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Molecular Techniques
Department of Stem Cells & Regenerative Medicine
ACECR
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DNA & RNA
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•DNA is a nucleic acid, made of long chains of nucleotides
Nucleotide
Phosphate group
Nitrogenous base
Sugar
Polynucleotide Sugar-phosphate backbone
DNA nucleotide
Phosphategroup
Nitrogenous base(A, G, C, or T)
Thymine (T)
Sugar(deoxyribose)
DNA and RNA are polymers of nucleotides
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Bases
• Adenine double ringed =
• Guanine
• Thymine single ringed =
• Cytosine
purines
pyrimidines
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Hydrogen bonds between bases hold the strands together: A and T, C and G
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Untwisting and replication of DNA
• each strand is a template for a new strand
helicase
5 end
Parental DNA
DNA polymerasemolecule
53
35
35
Daughter strandsynthesizedcontinuously
Daughter strandsynthesizedin pieces
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RNA is also a nucleic acid
– different sugar
– U instead of T
– Single strand, usuallyNitrogenous base
(A, G, C, or U)
Uracil (U)
Sugar(ribose)
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DNA molecule
Gene 1
Gene 2
Gene 3
DNA strand
TRANSCRIPTION
RNA
Polypeptide
TRANSLATIONCodon
Amino acid
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DNA of gene
PromoterDNA
RNA polymerase
Elongation
Termination
TerminatorDNACompleted RNA
RNApolymerase
GrowingRNA
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U C A G
U
C
A
G
GACU
GACU
GACU
GACU
UUUUUCUUAUUG
CUUCUCCUACUG
AUUAUCAUAAUG
GUUGUCGUAGUG
phe
leu
leu
ile
met (start)
val
UCUUCCUCAUCG
CCUCCCCCACCG
ACUACCACAACG
GCUGCCGCAGCG
ser
pro
thr
ala
UAUUACUAAUAG
CAUCACCAACAG
AAUAAC
AAGAAA
GAUGACGAAGAG
tyr
stopstop
his
gln
asn
lys
asp
glu
UGUUGCUGAUGG
CGUCGCCGACGG
AGUAGCAGAAGG
GGUGGCGGAGGG
cys
stoptrp
arg
ser
arg
gly
Firs
t B
ase
Third
Base
Second Base
Virtually all organisms share the same genetic code “unity of life”
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Techniques molecular biology Polymerase chain reaction (PCR)
Gel electrophoresis Macromolecule blotting and probing
Southern blotting Northern blotting Western blotting
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Polymerase Chain Reaction
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Polymerase Chain Reaction
Invented by Kary Mullis and his colleagues in the 1983.
Nobel prize 1993.
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PCR Reaction Components
Template: previously isolated and purified.
Two primers: to flank the target sequence)18-28 nucleotides).
Four deoxynucleosides triphosphate (dNTPs) : to provide energy and nucleosides for the synthesis of DNA.
Buffer system containing magnesium.
DNA polymerase.
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Thermal Cycler
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PCR Cycles
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Denaturation
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Annealing
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Elongation
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As amplification As amplification proceeds , the DNA proceeds , the DNA
sequence between primers sequence between primers doubles after each cycles doubles after each cycles (The amplification of the (The amplification of the
target sequence target sequence proceeding in an proceeding in an
exponential fashionexponential fashion ( 1 ( 1 2 4 8 2 4 8
16…………….)- up to 16…………….)- up to million of times the million of times the
starting amount until starting amount until enough is present to be enough is present to be
seen by gel seen by gel electrophoresis.electrophoresis.
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Agarose Gel Electrophoresis
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Since PCR amplifications can generate microgram
quantities of product, amplified fragments can
be visualized easily following staining with a
chemical stain such as ethidium bromide.
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Variants of PCR
Reverse transcriptase-PCR. Nested-PCR. Hot-start PCR. Quantitative PCR. ….
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Polymerase Chain Reaction: Uses
The polymerase chain reaction (PCR) is a technique widely used in:
Molecular biology, Microbiology,
Genetics, Diagnostics clinical laboratories,
Forensic science, Environmental science,
Hereditary studies, Paternity testing, and
Many other applications…
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Polymerase Chain Reaction clearly has the potential to become the routine laboratory method for diagnosis of a variety of human disorders :
Infectious Diseases: One area where the PCR technique will undoubtedly become a routine
method, is the detection of infectious agents, such as pathogenic bacteria, viruses or protozoa.
Cancer: Detection of malignant diseases by PCR. Recurrence of hematological cancers has also been evaluated. Detection of micro-metastasis in blood, lymph nodes and bone
marrow.
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Inherited disorders diagnosed using PCR protocols:
Alpha1 antitrypsin B thalassaemia Cystic fibrosis Duchenne muscular dystrophy Myotonic dystrophy Haemophilia A and B Huntington`s chorea Phenylketonuria Sickle cell anaemia Familial adenomatous polyposis
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Comparison of Southern, Northern, and Western analyses
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‘Southern’ hybridization named after Sir Edwin Southern
Developed in 1975
Southern Blotting
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Example – Looking for Gene X
Cell line 12 copies of Gene X
extract
DNA
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Example – Looking for Gene X
Cell line 2
extract
DNA
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Step 1. Restriction Enzyme Digestion
EcoR I EcoR I EcoR I EcoR I
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Step 1. Restriction Enzyme Digestion
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Step 2. Gel Electrophoresis
_ +
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Step 2. Gel Electrophoresis
_ +
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T G A A TC
A C AT T G
Step 3. DNA Denaturation
Eliminate hydrogen bonds with sodium hydroxide (NaOH)
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Step 4. Transfer DNA to Membrane
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Step 5. Making a Probe
A probe is a small (25-2000 bp) length of DNA or RNAComplementary to the sequence (gene) of interestLabeled for subsequent detection procedures
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Step 6. Pre-hybridization
Prehybridization bufferscontain ‘blocking reagents’that occupy available binding sites on the membrane
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Step 7. Hybridization
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Step 7. Hybridization
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Step 8. Washes
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Step 9. Anti-DIG
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Step 9. Anti-DIG
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Step 10. Washes
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Step 11. CSPD
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Step 12. Detection
• DIG-labeled probes emitting minute amounts of light (chemiluminescence)
• 32P-labeled probes emitting ß-particles
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Step 12. Detection
• DIG-labeled probes emitting minute amounts of light (chemiluminescence)
• 32P-labeled probes emitting ß-particles
• Autoradiography film can detect this radiation
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Example – Looking for Gene X
Cell line 2
extract
DNA
3 Copies
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Detection of the sickle-cell globin gene by Southern blotting
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The flow chart of Northern hybridization
Prepare RNA samples and run RNA gel
Northern transfer
Probe preparation
Prehybridization
Hybridization
Post-hybridization washing
Signal detection
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Any Question ?