You are on page 1of 36

Faculty

of Medicine
Department of Medical Biology Universitas Swadaya Gunung Jati

Role of genetic engineering in medicine &


introduction to molecular techniques
(gene identification)
Ariestya Indah Permata Sari, dr., M.Sc., M.Si.Med

2017
FM
UNSWAGATI

2
FM
UNSWAGATI

alleles at a G g G G g g
gene locus

Replication
R r R R r r

S s S S s s

t T t t T T

Homologous chromosomes

3
FM
UNSWAGATI

The human genetic material


§ 23 chromosome pairs

§ 3 billion basepairs (bp) = 3 x 109 bp

§ ±23.000 genes ≈ 1 x 108 bp


à Only 4% of the genome is
encoding proteins

4
FM
UNSWAGATI

Don’t you just love numbers?

§ Human = 6 x 1013 cells § All cells ≈ 1.2 x 1014 meters

= 1.2 x 1011 kms


§ Each cell = 46 chromosomes

≈ 400 000 light seconds


§=6x 109 bp

= 4 light days and 15 hours


§ = ±23.000 genes ≈ 2 m length
(0.013 light years)

≈ 400x return trip to the sun


5
FM UNSWAGATI

Genetic engineering
FM UNSWAGATI

Genetic engineering – Definition

§ Biotechnology
Technic which applies biological system (in organisms, cellular and molecular level) aiming
to obtain the expected result according to human needs.

§ Genetic engineering (Rekayasa genetika)


Biotechnology application by using gene/DNA manipulation.

§ Genetic engineering in medicine


Gene/DNA manipulation to obtain information regarding normal gene function and its
pathology in a disease; and to create a new prototype according to human needs (vaccine,
gene therapy, etc.)
FM UNSWAGATI

Biomedical importance
1. Rational approach to understanding the molecular 4. Human proteins can be produced
basis of a number of diseases in abundance for therapy
E.g: muscular dystrophy, cystic fibrosis, cancer, diabetes E.g: Insulin, growth hormone

2. Diagnostic testing & predict the risk of 5. Protein for vaccines


developing a given disease and individual response E.g: Hepatitis B vaccine

to pharmacological therapeutics
E.g: Ebola test, familial cancer 6. Forensic medicine
E.g: Method for identifying criminal
3. Gene therapy for potentially curing diseases suspect

caused by a single gene deficiency


E.g: thalassemia, adenosine dealinase deficiency
Murray RK, et al. 2009. A LANGE medical book: Harper’s illustrated
biochemistry. 28th ed. New York: The McGraw-Hill Companies, Inc
1856 1956
Gregor Mendel Tjio & Levan 1990-2003
Mendelian inheritance; Mendel Law I & II The right number of chromosome HGP (Human Genome
Project)
1877
1839 Flemming
Schleiden & Chromosome
Schwan identification 1977 1985
Cell à basic in the nucleus Sanger K. Mullis
unit of life Sequencing PCR

MILESTONES OF GENETICS & MOLECULAR GENETICS


1983
1859 1903
1953 JB Martin
Charles Darwin Sutton & Boveri
Watson & Crick 1st gene identification
Evolution theory; Chromosome contains
double helix responsible for genetic
The Origin of genes/blue print of life
DNA disease: Huntington
Species
Disease
1860-1868
1959
Haeckel
Leujeun dkk.
Heredity is transmitted via sperm & ovum
Human chromosomal disease(trisomy 21)
FM UNSWAGATI

Human
genome

Garland. 2008. Molecular basis of the cell.


