(r6) MEGAWHOP < Lab

---+ Megaprimer whole plasmid cloning
aka <nop>MEGAWHOP cloning %BR%
aka Overlap Extension PCR cloning

Adapted from Bryksin AV, Matsumura I. 2010. Overlap extension PCR Cloning: a simple and reliable way to create recombinant plasmids. _Biotechniques_.48(6):463-5.

---++ Purpose
To insert a DNA sequence into a plasmid without restriction enzymes.

---++ Experimental Steps

   * Create primers that amplify region of interest and hybridize with target plasmid
   * Perform a Phusion PCR with primers using the region of interest as template
   * Perform a second Phusion PCR using the products of the first PCR and the target plasmid as template
   * Digest Second PCR with Dpn1 to remove parental plasmid
   * Transform in _E coli_

     <img src="%ATTACHURLPATH%/genome_mod_figure.JPG" alt="genome_mod_figure.JPG" width='763' height='146' />


---++ Designing Primers
   <img src="%ATTACHURLPATH%/primers.png" alt="primers.png" width='374' height='204' />

Primers need to have two components
   * a region that amplifies the insert (A(or B), 20-25nt)
   * a region that targets the new plasmid (C(or D), 30-40nt)

The target plasmid regions should preferably be 50-200nt apart (C to D).

Order (A+C) primer and (B+D) primer.

---++ PCR Insert
Use stardard 25ul Phusion (or other high fidelity polymerase) protocol
   * PCR 1(25ul reaction)
   * 5 ul 5x Buffer
   * 1.5 ul  dntps
   * 1.25 ul primer (A+C)
   * 1.25 ul primer (B+D)
   * x ul template plasmid (<250ng)
   * ddH20 to 24.5 ul
   * then add 0.5 ul Phusion

Set elongation time according to size of insert.

Purify PCR products. This can either be done through a gel extraction or by adding Dpn1 directly to the Phusion reaction mixture after PCR, digesting at 37°C for 1 hour, and then doing a standard PCR clean up. Dpn1 works efficiently in a Phusion reaction mixture. 

---++ PCR Recombinant Plasmid
Use modified 10ul Phusion (or other high fidelity polymerase) protocol 
   * 2 ul 5x Buffer
   * 1 ul  dntps
   * 500 ng PCR insert product (Note, for optimal results, have a 250-fold molar excess of your megaprimer to your target plasmid).
   * ~10 ng  target plasmid
   * ddH20 to 9.5 ul
   * then add 0.5 ul Phusion

Adjust Elongation time for the length of the entire plasmid (90 seconds per kb). 

---++ Digest 
Once the reaction is complete, digest the Recombinant Plasmid PCR product with 0.5 ul Dpn1 at 37°C for one and a half hours to remove parental DNA.
---++ Transform
Heatshock 5ul of the Dpn1-digested MEGAWHOP reaction mixture into 25ul of chemically competent _E coli_.
Barrick Lab > ProtocolList > MEGAWHOP
Topic revision: r6 - 2014-06-16 - 18:33:00 - Main.JeffreyBarrick