RDT, Gene therapy, HGP

1. Recombinant DNA technology,
HGP,
GENE THERAPY
Dr. Monika Shekhawat, MBBS MD -Biochemistry

2. Contents
 Introduction
 Discovery
 Goals and objectives
 rDNA technology procedure
 Enzymes
 Vectors
 Techniques
 Applications
 Summary

3. Biotechnology may be defined as "the method by which a living
organism or its parts are used to incorporate a particular character
to another living organism".
“Genetic Engineering”
Recombinant DNA Technology
BI7.4 Describe applications of molecular technologies like recombinant DNA
technology, PCR in the diagnosis and treatment of diseases with genetic
basis.

4. Recombinant DNA technology
DNA molecules that are extracted from different
sources and chemically joined together;
for example DNA comprising an
animal gene may be recombined with DNA from a
bacterium

5. Discovery of recombinant DNA
technology
Discovery of DNA structure Watson & Crick in 1953
Isolation of DNA ligase in 1967
Isolation of REase in 1970
Paul Berg generated rDNA technology in 1972
Cohen & Boyer in 1973 produced first plasmid vector
capable of being replicated within a bacterial host

6. Goals of recombinant DNA technology
• To isolate and characterize a gene
• To make desired alterations in one or more isolated genes
• To return altered genes to living cells
• Artificially synthesize new gene
• Alternating the genome of an organism
• Understanding the hereditary diseases and their cure
• Improving human genome

7. Procedure of making rDNA
Isolating of DNA
Cutting of DNA
Joining of DNA
Amplifying of DNA

8. Isolating of DNA

9. Cutting of DNA
• DNA can be cut into large fragments by mechanical
shearing.
• Restriction enzymes are the scissors of molecular
genetics.

10. Restriction enzyme
• A special class of sequence-specific enzyme
• Found in bacteria
• Site-specific-cleave DNA molecules only at
specific nucleotide sequence
• RE recognize DNA base sequence that are
palindromic
• RE make staggered cuts with complementary
base sequences for easy ligation

11. Eco RI E Coli G AATT C
C TTAA G
Hind
III
Haemophillus
influenza
A AGCT T
T TCGA A
Taq I Thermus
aquaticus
T CG A
A GC T
Hpa I Haemophillus
parainfluenza
GTT AAC
CAA TTG
(The arrows show the site of the cut by the enzyme)
Specificity of Restriction Enzymes

12. EcoRI enzyme cuts the bonds marked with arrow.
This results in the sticky ends.

13. Joining DNA

14. Amplifying the recombinant DNA
• Transforming the recombinant DNA into a bacterial host strain.
• The cells are treated with CaCl2
• Cells are heat shocked at 42 degree C
• DNA goes into cell by a somewhat unknown mechanism.
• Once in a cell, the recombinant DNA will be replicated.
• When the cell divides, the replicated recombinant molecules go to both
daughter cells which themselves will divide later. Thus, the DNA is
amplified

15. Amplifying the recombinant DNA

16. Enzymes used in recombinant DNA technology
• Bind to DNA molecules
DNA ligase
• Cleaves DNA at specific sites
Type II restriction endonuclease
• Make a DNA copy of RNA molecule
Reverse transcriptase
• Fill single stranded gaps of DNA duplex
DNA polymerase I
• Adds a phosephate to the 5'-OH end of a polynucleotide
Polynycleotide Kinase
• Adds homopolymer tails to the 3'-OH ends
Terminal transferase
• Removes nucleotide residues from the 3' ends
Exonuclease III
• removes nucleotides from the 5' ends
Bacteriophage {lamda} exonuclease
• Removes terminal phosphates
Alkaline phosphatase

17. Vectors used in rDNA technology
• A vector is an area of DNA that can join another DNA
part without losing the limit for self-replication
• Should be capable of replicating in host cell
• Should have convenient RE sites for inserting DNA of
interest
• Should have a selectable marker to indicate which
host cells received recombinant DNA molecule
• Should be small and easy to isolate

18. Vectors used in rDNA technology
vectors
BAC
YAC
expression
cosmid
Lamda
phage
plasmid

19. Plasmid vector
• Plasmids are small, circular DNA molecules
that are separate from the rest of the
chromosome.
• They replicate independently of the
bacterial chromosome.
• Useful for cloning DNA inserts less that 20
kb (kilobase pairs).

20. Lambda phage vector
• Lambda phage vectors are recombinant
infections, containing the phage chromosome
in addition to embedded "outside" DNA.
• All in all, phage vectors can convey bigger DNA
groupings than plasmid vectors.

21. Cosmid vector
• Cosmids are hybrids of
phages and plasmids that
can carry DNA fragments
up to 45 kb.
• They can replicate like
plasmids but can be
packaged like phage
lambda

22. Expression vectors
• Expression vectors are
vectors that carry host
signals that facilitate the
transcription and
translation of an inserted
gene.
• They are very useful for
expressing eukaryotic
genes in bacteria.

23. Yeast artificial chromosomes (YAC)
• Yeast artificial chromosomes (YAC) are yeast
vectors that have been engineered to contain a
centromere, telomere, origin of replication,
and a selectable marker.
• They can carry up to 1,000 kb of DNA.
• they are useful for cloning eukaryotic genes
that contain introns.

