Knight:TOPO TA cloning

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Revision as of 11:49, 30 September 2005 by Reshma P. Shetty (talk | contribs)
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Efficient cloning of PCR products.



Reshma's procedure

(Note that the kit details a slightly different procedure which may give superior efficiencies.)

  1. Mix 1 μL PCR product (amplified with Platinum PCR supermix) with 0.5 or 1μL TOPO vector (0.5μL should be sufficient.)
  2. Incubate 5 mins on the bench top
  3. Place on ice
  4. Transform


  • Tom Knight claims you can cut the reaction volume in half and it will still work fine.
  • Use fresh PCR product for best results. (The A overhang tends to get chewed back over time ... even using day old PCR product can reduce efficiency.)
  • Your primers should NOT have 5' phosphates. They interfere with topoisomerase I.
  • From Tom Knight: As this article discusses, the 5' end of the PCR primer has a strong effect on the likelihood of 3' A addition to the PCR product when using Taq or Taq mixtures as enzymes during PCR. Since it is often necessary to add such an overhang to PCR products for cutting of an added cloning site, and since for such applications the sequence is immaterial, we should probably standardize that sequence to the A tail favoring sequence, GTTTCT for all PCR primers we make. This will favor a 3' A overhang on the PCR products, and allow TA cloning, or TOPO TA cloning of these products. Blunt end cloning could still be done by using Pfu or Phusion enzymes. I can't make any sense from the result about extending the primer sequence another base which is not specified. It seems to me this can not have any effect.



M. J. Brownstein, J. D. Carpten, and J. R. Smith. Modulation of non-templated nucleotide addition by taq dna polymerase: primer modifications that facilitate genotyping. Biotechniques, 20(6):1004–6, 1008–10, 1996.