Corum:Whole Plasmid PCR

Overview

Whole plasmid polymerase chain reaction (WP-PCR) protocol using PfuUltra II fusion HS DNA polymerase. It is imperative to use 5'-phosphorylated primers if the nicked DNA is going to be repaired downstream with ligase. PCR should be limited to templates of about 5 kb, but the protocol could probably be pushed up to 10 kb. See the PfuUltra II fusion manual.

Materials

For a 50 μL WP-PCR reaction:

• 37 μL H₂O
• 5 μL 10X PFU Ultra PCR buffer
• 5 μL 10 μM sense/antisense primer mix (0.5 μM final)
• 1 μL 12.5 mM (each) dNTP mix (0.25 mM final)
• 1 μL 5 nM plasmid template (0.1 nM final)
• 1 μL PfuUltra II fusion HS DNA polymerase

Procedure

1. In a PCR tube, add the components on ice in the order they are listed above. Mix gently and spin.
2. Perform the following thermocycling program:
   1. Initial melting: 95 °C 2 min
   2. Melting: 95 °C 20 s
   3. Annealing: T_a °C 20 s, where T_a = T_m - 5 °C
   4. Elongation: 72 °C 2 min / kb template
   5. Repeat steps 2-4 a total of 30 times
   6. Final elongation: 72 °C 30 min
   7. 12-16 °C hold
3. Verify product with gel electrophoresis.
4. Quantify product with quantifluore DNA quantification.

Notes

Please feel free to post comments, questions, or improvements to this protocol. Happy to have your input!

1. List troubleshooting tips here.
2. You can also link to FAQs/tips provided by other sources such as the manufacturer or other websites.
3. Anecdotal observations that might be of use to others can also be posted here.

Please sign your name to your note by adding '''*~~~~''': to the beginning of your tip.

References

Relevant papers and books

1. Sambrook, J and Russell, DW (2001) Molecular Cloning: A Laboratory Manual (Volume II) - Cold Spring Harbor Laboratory Press ISBN 0879695773

Contact

• Sean P Corum
• SC 12:50, 13 December 2012 (EST):

or instead, discuss this protocol.