2. Definition
īVisualization of specific DNA , RNA & protein among
many thousands of contaminating molecules requires
the convergence of number of techniques which are
collectively termed BLOT transfer .
3. Types of blotting techniques
ī1 ) Southern blotting ( to detect DNA )
ī2 ) Northern blotting ( to detect RNA )
ī3 ) Western blotting ( to detect protein )
4. Southern Blotting
īIn 1975 Edward Southern developed this technique
that is widely used to detect fragments of DNA .
ī This requires
1 ) Separation of DNA or DNA fragments by agarose
gel electrophoresis .
2 ) DNA fragments are blotted onto a strip of
nitrocellulose or a nylon membrane.
3 ) Identification by hybridization with a labeled
,complementary nucleic acid probe.
5. Definition
īSouthern blot a method for transferring DNA from an
agarose gel to nitrocellulose filter , on which the
DNA can be detected by suitable probe ( eg :
complementary DNA or RNA ) .
6. ProcedureīThe DNA sample is digested by restriction
endonucleases , producing small fragments & that are
amenable for analysis .
īFragments are seperated by agarose gel
electrophoresis or PAGE .
īThe mobility of nucleic acids in agarose gels is
influenced by agarose concentration , molecular size
& molecular conformation of the nucleic acid .
7. īAgarose concentration of 0.3 â 2 %are most effective
for nucleic acid separation .
īLike proteins nucleic acids migrate at rate that is
inversely proportional to the logarithm of their
molecular weight .
8. contd
īSeparated nucleic acids are visualized by fluorescent
dye ethidium bromide .
īThe agarose gel is soaked in a solution of dye &
washed for remain excess dye .
īillumination of the rinsed slab with UV light reveals
red orange stains where nucleic acids are located .
9. contdīEthidium bromide stains both single & double
stranded nucleic acids , the fluorescence is much
greater with double stranded molecules .
īThe electrophoresis can be performed with dye
incorporated in the gel & buffer .
īThis has the advantage that the gel can be
illuminated with UV light during electrophoresis to
view the extent of separation.
10. contdīThe mobility of DNA may be reduced by 10 -15 % in
the presence of ethidium bromide .
īEthidium bromide must be used with great care as it
is a potent mutagen .
īGloves should be worn at all times while using the
dye solutions or handling gels .
11. contdīNewer fluorescent SYBR dyes produced by molecular
probes offer several advantages , less toxic & 5 times
more sensitive than ethidium bromide.
īLabeled DNA with radioisotope P32
at 5â & 3â ends .
īP 32
is a strong β emitter .
īBands of labeled DNA on electrophoresis gel can
located by autoradiography .
12. contdīLabelling molecule before analysis with coenzyme
biotin , biotin forms a strong complex with enzyme
linked streptavidin .
īPAGE is useful for analysing small fragments of DNA
upto 3,50,00 daltons ( 500 bp ) in molecular size .
īLarge molecules of DNA could be separated by pulsed
field gel electrophoresis.
13. Blotting
īTransfer of DNA from gel to nitrocellulose
membrane done by
1 ) Weak acid treatment to depurinate &fragment
the DNA , thus make it smaller & easier to elute
from the gel .
followed by
2) Denaturate with strong base& neutralisation (
hydrolyzes phosphodiester back bone at
depurinated sites )
īsingle strands bind to membranes more
efficiently )
īA buffer is used to facilitate the transfer .
14. contdīOriginal methods of transfer relied on capillary action
.
īVaccum or preassure systems can be used to speed
the transfer .
īFaster & more efficient transfer is afforded by the use
of an electroblotter .
īElectroblotting process is usually completes in 1-4
hours .
15. Hybridization assaysīAll hybridization assays are based on the ability of
nucleic acids to form specific double stranded hybrids
.
īThe process requires
ī1 ) A probe that can target nucleic acids & allow for
specific complemenatary base pairing .
2) A method to detect any resulting double strands
nucleic acids .
