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  Section: Biotechnology Methods » Molecular Biology
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Chromatin Electrophoresis

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

  • 14 M Urea
  • 6 M NaCl
  • 0.05 M and 0.9 M acetic acid
  • Dialysis tubing
  • Electrophoresis apparatus
  • Prepared gels
  • 10 M urea-0.9 N acetic acid-0.5 M β-mercaptoethanol
  • 0.25% Coomassie Blue
  1. To some chromatin suspension add concentrated urea and concentrated NaCl separately to yield a final concentration of 7 M urea and 3 M NaCl.
  2. Centrifuge the clear solution at 85,500 xg for 48 hours at 4°C to pelletextracted DNA.
  3. Collect the supernatant and dialyze it against 0.05 M acetic acid (3 changes, 6 liters each at 4°C). Remove the dialyzed protein solution and lyophilize it to dryness.
  4. Meanwhile, set up a standard polyacrylamide gel, using 15% acrylamide (15%T:5%C) in 2.5 M urea and 0.9 M acetic acid. Set up the gel in the electrophoresis unit and run the gel at 2 mA/gel for 2 hours with no sample, using 0.9 M acetic acid for the running buffer.
  5. Dissolve the lyophilized protein from step 3 in 10 M urea-0.9 N acetic acid-0.5 M β--mercaptoethanol (to a final concentration of 500 micrograms protein per 100 µL of buffer) and incubate at room temperature for 12–14 hours prior to the next step.
  6. Apply 20 µL samples of the redissolved protein extract to 0.6 × 8.0 cm polyacrylamide prepared as in step 4.
  7. The gels are run against 0.9 M acetic acid in both upper and lower baths for approximately 3 hours at 100 V.
  8. Stain the gels for 1 hour in Coomassie Blue, rinse with water, destain, and store in 7% acetic acid.
  9. If densitometry measurements are made, 5 µg of pea bud fraction II, a protein, has a density of 1.360 density units × mm with a 95% confidence limit of 10%. By comparison, the density value can be used to quantitate the concentration of protein fractions in mg of your sample.

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