Molecular Biology Techniques
Outline
Restriction-enzyme analysis
The polymerase chain reaction (PCR)
DNA Fingerprinting
DNA sequencing
Blotting techniques
Recombinant DNA
Restriction Enzyme Analysis
aka restriction endonucleases
Recognizes specific base sequences and
cleaves
PALINDROMES
Two-fold rotational symmetry
Restriction Enzyme
Separation by gel
electrophoresis
Agarose (>20 kb)
PAGE (1 kb)
Visualization
Autoradiography
Ethidium bromide use to map the structure of a
DNA fragment
Electrophoresis
Electrophoresis
Electrophoresis
Stained gel result
Visualization may be achieved through UV dyes or radioactive agents
Polymerase Chain Reaction
A rapid and versatile in vitro method to amplify
defined target DNA within a heterogeneous
collection of DNA sequences (genomic DNA or
cDNA)
PCR Requirements
Template (genomic DNA or cDNA population)
Oligonucleotide primers
DNA polymerase (Taq polymerase)
dNTP
Thermal cycler
Cycles (25 – 30)
Denaturation
95o C
Separate strands
Annealing
50 – 70 oC (~5o C lower than Tm)
DNA Synthesis
70 – 75 oC (ideal temp for Taq polymerase)
thermus aquaticus (Taq)
Calculating the Tm
primerinTAofnumberCprimerinCGofnumberCT oo
m &2&4
5’ – ATTGCAAGTTCGGTAACCGG – 3’
Utility of PCR in Medical Diagnostics
Detection of bacteria and viruses by specific
primers
HIV virus in people who have not mounted an immune response
Mycobacterium tuberculosis bacilli
Detection of certain cancer cells
ras genes and leukemias caused by chromosomal rearrangement
Monitoring cancer chemotherapy
Utility of PCR in Forensics
DNA fingerprinting
Restriction fragment length polymorphisms
PCR-Based analysis
Can be used to determine biological parentage
Can be used to settle assault and rape cases
Steps:
1. Get DNA sample
2. Amplify with PCR
3. Cut with restriction enzyme
4. Run resulting fragments on gel electrophoresis
5. Analyze result
A sample with the
shorter DNA
fragments travels
through the gel faster
than a sample with
the larger fragments
DNA fingerprinting
DNA analysis can be used for catching criminals, establishing parentage, finding how closely organisms are related and many other applications.
The pattern of bands in a gel electrophoresis is known as a genetic fingerprint or a ‘genetic profile’
If a genetic fingerprint found in a sample of blood or other tissue at the scene of a crime matches the genetic fingerprint of a suspect, this can be used as evidence
A DNA sample can be obtained from the suspect using blood, cheek epithelial cells taken from the mouth lining or even the cells clinging to the root of a hair
V S S1 S2 S3
V Victim
S Sample from crime scene
S1 Suspect 1
S2 Suspect 2
S3 Suspect 3
More than 20 fragments from Suspect 1 match those taken from the crime scene
DNA profiles
Starting position of sample
1 2 3 4
Genetic fingerprint of …
1 mother
2 child
3 possible father A
4 possible father B
There is a match between one of the child’s restriction fragments and one of the mother’s. There is also a match between the child’s other fragment and one from possible father A.
Neither of the child’s restriction fragments match those of possible father B
Famous cases
In 2002 Elizabeth
Hurley used DNA
profiling to prove
that Steve Bing was
the father
of her child Damien
Famous Cases
Colin Pitchfork was
the first criminal
caught based on
DNA fingerprinting
evidence.
He was arrested in
1986 for the rape
and murder of two
girls and was
sentenced in 1988.
Famous Cases
O.J. Simpson was cleared of a double murder charge in 1994 which relied heavily on DNA evidence.
This case highlighted lab difficulties.
Sequencing by Sanger Dideoxy Method
Controlled
termination of
replication
Uses 2’,3’ dideoxy analog of nucleotide
Sequencing by Sanger Dideoxy Method
Fluorescence Detection
Automated DNA Sequencing
Southern blotting
Identification of restriction fragment
Southern blotting
Identification of restriction fragment
Recombinant DNA Technology
Constructing new combinations of unrelated
genes (ex. protein expression)
New combinations can be cloned by suitable
hosts
Covalent insertion of a DNA fragment from one
type of cell or organism into the replicating DNA
of another type of cell
Takes advantage of restriction enzymes and
DNA ligases
DNA ligase – catalyzes the formation of phosphodiester bond at a break in a DNA chain.
BASIC STEPS:
1. Selection of carrier
(ex. plasmid)
2. Cleaving the DNA
strand of the carrier
3. Insert DNA of
interest into the
carrier (creating
recombinant or
hybrid DNA)
4. Introduce hybrid
DNA to host cell
(transformation)
5. Screening of host
cells
Vectors = carriers of DNA fragments
Plasmids
Naturally occurring circular, double-stranded DNA that act as accessory chromosomes in bacteria; DNA fragments (15, 000 bp)
λ phage
Bacteriophage (virus) DNA; for larger
DNA fragments (23, 000 bp)
Yeast and bacterial artificial chromosome
Laboratory-designed carriers for larger
DNA fragments
Parts of bacterial plasmid
pBR322 Plasmid
Insertion can occur
in 3 restriction sites
Antibiotic resistance
Necessary for selection
DNA fragment Vector
How to construct
a recombinant
DNA:
Screening for
successful
transformation
Screening for successful transformation
Reference:
Garrett, R. and C. Grisham. Biochemistry. 3rd edition.
2005.
Berg, JM, Tymoczko, JL and L. Stryer. Biochemistry. 5th
edition. 2002.