BLOTTING

TECHNIQUES
Y . Sunaina M . Pharmacy Industrial Pharmacy 170211889011

ELECTROPHORESIS

Electrophoresis - the migration of charged molecules in an electric field though a solution or solid support We can separate DNA and RNA molecules by size using agarose gel electrophoresis

DNA (or RNA) samples loaded into wells

BLOTTING TECHNIQUES

Blotting Transfer of DNA, RNA or Proteins, typically from a electrophoresis gel to a membrane e.g. nitrocellulose. This membrane can then be subject to further techniques such as hybridization. Hybridization Process where two complementary single strands of nucleic acid (DNA or RNA) form a double helix.

BLOTTING TECHNIQUES

Southernblot for DNA analysis, requires electrophoresis

Northern blot for RNA analysis, requires electrophoresis Western blot for protein analysis, requires electrophoresis

Dot blot: no electrophoresis required for DNA/RNA/protein analysis

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FLOW CHART OF SOUTERN BLOTTING

Preparing the samples and running the gel Southern transfer Probe preparation Prehybridization Hybridization Post-hybridization washing Signal detection
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SOUTHERN BLOTTING

Transfer buffer

SOUTHERN BLOTTING

Step 1: Digest the dsDNA

The DNA is isolated & digested with restriction endonucleases. Results in production of dsDNA fragments of varying length depending on location of restriction sites.

 Step y

2: Run the digest.

Resulting fragments are separated through agarose gel electrophoresis. Standard DNA size markers should also be run - size of the sample fragments can be estimated Stain with ethidium bromide & visualized under UV light.
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depurination step is optional. y DNA fragments larger than 15kb are difficult to transfer y HCl used to remove the purines, reducing the size of the fragments 3: Denature the DNA The agarose gel is soaked in a basic solution, NaOH. After this , the base is neutralized before proceeding to the membrane transfer
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Step

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 Step
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4: Transfer the denatured DNA to a filter membrane

Nitrocellulose/nylon filter membranes used. Nylon has higher binding capacity & less fragile. In this, the DNA transfer is achieved by capillary action. Electrotransfer is less common. After this, the filter membrane should be exposed to UV light to cross link the DNA fragments to the membrane.
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Step 5: Hybridization Analysis y A) The membrane is soaked in a prehybridization buffer. prevents nonspecific binding of the probe
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B) It is then exposed hybridization probea single DNA fragment with a specific sequence. Contains a sequence that is complementary to the DNA sequence of interest. If the sequence of interest is present on the membrane, the probe will anneal to this sequence.

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Step 6 Post Hybridization After hybridization, excess probe is washed from the membrane The pattern of hybridization is visualized on Xray film by autoradiography in the case of a radioactive or fluorescent probe, / by development of color if a chromogenic detection method is used.

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APPLICATIONS

Diagnosis of HIV-1 infection Identify mutations, deletions, and gene rearrangements In prognosis of cancer and in prenatal diagnosis of genetic diseases

Investigation

of diseases with less obvious genetic transmission, such as ischaemic heart disease disease, hepatocellular carcinoma
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Malignant

The main use is to identity any changes in DNA sequencing or genes expressed, e.g. comparing genes expressed by a diseased cell to genes of an healthy cell. Restriction Fragment Length Polymorphism (RFLP) Polymorphism refers to the DNA sequence variation between individuals of a species. If the sequence variation occurs at the restriction sites, it could result in RFLP. example is the RFLP due to globin gene mutation
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RESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP)

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NORTHERN BLOTTING
RNA

was found not to bind with nitrocellulose filter. bands are blot transferred from the formaldehyde agarose gel into chemically reactive paper. aminobenzyloxymethyl cellulose paper prepared from whatmann filter paper number-540 after a series of uncomplicated reactions, is diazotized.
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RNA

An

 They

are hybridized & detected by autoradiography. are treated with SI nuclease and RNA ase which digests the single stranded RNA / DNA probe. of mRNA is revealed to the extent to which mRNA protects the nucleic acid probe.
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Hybrids

Structure

NORTHERN BLOTTING

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WESTERN BLOTTING
Extraction

of protein from transformed

cells Separation of protein by using SDS-PAGE where SDS acts as solvent for electrophoresis. Transfer of electrophoresed gel in a buffer at low temperature(400 c ) for half an hour. Blotting of proteins into nitrocellulose filter paper
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Placing of whatmann filter paper on a cathode plate followed by stack of coarse filter whatmann filter electrophoresed gel, nitrocellulose filter, whatmann filter paper, coarse filter stack, whatmann filter &anode plate Putting the complete set up in transfer tank containing sufficient transfer buffer Application of an electric field cause the migration of proteins from gel to nitrocellulose filter

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WESTERN BLOTTING

Hybridisation using radiolabelled antibodies(I123antibodies) Washing of the nitrocellulose filter with a wash solution (Tris-bufferd saline + Tween 20) Detection of hybridised sequences by autoradiography.

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WESTERN BLOTTING PROCEDURE

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DOT BLOTS AND SLOT BLOTS

Cloned /pure extracted DNAs to be tested are spotted adjacent to each other on a nitrocellulose membrane DNA blots thus produced are immobilized and denatured so that they are bound on membrane as single stranded DNA blots The membrane is then hybridized with a radioactively labelled probe (DNA or RNA). The dot representing sequence related to probe will light up by autoradiography

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ADVANTAGES

No steps involving digestion with enzyme, gel electrophoresis or transfer from gel to membrane are needed in this technique. Therefore it is more convenient , when no restriction sites are needed to be studied.

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DOT BLOTS FROM 25 HORDEUM SPECIES, SHOWING DIFFERENCE IN ABUNDANCE OF SEQUENCE RELATED TO PROBE PSC 119.

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An apparatus is used for placing spots on the membrane, through slots made in this equipment. Slot blots from genomic DNA of 10 Avena species, showing difference in abundance of sequences related to two different probes(pAvs 2, pAvs 6).

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Southern blotting Molecule detected Gel electrophoresis Gel pretreatment DNA (ds)

Northern blotting mRNA (ss)

Western blotting Protein

Agarose gel

Formaldehyde agarose gel _

Polyacrylamide gel _

Depurination Denaturation & Neutralization

Blotting method Capillary transfer

Capillary transfer

Electric transfer

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REFERENCES

PK Gupta., Elements of biotechnology, rastogi publications, Meerut,2005. (page no: 55-57) R.C.Dubey., A text book of biotechnology, Rajendra Ravindra printers ltd, Newdelhi,2006.(page no: 127-128) S.P.Vyas., Pharmaceutical biochemistry, CBS publishers ,Newdelhi,1998. (page no: 389) U.Satyanarayana, U.chakrapani, Biochemistry, Arunabhasen books & allied pvt. Ltd, 2007.(page no: 587589) Robert k.Murray, Daryl k.Granner, Peter A.Mayer, Victor W.Rodwell. Harpers illustrated biochemistry, Lange medical publications,1998.(page no. 403-404) http://en.wikipedia.org/wiki/Western_blot
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Thank you
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