Preparation of Genomic DNA from Bacteria

Abstract

MINIPREP OF BACTERIAL GENOMIC DNA Bacteria from a saturated liquid culture are lysed and proteins removed by digestion with proteinase K. Cell wall debris, polysaccharides, and remaining proteins are removed by selective precipitation with CTAB, and high-molecular-weight DNA is recovered from the resulting supernatant by isopropanol precipitation. Materials TE buffer (APPENDIX 2) 10% sodium dodecyl sulfate (SDS) 20 mg/ml proteinase K (stored in small single-use aliquots at −20°C) 5 M NaCl CTAB/NaCl solution 24:1 chloroform/isoamyl alcohol 25:24:1 phenol/chloroform/isoamyl alcohol (UNIT 2.1) Isopropanol 70% ethanol 1. Inoculate a 5-ml liquid culture with the bacterial strain of interest. Grow in conditions appropriate for that strain (i.e., appropriate medium, drug selection, temperature) until the culture is saturated. This may take several hours to several days, depending on the growth rate. 2. Spin 1.5 ml of the culture in a microcentrifuge for 2 min, or until a compact pellet forms. Discard the supernatant. 3. Resuspend pellet in 567 µl TE buffer by repeated pipetting. Add 30 µl of 10% SDS and 3 µl of 20 mg/ml proteinase K to give a final concentration of 100 µg/ml proteinase K in 0.5% SDS. Mix thoroughly and incubate 1 hr at 37°C. The solution should become viscous as the detergent lyses the bacterial cell walls. There should be no need to predigest the bacterial cell wall with lysozyme. 4. Add 100 µl of 5 M NaCl and mix thoroughly. This step is very important since a CTAB–nucleic acid precipitate will form if salt concentration drops below about 0.5 M at room temperature (Murray and Thompson, 1980). The aim here is to remove cell wall debris, denatured protein, and polysaccharides complexed to CTAB, while retaining the nucleic acids in solution. 5. Add 80 µl of CTAB/NaCl solution. Mix thoroughly and incubate 10 min at 65°C.