FM UNSWAGATI

Recombinant DNA technology


§ DNA isolation & manipulation
§ Makes chimeric molecules
§ Involves several unique techniques and reagents
Several important reagents:
üRestriction enzymes
üDNA ligase
üDNA polymerase
FM UNSWAGATI

Genetic engineering techniques

1. Gene identification
§ Polymerase chain reaction (PCR) & electrophoresis
§ Restriction fragment length polymorphism (RFLP)
§ Hybridization: Western, southern, northern blot
§ DNA sequencing

2. Gene cloning

3. Transgenic animal
FM UNSWAGATI

Gene identification: Polymerase chain reaction


(PCR)
§ Gene identification by amplifying DNA
sequence using primers compatible to DNA
target.
§ Principle: amplification of target DNA by
using thermal cycler

Target DNA
FM UNSWAGATI

Step 1 (94oC)
Denaturation
dsDNA to ssDNA

Step 2 (56-60oC)
Annealing
Primers onto template

Step 3 (72oC)
Extension
dNTPs extend the 2nd strand

extension products in one cycle serve as template in the next cycle


PCR Animation

Process

Denature

Anneal Primer

Replicate
DNA

1st cycle 2nd cycle 3rd cycle


FM UNSWAGATI

Gene identification: Polymerase


chain reaction (PCR) – cont.

§ Requires:
§ DNA template
§ A pair of primers
§ DNA polymerase (thermostable; obtained from
thermophilic bacteria) à Thermus aquaticus
§ Taq polymerase

§ dNTP
§ Thermal cycler (PCR machine)
FM UNSWAGATI

Gene identification:
§ To separate charged cells/molecules component Electrophoresis
(protein, nucleotide).
§ Principle: charged molecule in electric field will
migrate to opposite electrode. DNA is negatively
charged, will migrate to anode.
§ Samples are loaded into well in one of the plate
site
§ Velocity of the migration depends on:
§ Charged level
large moderate small
§ Molecule’s size
§ Molecule’s shape
§ Supporting media: Agarose/polyacrylamide gel &
Buffer
FM UNSWAGATI

Electrophoresis

Loading the sample


FM UNSWAGATI

Amplification result of Y chromosome fragment with PCR technic

N O N O N O N O M
1 2 3 4 5 6 7 8 9

800 bp 1000 bp
472 bp
500 bp
326 bp
311 bp

Y chromosome fragment amplification: sY14, sY84, sY143, and RBM1 in


Indonesian males with normozoospermia (N) and oligozoospermia (O).
Well no. 1-2 = sY14 3-4 = sY84
5-6 = sY143 7-8 = RBM1
9 = Marker 100 bp
FM UNSWAGATI

Gene identification: identify DNA variant


FM UNSWAGATI

Gene identification: identify DNA variant


FM UNSWAGATI

Gene identification: identify DNA variant by


RFLP (Restriction fragment length polymorphism)
difference in homologous DNA sequences that can be
detected by the presence of fragments of different
lengths after digestion of the DNA samples in question
with specific restriction endonucleases

§ Detection of gene polymorphism (variant in a gene) by using restriction


enzyme

§ E.g:
Polymorphism in exon 10 of FSH receptor gene in position 680th
nucleotide à resulting in 2 different amino acids: Ser & Asn.
AACC CGGGAG AACC AGGGAG
TTGGGC CCTC TTGGGT CCTC
FM UNSWAGATI

Gene identification: RFLP (Restriction fragment


length polymorphism) – cont.

§ PCR product of FSHR gene exon 10 in position 680


AACC CGGGAG AACC AGGGAG
TTGGGC CCTC TTGGGT CCTC

§ Cut by BsrI restriction enzyme


5’CC CGGG 3’
3’GGGC CC 5’
FM UNSWAGATI

§ RFLP Electrophoresis result:


homozygous serin/serin : one band (300 bp)
homozygous asparagin/asparagin: 2 bands (200 bp & 100 bp)
heterozygous serin/asparagin : 3 bands (100bp, 200bp & 300 bp)
a b c d

1 kb a. Marker
b. Ser/Ser
500bp c. Asn/Asn
d. Ser/Asn
100bp
FM UNSWAGATI

Application in forensic medicine

§ Variation in DNA for identification of an


individual: criminals or biological relationship.

