Preparation of High-Molecular-Weight Human DNA Restriction Fragments in Agarose Plugs


Molecular Biology
  The Central Dogma
  Protein Synthesis in Cell Free Systems
  Polytene Chromosomes of Dipterans
  Salivary Gland Preparation (Squash Technique)
  Extraction of Chromatin
  Chromatin Electrophoresis
  Extraction and Electrophoresis of Histones
  Karyotype Analysis
  In Situ Hybridization
  Culturing Peripheral Blood Lymphocytes
  Microslide Preparation of Metaphases for In-Situ Hybridization
  Staining Chromosomes (G-Banding)
  Nucleic Acids
  Extraction of DNA from Bovine Spleen
  Purification of DNA
  Characterization of DNA
  DNA-Dische Diphenylamine Determination
  Melting Point Determination
  CsCl-Density Separation of DNA
  Phenol Extraction of rRNA (Rat liver)
  Spectrophotometric Analysis of rRNA
  Determination of Amount of RNA by the Orcinol Method
  Sucrose Density Fractionation
  Nucleotide Composition of RNA
  Isolation of Genomic DNA—DNA Extraction Procedure
  Isolation of Genomic DNA from Bacterial Cells
  Preparation of Genomic DNA from Bacteria
  Extraction of Genomic DNA from Plant Source
  Extraction of DNA from Goat Liver
  Isolation of Cotton Genomic DNA from Leaf Tissue
  Arabidopsis Thaliana DNA Isolation
  Plant DNA Extraction
  Phenol/Chloroform Extraction of DNA
  Ethanol Precipitation of DNA
  Isolation of Mitochondrial DNA
  Isolation of Chloroplast DNA
  DNA Extraction of Rhizobium (CsCl Method)
  Isolation of Plasmids
  RNA Isolation
  Preparation of Vanadyl-Ribonucleoside Complexes that Inhibit Ribonuclease Activity
  RNA Extraction Method for Cotton
  Isolation of RNA from Bacteroids
  Isolation of RNA from Free-Living Rhizobia
  Estimation of DNA purity and Quantification
  Fungal DNA Isolation
  Methylene Blue DNA Staining
  Blotting Techniques—Southern, Northern, Western Blotting
  Preparing the Probe
  Southern Blotting (First Method)
  Southern Blotting (Second Method)
  Western Blotting
  Western Blot Analysis of Epitoped-tagged Proteins using the Chemifluorescent Detection Method for Alkaline Phosphatase-conjugated Antibodies
  Southern Blot
  Southern Analysis of Mouse Toe/Tail DNA
  Northern Blotting
  Restriction Digestion Methods—Restriction Enzyme Digests
  Restriction Digestion of Plasmid, Cosmid, and Phage DNAs
  Manual Method of Restriction Digestion of Human DNA
  Preparation of High-Molecular-Weight Human DNA Restriction Fragments in Agarose Plugs
  Restriction Enzyme Digestion of DNA
  Electroelution of DNA Fragments from Agarose into Dialysis Tubing
  Isolation of Restriction Fragments from Agarose Gels by Collection onto DEAE Cellulose
  Ligation of Insert DNA to Vector DNA
  PCR Methods (Polymerase Chain Reaction)
  Polymerase Chain Reaction
  DNA Amplification by the PCR Method

To prepare intact mammalian chromosomal DNA for use in pulsed-field electrophoresis mapping experiments, using rare cutting restriction enzymes.

Time Required
4 days.

Phenylmethylsulfonyl fluoride (PMSF)

Day 1–2

  1. Place freshly grown mammalian cells in a 15-µL Falcon tube and centrifuge in a Beckman tabletop centrifuge at 1000 rpm for 15 minutes. Pour off supernatant, and resuspend pellet in 10 mL of phosphate buffered saline (PBS). Centrifuge at 1000 rpm for 15 minutes again, then resuspend in PBS to achieve a cell concentration of 1–2 x 107 cells/mL (refer to methods in tissue culture regarding hemocytometer for cell counting procedure).
  2. Mix an equal volume of cells (1–2 µL) with premelted 1% low gelling agarose which has been cooled to 45°;C–50°;C, using a Pasteur pipette; immediately distribute the mixture to plug molds for the CHEF apparatus. Place the mold on ice for 15 minutes.
  3. Remove plugs, then incubate in 6 well tissue culture plates (5 µL/well, several plugs/well) in ESP solution at 50°;C with gentle shaking for 2 days; be sure to seal the 6 well plate securely with parafilm to prevent evaporation of the samples. Plugs can now be stored in ESP at 4°;C, or one can proceed as follows.
Day 3
  1. For each digest condition, use approximately ¼ of a plug, roughly the size that would fill a well on the CHEF DR apparatus. Place each in 1 mL of 1-mM PMSF (caution: extremely toxic to mucous membranes, do not inhale or allow contact with skin) diluted from 0.1 M stock in TE (pH 8), and slowly rotate plates at room temperature for 2 hours. Replace with new PMSF aliquot and repeat. Remove PMSF, and wash in 1 mL of TE (pH 8) 3 times for 1–2 hours each by slow rotation at room temperature.
  2. Place each plug in 250µL of appropriate restriction buffer (1X) in eppendorf tubes at room temperature for 30 minutes. Aspirate buffer carefully, then replace with fresh buffer and hold at room temperature for 30 minutes. Replace with 250µL of fresh buffer, then add 25 µg of BSA to each tube. Add 20 units of enzyme per mg of DNA to tubes containing the appropriate buffer (¼ of one plug should be approximately equal to 5–10 µg of DNA if the cell counts are correct). Incubate overnight at the appropriate temperature; additional enzyme can be added the next morning and incubation carried out for 4 more hours if so desired.
Day 4
  1. Replace buffer with 1 mL of ES solution, and incubate at 50°;C for 2 hours with gentle shaking.
  2. Replace ES with 250 µL ESP solution and incubate at 50°;C for an additional 2 hours.
  3. Load the plugs into a gel poured for the CHEF DR apparatus. Run under conditions appropriate for the fragment sizes expected. Fragments in the 200–2200 kb size range can be effectively separated on a 1.0% agarose gel run at 200 V with a switch time of 60 seconds for 15 hours, and 90 seconds for 9 hours.

  • ESP solution:
    0.5 M EDTA, pH 9.0–9.5
    1% sodium laurylsarcosine
    1 mg/mL Proteinase K
  • PMSF stock:
    0.1 M PMSF in 2-Propanol
  • ES solution:
    0.5 M EDTA, pH 9.0–9.5
    1% sodium laurylsarcosine