Smolke:Protocols/Insert prep

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Revision as of 13:43, 15 October 2009 by Yvchen (talk | contribs) (Notes)

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  • Prepare 5 x 100-ul PCR reactions for each insert
    • 400 ul water
    • 50 ul 10x Taq buffer
    • 16 ul 5 mM MgCl2
    • 10 ul dNTP
    • 10 ul Fwd primer
    • 10 ul Rev primer
    • 250 ng plasmid
    • 10 ul 1:10 Taq DNA polymerase
  • After PCR, combine products from the five tubes, and run 5 ul on a gel to verify product length
  • Purify and concentrate PCR products by phenol-chloroform extraction and ethanol precipitation
  • Resuspend inserts to appropriate volume for digestion reaction


  • Amplification rates:
    • Taq: 0.5-1 min/kb (YC). 1 min/kb (JKM)
    • Pfu: 2 min/kb (JKM)
    • PfuUltra: 1 min/kb (JKM)
    • PfuUltraII: 0.25 min/kb (JKM)
    • MutazymeII: 2 min/kb (JKM)
  • Size: I consider this massively oversized. In my experience, 50uL of PCR products (~3ug product) is more than sufficient for cloning. -Josh
    • I think this depends on what you're cloning. My inserts tend to be <150 bp, which makes it difficult to purify without loss downstream, hence the large volume that I generally use.
  • Polymerase: I use Pfu (>500bp) or PfuUltraII (>~3kb) for any lengthy PCR that I intend to clone. -Josh
  • Magnesium: I have never felt a need to vary my magnesium concentration on a reaction-by-reaction basis. So I mix my Taq buffer using a standard amount of magnesium (2mM, personally), and save an extra step. The magnesium concentration given above (0.16mM) seems way too low. -Josh