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Multiplex PCR
Advantages:
• This technique has the potential to produce
considerable savings in time and effort within the
laboratory
Disadvantages:
• Optimization is difficult; since many sets of
forward and reverse primers are to be designed
for use.
• Increases cost.
• Presence of multiple primer may lead to cross
hybridization with each other and the possibility
of mis-priming with other templates.
Annealing temperatures for each of the primer
sets must be optimized to work correctly within a
single reaction, and amplicon sizes, i.e., their base
pair length, should be different enough to form
distinct bands when visualized by gel
electrophoresis. Alternatively, if amplicon sizes
overlap, the different amplicons may be
differentiated and visualised using primers that
have been dyed with different colour fluorescent
dyes.
Blotting Techniques
Nitrocellulose membranes are a popular
matrix used in protein blotting because of
their high protein-binding affinity,
compatibility with a variety of detection
methods (chemiluminescence, chromogenic,
and fluorescence), and the ability to
immobilize proteins, glycoproteins, or nucleic
acids.
Southern blotting
Method
- Restriction endonucleases are used to cut high-
molecular-weight DNA strands into smaller
fragments.
- The DNA fragments are then electrophoresed on
an agarose gel to separate them by size.
- The DNA gel is placed into an alkaline solution
(typically containing sodium hydroxide) to denature
the double-stranded DNA. The denaturation in an
alkaline environment may improve binding of the
negatively charged thymine residues of DNA to a
positively charged amino groups of membrane,
separating it into single DNA strands for
later hybridization to the probe, and destroys any
residual RNA that may still be present in the DNA.
- A sheet of nitrocellulose (or,
alternatively, nylon) membrane is placed on top of
the gel. Pressure is applied evenly to the gel by
placing a stack of paper towels and a weight on top of
the membrane and gel, to ensure good and even
contact between gel and membrane. Buffer transfer
by capillary action from a region of high water
potential to a region of low water potential (usually
filter paper and paper tissues) is then used to move
the DNA from the gel onto the membrane. the DNA
binds to the membrane due to the negative charge of
the DNA and positive charge of the membrane.
- The membrane is then baked in a vacuum or regular
oven at 80 °C for 2 hours (standard conditions;
nitrocellulose or nylon membrane) to permanently
attach the transferred DNA to the membrane.
- The membrane is then exposed to a hybridization
probe—a single DNA fragment with a specific
sequence. The probe DNA is labelled so that it can
be detected, usually by
incorporating radioactivity or tagging the
molecule with a fluorescent dye.
- After hybridization, excess probe is washed from
the membrane, and the pattern of hybridization is
visualized on X-ray film by autoradiography in the
case of a radioactive or fluorescent probe.
Northern Blotting
Western blotting or immunoblotting
A technique in which proteins are separated by
gel electrophoresis and transferred to a
membrane sheet. A specific protein is then
identified through its reaction with a labeled
antibody.
PROCEDURE
- The proteins of the sample are separated using gel
electrophoresis (PAGE, Poly Acrylamide Gel
Electrophoresis) and are then transferred onto nitro
cellulose to which they bind.
- Then radiolabelled specific antibody is added on such
membrane and it binds only to specific complementary
protein.
- The antibody is labelled with iodine-125 and the
signal is detected again with autoradiography.
-If radio active label is not used, bound antibody may
be detected by a second antibody tagged with an
enzyme, which allows to visualize the protein-Ab1-
Ab2 complex.
lec 7 - blotting + multiplex pcr biochemistry..pptx
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lec 7 - blotting + multiplex pcr biochemistry..pptx

  • 2. Advantages: • This technique has the potential to produce considerable savings in time and effort within the laboratory Disadvantages: • Optimization is difficult; since many sets of forward and reverse primers are to be designed for use. • Increases cost. • Presence of multiple primer may lead to cross hybridization with each other and the possibility of mis-priming with other templates.
  • 3.
  • 4. Annealing temperatures for each of the primer sets must be optimized to work correctly within a single reaction, and amplicon sizes, i.e., their base pair length, should be different enough to form distinct bands when visualized by gel electrophoresis. Alternatively, if amplicon sizes overlap, the different amplicons may be differentiated and visualised using primers that have been dyed with different colour fluorescent dyes.
  • 5.
  • 7.
  • 8.
  • 9.
  • 10. Nitrocellulose membranes are a popular matrix used in protein blotting because of their high protein-binding affinity, compatibility with a variety of detection methods (chemiluminescence, chromogenic, and fluorescence), and the ability to immobilize proteins, glycoproteins, or nucleic acids.
  • 12.
  • 13.
  • 14.
  • 15. Method - Restriction endonucleases are used to cut high- molecular-weight DNA strands into smaller fragments. - The DNA fragments are then electrophoresed on an agarose gel to separate them by size. - The DNA gel is placed into an alkaline solution (typically containing sodium hydroxide) to denature the double-stranded DNA. The denaturation in an alkaline environment may improve binding of the negatively charged thymine residues of DNA to a positively charged amino groups of membrane, separating it into single DNA strands for later hybridization to the probe, and destroys any residual RNA that may still be present in the DNA.
  • 16. - A sheet of nitrocellulose (or, alternatively, nylon) membrane is placed on top of the gel. Pressure is applied evenly to the gel by placing a stack of paper towels and a weight on top of the membrane and gel, to ensure good and even contact between gel and membrane. Buffer transfer by capillary action from a region of high water potential to a region of low water potential (usually filter paper and paper tissues) is then used to move the DNA from the gel onto the membrane. the DNA binds to the membrane due to the negative charge of the DNA and positive charge of the membrane. - The membrane is then baked in a vacuum or regular oven at 80 °C for 2 hours (standard conditions; nitrocellulose or nylon membrane) to permanently attach the transferred DNA to the membrane.
  • 17. - The membrane is then exposed to a hybridization probe—a single DNA fragment with a specific sequence. The probe DNA is labelled so that it can be detected, usually by incorporating radioactivity or tagging the molecule with a fluorescent dye. - After hybridization, excess probe is washed from the membrane, and the pattern of hybridization is visualized on X-ray film by autoradiography in the case of a radioactive or fluorescent probe.
  • 18.
  • 20.
  • 21. Western blotting or immunoblotting A technique in which proteins are separated by gel electrophoresis and transferred to a membrane sheet. A specific protein is then identified through its reaction with a labeled antibody.
  • 22. PROCEDURE - The proteins of the sample are separated using gel electrophoresis (PAGE, Poly Acrylamide Gel Electrophoresis) and are then transferred onto nitro cellulose to which they bind. - Then radiolabelled specific antibody is added on such membrane and it binds only to specific complementary protein. - The antibody is labelled with iodine-125 and the signal is detected again with autoradiography. -If radio active label is not used, bound antibody may be detected by a second antibody tagged with an enzyme, which allows to visualize the protein-Ab1- Ab2 complex.