GoTaq PCR

Materials required

Add the following as mentioned below to make up to a final volume of 50 µl in the PCR tube:

1. 32.5 µl of distilled H₂O
2. 10 µl of 5x GoTaq Buffer
3. 1 µl of dNTPs
4. 2.5 µl forward primer
5. 2.5 µl backward primer
6. 1 µl template DNA
7. 0.5 µl of GoTaq polymerase

Conditions for ThermoCycler

After putting the PCR tubes in the thermocycler, set the thermocycler's condition as mentioned below:

1. Initialise - 95°C for 2 minutes.
2. Denature - 95°C for 30 seconds.
3. Anneal - ~°C for 30 seconds (depends upon the melting temperature, Tm, of template)
4. Extension - 75°C for 30 seconds
5. Extension finish - 75°C for 5 minutes
6. Hold - 4°C

Steps 2 to 4 are repeated for 30 cycles before continuing to step 5.

Note Extension time depends on size of DNA and time used is 30 seconds/kb.

Note PCR is best when everything is kept on ice!

Note Melting temperatures, Tm, for annealing step of primers is important and can have a big effect on the product formed.

Phusion PCR

Materials required

Add the following as mentioned below to make up to a final volume of 50µl in the PCR tube:

1. 27.5 µl of distilled H₂O
2. 10 µl of 5x Buffer
3. 1 µl of dNTPs
4. 5 µl forward primer
5. 5 µl backward primer
6. 1 µl template DNA
7. 0.5 µl of Phusion polymerase

Conditions for ThermoCycler

After putting the PCR tubes in the thermocycler, set the thermocycler's condition as mentioned below:

1. Initialise - 98°C for 30 seconds.
2. Denature - 98°C for 10 seconds.
3. Anneal - Depends on the melting temperature, Tm of the primer and it lasts for 20 seconds.
4. Extension - 72°C (The extension time depends on the the size of the fragment which is to be amplified).
5. Extension finish - 72°C for 5-10 minutes
6. Hold - 4°C

• Some important points to note while performing Phusion PCR are as following:

1. Annealing temperature of the primer depends on the GC content and thus before setting up the thermocycler, check the melting temperature once again online or on the notes provided by the company which made the primers.
2. Rate of extension by Phusion polymerase is 1Kb/ 30 seconds and thus always set extension time based on the size of the fragment you are planning to amplify.

Steps 2 to 4 are repeated for 30 cycles before continuing to step 5.

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