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Method: Alkaline Lysis Minipreps of Plasmid or Cosmid DNA

May 1 1990

C. Helms


Principle:

Special solutions required:

Time required:

Procedure:

Day 1

  1. Inoculate 5 ml of LBM medium containing 50 ug /ml ampicillin (use 200 ug / ml for cosmids) with a single bacterial colony containing the desired plasmid or cosmid. Incubate at 37 degrees C overnight on a roller drum.

Day 2

  1. Spin down cells at 2500 rpm in Beckman low speed centrifuge (e. g. the J-6) for 15 minutes. Discard supernatant.

  2. Resuspend each pellet in 200 ul GTE solution. Transfer samples to labeled eppendorf tubes. Incubate at room temperature for 5 minutes.

  3. Add 400 ul of a freshly prepared solution of lysis solution. Mix gently. Place on ice for 5 minutes.

  4. Add 300 ul of an ice-cold solution of 3 M potassium acetate (see recipe at end of procedure). Mix gently. Place on ice for 5 minutes.

  5. Centrifuge for 1 minute at 4 degrees C. Transfer the supernatant to a clean tube.

  6. Add 0.6 volume (540 ul) isopropanol to the supernatant mix and incubate at room temperature for 2 minutes. Pellet the nucleic acid (a 1 minute microcentrifuge spin top speed). Discard the supernatant.

  7. Wash the pellet twice with 1 ml 70% ethanol. Spin for 1 minute and discard the supernatant.

  8. Dry the pellet for 10 minutes in the lyophilizer or allow to air dry. Resuspend in 50 ul TE pH 7.5. Add 1 ul of a 10 mg/ml solution of RNAase and incubate for 30 minutes at room temperature.

  9. Assay the DNA on a minigel with appropriate concentration standards before restricting the DNA. The expected yield is 5-10 ug plasmid DNA or 2-5 ug cosmid DNA from 5 ml of culture.

    NOTE: This procedure can be scaled up many fold. For cell culture volumes over 25 mls reprecipitate with isopropanol after step 9 since a great deal of KOAc is still held in large pellets (which lowers pH). Before banding the DNA in CsCl check that the DNA solution is of neutral pH.

Solutions:

  1. GTE solution:

       stock solution            volume      final concentration    40%  sterile glucose      2.27 ml         50 mM   0.5 M EDTA, pH 8           2.0 ml         10 mM   1M Tris-HCl, pH 8          2.5 ml         25 mM   sterile ddH2O            93.23 ml   Total:                   100.0 ml   Use all sterile stock solutions. Store at 4 degrees C.  

  2. Lysis Solution:

       stock solution          	volume     final concentration 	   1N NaOH	                2.0 ml          0.2 N   10% SDS	                1.0 ml           1%    sterile ddH2O                 7.0 ml   Total:                       10.0 ml   Prepare fresh solution prior to use.  
  3. 3 M Potassium Acetate:

       stock solution             volume	 	   5 M KOAc                    60 ml    glacial acetic acid       11.5 ml    ddH2O 	            28.5 ml        		             100 ml  Filter sterilize.  The resulting solution is 3 M potassium and 5 M acetate and has a pH of about 4.8.  
  4. RNAase (10 mg/ml):

        Dissolve 100 mg RNAase A (pancreatic RNAase)    in 10 ml 10mM Tris-HCl 15 mM NaCl.    Heat to 100 degrees C (in a beaker of    boiling water) for 15 minutes.  Cool    slowly to room temperature. Dispense into    aliquots and store at -20 degrees C.  

References:

Sambrook J. Fritsch E.F. and T. Maniatis (1989). Molecular Cloning A Laboratory Manual. Second edition. Cold Spring Harbor Laboratory Press pp.1.25-1.28.