Difference between revisions of "Richard Lab:Amplified insert assembly"

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#[[Richard Lab:Ligation|Ligate]] (Don't forget to kill the ligation).
#[[Richard Lab:Ligation|Ligate]] (Don't forget to kill the ligation).
#[[Richard Lab:Electroporation of E. coli|Transform]].
#[[Richard Lab:Electroporation of E. coli|Transform]].
#Plate on plates with the same antibiotic as the "vector" resistance.

Revision as of 12:29, 18 January 2011

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This is what Mike calls "New Standard Assembly" and is a method of "bio-bricking" two biological parts (i.e. pieces of DNA) together. For more information on bio-bricking see this link. This method combines the ease and speed of 3A assembly with the fidelity of standard assembly. Major benefits of this assembly method over other assembly methods include:

This protocol is typically used to do bio-brick assembly with restriction sites consisting of the following configuration:


Ocassionally other enzymes (e.g. BamHI or HindIII) are used to make protein fusions.

The two parts you want to assemble will be labeled "insert" and "vector" and will be initially contained on separate plasmids. The eventual goal of assembly is to get these parts on the same plasmid next to one another.


  1. Miniprep both "insert" and "vector" from their respective cultures using a kit or this protocol (30 mins).
  2. PCR the "insert" plasmid (This will take about 2 hrs, but start the vector digest right away).
  • Use a high-fidelity polymerase (e.g. pfu Turbo or Deep Vent).
  • Use the same primers you use for colony PCR (Annealing Temp of 55°C).
  1. Digest the "vector" for 2 hours.
  2. Purify the PCR product using a kit or this protocol.
  3. Digest insert for 1 hour (adding DpnI along with the other restriction endonucleases).
  4. Add 1μL Antarctic Phosphatase and 6μL AP Buffer to the "vector" digest and incubate until the "insert" digest is done.
  5. Kill all reactions by incubating for 20 mins at 80°C.
  6. Ligate (Don't forget to kill the ligation).
  7. Transform.
  8. Plate on plates with the same antibiotic as the "vector" resistance.
  9. Celebrate.

This entire process should take around 6 hours as many steps overlap.


  • The DpnI eliminates any background from the insert PCR.
  • The phosphatase eliminates any background vector.
  • The "vector" will be digested for a total of thee hours (including nearly one hour with Antarctic Phosphatase)
  • The "insert" will only be digested for one hour. This is okay as there is a lot of it.
  • Detractors of this method may say that it's risky to PCR the inserts because of mutations. We say:
    • This hasn't been a problem for us.
    • This is why we use a high-fidelity polymerase
    • We're sequencing the constructs anyway so we'd spot any mutations.



or instead, discuss this protocol.

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