Top : Molecular Biology : Isolation of Plasmid DNA

Isolation of Plasmid DNA

Author: Saji Menon
Affiliation: Birla Institute of Scientific Research
Source: Protocol Online
Date Added: Sun Mar 22 2009
Date Modified: Sun May 17 2009
Abstract: A simple method to isolate plasmid DNA

Reagents and solutions

  1. Alkaline Solution I
    50 mM glucose
    25 mM Tris HCl (pH 8.0)
    10 mM EDTA (pH 8.0)
  2. 10 mg/ml lysozyme
  3. Alkaline Solution II
    0.2 N NaOH (2.0 ml of 10 N NaOH in 100ml double distilled water)
    1.0% SDS
  4. Alkaline Solution III
    5 M Potassium acetate
    Glacial acetic acid
    Autoclaved water
  5. TE buffer
    10 mM Tris HCl (pH 8.0)
    1.0 mM EDTA (pH 8.0)
  6. Ring stand with clamp
  7. 26 gauge needle
  8. 1 cc syringe
  9. Dialysis buffer
    1 M Tris HCl (pH 7.5)
    0.5 M EDTA (pH 8.0)
    Autoclaved distilled water (1L)
  10. Ampilcillin 100 g/ml
  11. Ice cold Isopropyl alcohol
  12. Cesium chloride as per Plasmid DNA sample
  13. Dialysis tubings (Nylon)
  14. 5 M NaCl
    29.22 g NaCl in 75 ml water and bring the volume to 100 ml.
  15. Isoamyl alcohol
  16. Luria Broth media
    1 gm Tryptone
    0.5 gm Yeast extract
    1 gm Sodium chloride
    Deionised water 75 ml
    Shake all the solutes until dissolved. Adjust the pH to 7.0 with 5 N NaOH. Bring the volume of the solution to 100 ml with deionised water and sterilize it by autoclaving it for 20 minutes at 15 psi.


Isolation of Plasmid DNA

  1. Pick up a colony of bacteria and inoculate it in a conical flask containing 100 ml autoclaved Luria broth media supplemented with antibiotic (Ampicillin 100 g/ml) and incubate overnight in a 37C shaking water bath at 250 rpm.
  2. Pour the culture in a 2.0 ml centrifuge tube and centrifuge at 5000 rpm for 20 minutes.
  3. Discard the supernatant and wash the pellet in 1.0 ml double distilled water. Centrifuge the solution at 1000 rpm for 5 minutes.
  4. Discard the supernatant and resuspend the pellet in 250l cold alkaline solution I (stored at 4C). Mix properly so that the pellet dissolves.
  5. Add 20 mg of lysozyme in the above solution and mix well. Allow it to incubate on ice for 15 minutes.
  6. Add 500 l of alkaline solution II and mix properly. Mix the solution by flicking.
  7. Now add 250 l of alkaline solution III and incubate it on ice for 15 minutes.
  8. Centrifuge the sample at 5000 rpm for 10 minutes and filter the supernatant into an autoclaved 2.0 ml centrifuge tube.
  9. Fill the tube with the same amount of ice-cold isopropyl alcohol (stored at-20C) and incubate in cold (-20C) for 30 minutes.
  10. Centrifuge the sample at 5000 rpm for 15 minutes. Discard the supernatant and air dry the pellet.
  11. Resuspend the pellet in 500 l TE buffer.
Purification of Plasmid DNA using Cesium Chloride

  1. When the pellet is suspended completely, measure the mass of plasmid DNA by using a balance. For every gram of plasmid DNA solution, add 1.0 gm of solid cesium chloride. Warm the solution at 30C to dissolve the CsCl salt.
  2. Add 5 l of 10mg/ml ethidium bromide to the above plasmid DNA solution.
  3. Centrifuge the sample at 50,000 rpm for 10-15 hours at 20C in an ultracentrifuge.
  4. After the first run is complete remove the tube carefully and place it in the clamp and insert a needle just below the band. Remove the cap on the tube and pull out the band with the help of needle and syringe.
  5. Place the sample in another ultra centrifuge tube and fill the tube with a solution of cesium chloride and TE. Spin at 50,000 rpm for 5 hours.
  6. When the run is complete follow the above instructions for removing the bands.
  7. Place the bands in a centrifuge tube and add equal volumes of TE and mix well. Now add isoamyl alcohol twice the volume of sample in the tube. Shake well and allow the phases to separate.
  8. Pipet off the top pink layer and repeat the extraction with isoamyl alcohol until the top layer is clear and transparent.

Dialysis of Plasmid DNA

  1. Prepare pieces of dialysis tubing by rinsing very well in autoclaved distilled water. Tie one end of the tube and carefully suspend he extracted plasmid DNA band into the tubing. Tie the other end too and place the sample in dialysis buffer.
  2. Dialyze for at least 6 hours at 4C using a magnetic stirrer. Repeat the process in new buffer solution.
  3. Once the dialysis is complete, remove the liquid from the tubing and transfer it into another tube.
  4. Add 1/10 volume of 5 M NaCl and twice the volume of pure ethanol.
  5. Centrifuge the samples for 20 minutes at 5000 rpm at 4C.
  6. Discard the supernatant, leaving the pellet.
  7. Rinse with 95% Ethanol and resuspend the pellet in 100 μl of TE buffer (pH 8.0) or autoclaved distilled water.

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