Restriction enzymes and DNA-modifying enzymes were purchased from Promega and used according to the manufacturer’s recommendations. Standard PCR amplifications were performed with BioTaq DNA polymerase (Bioline).
When necessary, high fidelity and blunt-ended PCR products were amplified with Expand High Fidelity (Roche) and Accuzyme (Bioline) DNA polymerases, respectively. All oligonucleotides (Sigma) used in the study are listed in Table 2. PCR products were purified with the High Pure PCR Product Purification Kit (Roche). Daporinad in vitro When high concentrations of purified PCR products were required, a MinElute PCR Purification Kit (Qiagen) was used. All the recombinant plasmids obtained in the study, and the PCR products indicated, were sequenced by the Macrogen sequencing service (Seoul, Korea). Electroporation All strains were made electrocompetent as follows. Bacterial overnight cultures were grown in LB broth and subcultured at a dilution of
1:20 in 100 ml of fresh LB medium. Cultures were grown at an OD600 of 0.8 and then incubated on ice for 10 min. Cells were pelleted by centrifugation and then washed 3 times with 10% (v/v) glycerol and finally resuspended in 500 μl of 10% (v/v) glycerol. An aliquot of 100 μl ALK inhibitor drugs of the cell suspension was mixed with the recombinant DNA (up to 20 μl). The mixture was placed in a pre-chilled sterile electroporation cuvette (1 mm electrode gap, Bio-Rad) and immediately pulsed by use of a Bio-Rad Gene Pulser (1.8 kV, 200 W, and 25 μF). The mixture was incubated at 37°C for 1 h with 1 ml of LB broth. Cells were spread on LB agar containing the appropriate antibiotics and incubated at 37°C. Knockout construction by gene replacement The upstream
and downstream regions SPTLC1 (approximately 0.5 kbp each) of the target gene were amplified from genomic DNA of A. baumannii ATCC 17978 strain using primer pairs upFW + upintRV and dwintFW + dwRV (Figure 6), respectively. The kanamycin cassette was amplified using primers Kmup and Kmdw (Table 2) and the pCR-BluntII-TOPO vector (Invitrogen) as a template. The upintRV and dwintFW primers (Figure 6) contained, at their 5′ ends, an AR-13324 mw extension of approximately 20 nucleotides homologous to the Kmup and Kmdw primers, respectively. The three PCR products obtained in the first step were mixed at equimolar concentrations and subjected to a nested overlap-extension PCR with FWnest and RVnest primers (Figure 6) to generate a kanamycin resistance cassette flanked by both the upstream and the downstream gene homologous regions. The nested overlap-extension PCR was carried out with an Expand High Fidelity Taq DNA polymerase (Roche), according to the manufacturer’s recommendations; the conditions used were as follows: 94°C for 15 s, 40°C for 1 min, 72°C for 2 min (10 cycles); 94°C for 15 s, 55°C for 1 min, 72°C for 3 min (20 cycles), and a final extension at 68°C for 10 min. Electroporation of the A.