Corum:Whole Plasmid PCR

Overview

Whole plasmid PCR protocol using PFU Ultra DNA polymerase. PFU ligase is used in the reaction to repair the nicked plasmid products as PCR proceeds. It is imperative to use 5'-phosphorylated primers for the ligase to repair the nicks.

Materials

For a 50 μL whole plasmid PCR PCR reaction:

• 37 μL H₂O
• 5 μL 10X PFU Ultra PCR buffer
• 5 μL 100 μM sense/antisense primer mix (10 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 PFU Ultra II high-fidelity DNA polyermerase

Procedure

1. In a PCR tube, mix the components on ice in the order they are listed above.
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 12-20 times (20 is standard).
   6. Final elongation: 72 °C 30 min
   7. 12 °C hold
3. Verify product with gel electrophoresis.
4. Quantify product with quantifluore DNA quantification.

Notes

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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 18:46, 23 July 2012 (EDT):

or instead, discuss this protocol.