles:

       	98oC, 10 seconds
       	55oC, 30 seconds
       	72oC, 30 seconds

1 cycle:

       	72oC, 10 minutes

10. Parafilm your bacterial plates from last week and store in the fridge until we analyze the PCR reactions. Place your new plate of bacteria (#1-8) into the 37C incubator (remember to place the plate upside down). If the PCR reactions indicate that we have an insert of the correct size, we can come back to these cultures to regrow the bacterial cells with the plasmid to send the plasmid for DNA sequencing.

Pouring Gels

Pouring a Gel:

1. Weigh out 0.5 g of agarose on a piece of weigh paper. Transfer to an Erlenmeyer flask. Add 50 ml of 1X TAE.
2. Place the flask in the microwave and heat until the agarose is completely transparent and colorless.
3. Allow the agarose to cool -this will take about 10 min.
4. While the agarose is cooling, place the gel tray into the gel box and add the comb.
5. When the agarose is cool, add 5 ul of Gel Red to the melted agarose
6. Swirl the agarose to incorporate the Gel Red and pour the agarose into the gel tray.
7. Allow the gel to solidify for 15-20 minutes. During this time, you prepare your samples (below).

Gel electrophoresis

Preparing your samples:

1. Gather your colony screening PCR products. They should be:

    1. Colony 1

    2. Colony 2

    3. Colony 3

    4. Colony 4

    5. Colony 5

    6. Colony 6

    7. Positive control
    8. Negative control

2. To each tube, add 5 ul of 6X DNA loading dye.

Running a Gel:

1. Into lanes 1-8, load 11 ul of each of your PCR products (mixed with water and dye).
2. Into lane 9, load 10 ul of the DNA ladder (premixed with water and dye)
3. Place the lid with electrodes onto the gel box, and set voltage to 100V.
4. Run gel approximately 30 minutes or until the dye is 2/3 of the way down the gel, then take a picture.

5. When done, you want to check that:

    •There are no DNA bands in the NC lane of the gel (lane 8)
    •There is a DNA band in the PC lane of the gel (lane 7). This should be ~426 base pairs in length. 
    •The colony screening PCR products (lanes 1-6) are full-length. A full-length product should give a band of ~426 bp.

Be sure to check the size of your PCR products in comparison to the DNA ladder (NEB 100 bp ladder, pictured below: