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Recombination Cloning in Bacteria
The following approach to high throughput subcloning using recombination in bacteria was developed in theFinley lab at Wayne State University by Jodi Parrish and Tom Limjindaporn (1).
Introduction
Co-transformation of a recA+ E. coli strain with a linearized plasmid and a linear fragment of DNA having
ends homologous to the plasmid, can result in insertion of the DNA fragment into the plasmid byrecombination. This approach has been used to subclone open reading frames (ORFs) and other DNA
fragments into plasmid vectors (1,2,3). We haveOR F
optimized this as an approach to rapidly subclone
PCR products into a variety of vectors, including
yeast vectors and E. coli expression vectors. We
have shown that PCR products with as little as 21linearized
bp of homology to the vector at either end can bevector
subcloned by recombination with good efficiency
and fidelity. In one project, for example, we have
Selectablesubcloned 1,184 different ORFs. The cloning
Markerefficiency observed was 75% (E. coli transformant
colonies (%) containing recombinant plasmids withcompetentinserts). Cloning fidelity was around 93% (based
E. colion DNA sequence of the region around the 5’
insertion site for 1126 clones). Included below areprotocols adapted for high throughput subcloning
and also for cloning individual and small sets of ORFs into expression vectors.

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Critical Parameters
1. The vector should be linearized by digesting with one or more unique restriction enzymes to completion.
Uncut vector in the prep will lead to a high background of E. coli transformants having no inserts in thevector.
2. We generally digest the vector with two different restriction enzymes that have nearly adjacent
recognition sites in the cloning region. This produces non-compatible sticky ends, which reduces thebackground of vector recircularization without insert. If digesting with a single enzyme, treatment withalkaline phosphatase is recommended. After linearization purification of the vector is recommended.
3. ORFs tagged with the vector homology regions can be generated by PCR using primers containing anadditional 21 bases of the vector sequence 5’ to the ORF-specific sequence. We refer to the vector
homology regions as Recombination Tags (5RT and 3RT). The 21 bases should correspond to thevector sequence adjacent to the restriction site, but not including the sticky ends. We have found that
longer tags are usually not necessary. However, recombination tags longer than 21 bases increases thetransformation efficiency. Longer tags can be added in the PCR primer or by performing a secondary
PCR.
4. The PCR products can be used directly in the transformation without further purification. However,using ethanol precipitated PCR products increases the transformation efficiency (1,2). Other methods ofpurification may also result in increased efficiency (2).
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5. The total amount of vector, and the ratio of vector to insert are important and may vary with the vector
and insert used. For a typical 10 kb yeast vector or a 6 kb E. coli pET-derived vector, and inserts from100 to 3000 bp, we have used 50 ng vector and 50 ng of PCR product.
6. We have tried a number of different E. coli strains and found that KC8 works best under someconditions. KC8 outperformed BUN10 (recB21 recC22 sbcA23), V324 (recD1009), MG1655, andDH5α(1).
7. Other methods for transformation of E. coli may be used (2,3). The chemical method outlined below isparticularly effective for high throughput cloning because it enables small volume transformations in 96well plates.

PROTOCOLS:I). Preparation of Competent Cells1
1. Streak the appropriate E.coli strain (preferablyKC8) on an LB plate2 and incubate overnightat 37oC.

5. Gently resuspend the cells in 25 ml of icecold, filter-sterilized TSB.
6. Incubate for 10 min on ice2

2. Inoculate a single colony in 5 ml of LB andincubate overnight at 37oC in a shaking
incubator.
3. Transfer the 5-ml culture to 500 ml of LB andincubate for 3 h or until the OD600 is 0.5.
4. Centrifuge the cells in two sterile 250-ml
tubes for 15 min at 4oC at 3500 rpm.

7. Aliquot the cells (500µl/tube) and quickfreeze in dry ice-ethanol.
8. Store at –80oC.
9. Determine the transformation efficiency. Use
protocol below, but use uncut vector and noinsert DNA.

II). High-throughput Cloning via Transformation of PEG-DMSO CompetentCells
1. Array 10 µl (≈50 ng) of each of the tagged PCR products into a 96-well PCR plate.
2. Add 25 µl of 2X KCM and 10 µl of sddH2O to each well and mix by pipetting up and down 3times.
3. Add 5 µl (≈50 ng) of linearized vector DNA and mix by pipetting up and down 3 times.
4. Thaw the E. coli chemo-competent cells on ice.
5. Add 50 µl of cells to each well of the 96-well PCR plate and mix by pipetting up and down 3times.
6. Seal the plate with foil and incubate for 30 min in an ice-ethanol bath.
7. Incubate for 10 min at room temperature.
8. Add 80 µl of LB, mix by pipetting up and down 3 times. Incubate for 2 h at 37oC.

29. Plate all (195 µl) of the cells onto dried 6-well culture LB plates3 containing 3.2 ml LB plus
antibiotic in each well.
10. Incubate overnight at 37oC4.

III). Cloning individual or small sets of ORFs via Transformation of PEGDMSO Competent Cells (low throughput)
1. Thaw the chemocompetent cells on ice.
2. To 25 µl of 2x KCM add 5µl (50 ng) oflinearized vector DNA, and 5 µl (50 ng) oftagged PCR product (insert). Raise volume to50µl with sddH2O (add 15 µl sddH2O).

5. Add 500 µl of LB, mix, and incubate for 1-1.5
h at 37oC.
6. Pellet the cells in microcentrifuge. Pour off
most of the supernatant except for about 200µl. Use this to resuspend the pellet.

3. Add 50 µl of cells, mix gently, and incubatefor 20 min on ice.

7. Plate all of the cells on one LB platecontaining the appropriate antibiotic.

4. Incubate for 10 min at room temp.

8. Incubate overnight at 37oC4

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This transformation protocol uses the Chemo-competent Bacteria Preparation & Transformation Protocol described in:
Walhout et al, 2000, Methods in Enzymology, 328:575-592.
2If using E. coli KC8, then include kanamycin (20 µg/ml).

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We use Costar 6-well cell culture cluster plates from Corning Incorporated (catalog number 3506).

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We have observed for two-hybrid vectors cut with two enzymes (BamH1 & EcoR1), and with PCR inserts containing 21 bp
homology tags, anywhere from 4–80 colonies. Typically around 80% of these contain vector + insert (determined usingPCR). Note that a control transformation using the linearized vector but no insert ideally should yield no greater than 1 – 10colonies.

Reagents
TSB

5xKCM

1. LB-HCL (pH6.1)

1. 0.5 M KCL*** get better result in pH 6.1

2. 150 mM CaCl2

2. 10% (w/v) PEG (mol wt = 3,400)

3. 250 mM Mg Cl2

3. 5% (v/v) DMSO
4. 10% (v/v) glycerol
5. 10mM MgCl2
6. 10mM MgSO4

Literature Cited
1. Parrish, J. R., T. Limjindaporn, R. Finley, Jr. High-throughput cloning of Campylobacter jejuni
ORFs by in vivo recombination in Escherichia coli. J. Proteome Research. 3:582-586 (2004).
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2. Oliner, J. D., K. W. Kinzler, and B. Vogelstein. In vivo cloning of PCR products in E. coli.
Nucleic Acids Research. 21:5192-5197 (1993).
3. Bubeck, P., M. Winkler, and W. Bautsch. Rapid cloning by homologous recombination in vivo.
Nucleic Acids Research. 21:3601-3602 (1993).

Contact Information:
Jodi Parrish
Center for Molecular Medicine & Genetics
Wayne State University School of Medicine
540 East Canfield Ave
Detroit, Michigan 48201
Phone (313) 577-1309
Fax (313) 577-5218
E-mail: jparrish@genetics.wayne.edu
Web: http://proteome.wayne.edu

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