§ Use of microsatellite markers (Alec Jeffreys,


1984) à DNA fingerprinting.

§ Variations are visualized as band patterns after


electrophoresis.

§ Each person has a unique pattern, except


identical twins.
FM UNSWAGATI

Application in paternity test

Who are their parents/sons/daughters?


FM UNSWAGATI

Gene identification: Hybridization

§ Detect certain sequence/fragment (DNA, RNA, or protein) by


creating its hybrid (couple between two complementary strands)
§ The detected fragment will be marked by a probe
§ Types:
1. DNA hybridization (southern blot)
2. RNA hybridization (northern blot)
3. Protein hybridization (western blot)
FM UNSWAGATI

Southern blot
hybridization

Hybridization
FM UNSWAGATI
FM UNSWAGATI

Gene identification: DNA sequencing (cont’)


FM UNSWAGATI

Gene identification: DNA


sequencing
§ Principle: amplify DNA using DNA
template identified by DNA polymerase.
Incorporation of nucleotides in new
strand is terminated by ddNTP.
FM UNSWAGATI

Important reagents: Restriction enzymes


§ Endonuclease
§ Cut DNA chains at specific locations (palindromic 4-7 bp)
§ Result: unique DNA fragment in a sequence-specific manner
§ Isolated from bacteria
§ Protect the host bacterial DNA from the genome of foreign organism
§ Named after the bacterium from which they are isolated
§ EcoRI à isolated from Escherichia coli strain RY13 which is 1st discovered
§ BamHI à isolated from Bacillus amyloliquefaciens strain H which is 1st discovered

§ DNA cut ends result:


§ Sticky ends (overlapping/cohesive)
§ Blunt ends
Murray RK, et al. 2009. A LANGE medical book: Harper’s illustrated
biochemistry. 28th ed. New York: The McGraw-Hill Companies, Inc
FM UNSWAGATI

Blunt ends

Sticky ends
FM UNSWAGATI

Restriction enzymes
FM UNSWAGATI

Important reagents: DNA ligase & DNA polymerase


DNA ligase
§ Isolated from cell culture or bacteria
§ Ligates 2 fragments of DNA by catalyzing bonds between DNA molecules

DNA polymerase I
§ Isolated from bacteria
§ Incorporates nucleotides to complementary template DNA to synthesizing
new dsDNA; generates blunt ends from sticky ends.
Murray RK, et al. 2009. A LANGE medical book: Harper’s illustrated biochemistry. 28th ed. New York: The McGraw-Hill Companies, Inc
“Tempora Mutantur Nos et Mutantur In Illis”
“Time changes and we change with them”

Thank you, questions?


References
1. Albert B, et al. 2002. Molecular biology of the cell. 4th edition. New York: Garland Publishing, Inc.
2. Murray RK, Bender DA, Botham KM, Kennelly PJ, Rodwell VW, and Weil PA. 2009. A LANGE medical book: Harper’s illustrated biochemistry. 28th ed.
New York: The McGraw-Hill Companies, Inc.
3. Permata Sari AI, Farhat R, Ladeveze V, Faradz SM, Kitzis A. Genetic counseling in the couple with compound heterozygous carrier based on the
result of mutation effect analysis on cystic fibrosis transmembrane conductance regulator (CFTR) protein. Ann Transl Med 2015; 3(S2):AB174.
4. Primrose SB and Twyman RM. 2004. Genomics: Applications in human biology. Oxford: Blackwell Publishing Company.
5. Sambrook J, Fritsch EF, and Maniatis T. 1989. Molecular cloning: A laboratory manual. Cold Spring Harbor Laboratory Press.
6. Snustad DP and Simmons MJ. 2003. Principles of genetics. 3rd edition. New York: John Willey & Sons Inc.
7. Srachan T and Read AP. 1996. Human molecular genetics. New York: John Willey & sons. Inc.
8. Thompson J and Thompson MW. 1997. Genetics in medicine. Philadelphia: WB Saunders Company.