Knight:TOPO TA cloning

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Revision as of 11:50, 10 January 2006 by Reshma P. Shetty (talk | contribs) (References)
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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.
  • Reshma Shetty was generating some PCR fragments via annealing and primer extension and trying to cut with BioBricks enzymes and clone but the reactions were failing. Switching to TOPO TA cloning solved the problem.
  • In order for your part to be in BioBricks format after TOPO TA cloning, you must have the full BioBricks ends on your primers.
  • Austin Che observed anecdotally that he had a greater percentage of correct clones when he screened colonies from Kan plates rather than Amp plates.



  • 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. PMID 8780871.
  • Shuman S. Recombination mediated by vaccinia virus DNA topoisomerase I in Escherichia coli is sequence specific. Proc Natl Acad Sci U S A. 1991 Nov 15;88(22):10104-8. PMID 1658796
  • Cheng C, Shuman S. DNA strand transfer catalyzed by vaccinia topoisomerase: ligation of DNAs containing a 3' mononucleotide overhang. Nucleic Acids Res. 2000 May 1;28(9):1893-8. PMID 10756188
  • Shuman S. Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase. J Biol Chem. 1994 Dec 23;269(51):32678-84. PMID 7798275
  • US Patent 6,916,632 on topoisomerase-mediated cloning using a 5' overhang and blunt end. pdf html