16. contd
ī Conditions of high stringency in hybridization
assay are
1) Low salt concentration ,
2) High formamide levels ,
3) High temparature .
As the stringency of the assay is lowered
increasing number of base mismatches are tolerated .
conditions of high stringency require exact base
pairing .
17. īThe time required to hybridize the probe to a given
fraction of the target remains proportional to the
probe concentration .
īThe rate of hybridization reaction is influenced by
temperature & ionic strength.
īAbove the Tm no stable hybrids are present .
īDivalent cations like Mg+2
have stronger effect on
hybridization .
18. contd
īUnbound probes are removed by washing
īProbe bound to the membrane is detected by
autoradiogarphy , which reveals the DNA fragments
to which the probe hybridized .
19. ApplicationsīSouthern blots are used in gene discovery,
mapping , evolution & development studies ,
diagnostics & forensics .
īDeletions / insertions .
īpointmutations / polymorphisms .
īStructural rearrangements .
īAllow for determination of molecular weights of
restriction fragments .
īPresence of particular bit of DNA in the sample.
20. Northern blotting
īNorthern blotting is a technique for detection of
specific RNA sequences .
īDeveloped by James alwine & George stark.
īRNA molecules have defined length & much
shorter than genomic DNA it is not necessary to
cleave RNA before electrophoresis .
īRNA is more susceptible to degradation than
DNA .
īRNA sample are separated based on size by gel
electrophoresis .
21. contdīRNA is blotted on to a nylon positively charged
membrane .
īThe membrane is placed in a hybridization buffer
with a labeled probe ( usually DNA )
īLabeled probe is detected by autoradiography
īExpression patterns of sequences of interest in
different samples can be compared .
22. Applications
īA standard for direct study of the gene expression at
the level of mRNA .
īDetection of mRNA transcript size .
īStudy of RNA splicing â can detect alternatively
spliced transcripts .
īStudy RNA half life
23. Disadvantages
īTime consuming procedure .
īRNA samples can be degraded by RNases .
īUse of radioactive probes .
īDetection with multiple probes is a problem .
24. Western blottingīWestern blotting is an immunoblotting technique
which rely on the specificity of binding between the
molecule of interest & a probe to allow detection of
molecule of interest in a mixture of many other
similar molecules .
īIn western blotting the molecule of interest is a
protein & the probe is typically an antibody raised
against that particular protein .
25. Contd
īSDS PAGE technique is a prerequisite for western
blotting .
īProtein sample is subjected to electrophoresis on SDS
polyacrylamide gel .
īElectroblotting transfers the separated proteins from
the gel to the surface of nitrocellulose membrane .
26. contd
īBlot is incubated with generic protein ( such as
milk protein )which binds to any remaining sticky
places on the nitrocellulose .
īAn antibody which is specific for the protein of
interest ( the primary antibody Ab 1 ) is added to the
nitrocellulose sheet & reacts with the antigen . Only
the band containing protein of interest binds the
antibody forming a layer of antibody molecules .
27. contd
īFollowing several rinses for removal of nonspecifically
bound Ab1 , the Ab1 â antigen complex on the
nitrocellulose sheet is incubated with second
antibody Ab2 , which specifically recognizes the Fc
domain of the primary antibody & binds it . Ab 2 is
radioactive labeled or is covalently linked to reporter
enzyme which allows to visualize protein â Ab1 â Ab2
complex .
28. Applications
īThe confirmatory HIV test employs a western blot to
detect anti HIV antibody in a human sample .
īProteins from known HIV infected cells are separated
& blotted on a membrane then the serum to be tested
is applied in the primary antibody incubation step.
īFree antibody is washed away & a second anti human
antibody linked to an enzyme signal can be added .
29. contd
īThe stained bands then indicate the proteins to
which the patient serum contains antibody .
īWestern blot is also used as definitive test for bovine
spongiform encephalopathy . ( mad cow disease )
īSome forms of Lyme disease testing employs western
blotting .