FLP Recombination in E. coli

Commonly used to eliminate the Kanamycin resistance cassette from E. coli strains from the Keio collection.

Day 1: Transform recombinase plasmid

  1. Make electrocompetent cells of the desired E. coli strain.
  2. Transform with pCP20. This plasmid has a temperature-sensitive origin of replication, confers ampicillin resistance, and encodes the FLP recombinase.
  3. Add 500 l SOC and incubate in a 1.7 ml tube shaking on its side at ≥120 rpm for 1 hr at 30C to allow antibiotic resistance induction.
  4. Plate 20 l of the culture on an LB + Amp plate, save the rest for additional plating if necessary.
  5. Grow overnight at 30C.

Expected results:

  1. 50-100 colonies expected by 18-20 hours.
  2. ALERT! Plate may take 18+ hours to be able to see colonies. DO NOT assume failure if no colonies seen first thing in morning

Day 2: Induce recombination

  1. Pick a single colony from the LB + Amp plate.
  2. Inoculate into 5 ml of LB in a test tube.
  3. Grow overnight at 43C to induce FLP recombinase expression and select for loss of pCP20.

Day 3: Plate to get single candidate recombinants

  1. Make a 106 dilution of the overnight culture via 3 wet DTs (100 l into 9.9 ml each time).
  2. Plate 50 l of this dilution on LB. This should yield a couple hundred colonies.
  3. Grow overnight at 30C to prevent partial loss of plasmid from colonies founded by cells that did not lose plasmid.

Expected results: ~200 colonies on LB plates.

Day 4: Screen for genomic recombination and plasmid loss

  1. Patch six individual colonies from this plate onto LB + Kan, LB + Amp, and LB plates. Do the patching by picking a colony and then streaking a small spot on each plate in this order. Be sure you patch on LB last. Failure to grow can sometimes occur because no cells were transferred to the later plates. This order ensures that, if you get the desired growth on the last plate and no growth on the LB + Kan and LB + Amp plates, it was not due to "running out" of cells in the later patches.
  2. Grow overnight at 37C for LB and LB + Kan and grow at 30C for LB + Amp plates.

  • NOTE: If 5mL LB is inoculated for each colony, a day can be saved. If LB culture grows, but LB plate does not, left with a choice of if you believe patching was bad or contamination.

Expected results: Most if not all patches should be completely Kanamycin and Ampicillin sensitive.

Day 5: Grow up successful recombinants (can be skipped, see note in Day 4)

  1. Inoculate 5 ml LB from patches on LB plates that score as sensitive to both antibiotics.
  2. Grow overnight at 37C, shaking at 120 rpm.

Day 6: Archive clones

  1. Freeze and archive copies of the newly created strain, there the Kan cassette has been eliminated from between the FRT sites. To guard against mutations that may occur during strain construction, it may be wise to archive and test the fitness of several separate colonies (patches).


  1. Datsenko, K.A., and Wanner, B.L. (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. U.S.A. 97: 6640-6645.
  2. Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K.A., Tomita, M., Wanner, B.L., and Mori, H. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 0008.
  3. Keio Strain construction details
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Contributors to this topic edittopic JeffreyBarrick, DanielDeatherage, SteveSowa
Topic revision: r11 - 12 Dec 2016 - 21:23:12 - Main.DanielDeatherage
Lab.ProcedureFLPFRTRecombination moved from Lab.ProcedureGeneKnockout on 26 Mar 2012 - 17:00 by Main.JeffreyBarrick - put it back
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