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  Section: Biotechnology Methods » Molecular Biology
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Preparing the Probe

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

Radioactive DNA probes for Southerns and Northerns
The objective is to create a radioactive copy of a double-stranded DNA fragment. The process usually begins with a estriction fragment of a plasmid containing the gene of interest. The plasmid is digested with particular restriction enzymes and the digest is run on an agarose gel. Since a plasmid is usually less than 20 kbp long, this results in 2 to 10 DNA fragments of different lengths. If the restriction map of the plasmid is known, the desired band can be identified on the gel. The band is then cut out of the gel and the DNA is extracted from it. Because the bands are well separated by the gel, the isolated DNA is a pure population of identical double-stranded DNA fragments.
The DNA restriction fragment (template) is then labeled by random hexamer labeling:
  1. The template DNA is denatured; the strands are separated by boiling.
  2. A mixture of DNA hexamers (6 nucleotides of ssDNA) containing all possible sequences is added to the denatured template and allowed to base-pair. They pair at many sites along each strand of DNA.
  3. DNA polymerase is added along with dATP, dGTP, dTTP, and radioactive dCTP. Usually, the phosphate bonded to the sugar (the a-phosphate, the one that is incorporated into the DNA strand) is synthesized from phosphorus-32 (32P), which is radioactive.
  4. The mixture is boiled to separate the strands and is ready for hybridization.
    This process is diagrammed below (labeled DNA shown in gray):

This produces a radioactive single-stranded DNA copy of both strands of the template for use as a probe.

Radioactive Antibodies for Westerns

Antibodies are raised by injecting a purified protein into an animal, usually a rabbit or a mouse. This produces an immune response to that protein. Antibodies isolated from the serum (blood) of that rabbit will bind to the protein used for immunization. These antibodies are protein molecules and are not themselves radioactive.

They are labeled by chemically modifying the side chains of tyrosines in the antibody with iodine-125 (125I), which is radioactive. A set of enzymes catalyzes the following reaction:
antibody-tyrosine + 125I– + H2O2 → H2O + 125 iodo-tyrosineantibody

Enzyme-conjugated Antibodies for Westerns
Antibodies against a particular protein are raised as above and labeled by chemically cross-linking the antibody molecules to molecules of an enzyme. The resulting antibody-enzyme conjugate is still able to bind to the target protein.

In all 3 blots, the labeled probe is added to the blocked filter in buffer and incubated for several hours to allow the probe molecules to find their targets.

After hybrids have formed between the probe and target, it is necessary to remove any probe that is on the filter that is not stuck to the target molecules.

Because the nitrocellulose is absorbent, some of the probe soaks into the filter and must be removed. If it is not removed, the whole filter will be radioactive and the specific hybrids will be undetectable.

To do this, the filter is rinsed repeatedly in several changes of buffer to wash off any unhybridized probe.


In Southerns and Northerns, hybrids can form between molecules with similar but not necessarily identical sequences (For example, the same gene from 2 different species). This property can be used to study genes from different organisms or genes that are mutated. The washing conditions can be varied so that hybrids with differing mismatch frequencies are maintained. This is called “controlling the stringency”—the higher the wash temperature, the more stringent the wash and the fewer mismatches per hybrid allowed.

Detecting the Probe-Target Hybrids
At this point, you have a sheet of nitrocellulose with spots of probe bound wherever the probe molecules could form hybrids with their targets. The filter now looks like a blank sheet of paper—you must now detect where the probe has bound.

If the probe is radioactive, the radioactive particles that it emits can expose x-ray film. If you press the filter up against x-ray film and leave it in the dark for a few minutes to a few weeks, the film will be exposed wherever the probe bound to the filter. After development, there will be dark spots on the film wherever the probe bound.

Enzymatic Development
If an antibody-enzyme conjugate was used as a probe, this can be detected by soaking the filter in a solution of a substrate for the enzyme. Usually, the substrate produces an insoluble colored product (a chromogenic substrate) when acted upon by the enzyme. This produces a deposit of colored product wherever the probe bound.



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