24. Bacterial artificial chromosomes (BAC)
• Bacterial artificial
chromosomes (BAC) are
bacterial plasmids derived
from the F plasmid.
• They are capable of
carrying up to 300 kb of
DNA.

25. Techniques used in rDNA technology
• Gel electrophoresis
• Cloning libraries
• Restriction enzyme mapping
• PCR
• Nucleic Acid Hybridization
• DNA Microarrays

26. Gel electrophoresis
 Gel electrophoresis – DNA fragments of different
sizes can be separated by an electrical field applied
to a “gel”.
The negatively charged DNA migrates away from the
negative electrode and to the positive electrode.
The smaller the fragment the faster it migrates.

27. Cloning libraries
• Libraries are collection of DNA clones in a certain
vector.
• The goal is to have each gene represented in the
library at least once.
• Genomic - made from RE DNA fragments of total
genomic DNA
• cDNA (complementary DNA) – made from DNA
synthesized from mRNA

28. PCR
• Allows the isolation of a specific segment of DNA
from a small DNA (or cell sample) using DNA
primers at the ends of the segment of interest.

29. Restriction enzyme mapping
• Frequently it is important to have a restriction enzyme site
map of a cloned gene for further manipulations of the gene.
• This is accomplished by digestion of the gene singly with
several enzymes and then in combinations.
• The fragments are subjected to gel electrophoresis to
separate the fragments by size and the sites are deduced
based on the sizes of the fragments.

30. Restriction map of DNA from lambda bacteriophage. The numbers
denote the length of restriction fragment in kbp.

31. Nucleic Acid Hybridization
• A Southern blot allows the detection of a gene of
interest by probing DNA fragments that have been
separated by electrophoresis with a “labeled” probe.
• Northern Blot (probe RNA on a gel with a DNA
probe)
• Western Blot (probe proteins on a gel with an
antibody)

32. DNA Microarrays
• vast majority of the protein-
encoding qualities onto a
microarray chip, utilizing
innovation in light of the DNA
silicon chip industry.
• The chip can be utilized to
hybridize to cell RNA, and
measure the statement rates of a
substantial number of qualities
in a cell.

33. 1. Quantitative Preparation of Bio-molecules
If molecules are isolated from higher organisms, the
availability will be greatly limited. For example, to get 1 unit of
growth hormone, more than 1000 pituitaries from cadavers are
required. By means of recombinant technology, large scale
availability is now assured.
2. Risk of Contamination is Eliminated
It is now possible to produce a biological substance without any
contamination. Hepatitis, caused by the hepatitis B virus
(HBV), is highly contagious. Originally the virus was isolated
from pooled blood.
Applications of Recombinant Technology

34. Scheme to produce
recombinant human
insulin.

35. ‰
Selected list of proteins produced by recombinant DNA technology
• Recombinant human insulin to treat diabetes mellitus
• Recombinant human growth hormone (HGH)
• ‰
Other human hormones (e.g. FSH)
• Recombinant blood clotting factor VIII and other clotting factors (Factor IX) for
treatment of hemophilia
• Recombinant vaccines, such as hepatitis B vaccine, HPV vaccine
• Cytokines and growth factors (interferon, interleukins)
• Monoclonal antibodies and other related products (rituximab, trastuzumab, etc.)
• Recombinant enzymes (acid alpha-glucosidase, alpha-L-iduronidase)
• Recombinant HIV protein for HIV ELISA testing
• Tissue plasminogen activator, used to treat strokes

36. • ANTIBI0TICS AND DRUG DEVELOPMENT
• RECOMBINANT HORMONES AND ENZYMES
• DROUGHT AND INSECT RESISTANT CROPS
• BIOFERTILIZERS AND BIOINSECTISIDES
Applications of Biotechnology

37. • International effort started in 1990
Goals
• Sequencing the entire genome
One set of human DNA contains 3 billion base pairs and about
10,000genes.
• US department of Energy and US National Institute of Health
started the project in 1990.
• James Watson headed the project first, later Francis Collins
succeeded him.
• The project included scientists from 16 countries world wide.
• In 1997, Craig Ventor of Celera Genomics had independently
embarked on the project and hastened the completion of the
project by 2002
Human Genome Project

38. • 1995- Gene map of human DNA published.
• 1998 – human chromosome 5 was sequenced
• 1999- human chromosome 16 was sequenced
• 2000- Preliminary work draft announced.
• 2002- HGP completed.
• The book of Human life contains 23 chapters which represent
23 chromosomes.
Human Genome Project

39. It is now possible to isolate any human gene of interest. Many
previously unknown genes have been identified.
Pharmacogenomics is emerged from the genome project; it is the
use of genetic information toward the development of new drugs
and their targets of action.
In 2003, the National Human Genome Research Institute initiated
the ENCODE (Encyclopedia of DNA Elements) Project, to identify
all the functional elements of the genome.
Human Genome Project

40. The word CRISPR (pronounced as crisper) stands for “clusters of
regularly interspaced short palindromic repeats”. Cas stands for
“CRISPR-associated system”. CRISPR and cas proteins form
CRISPR/Cas systems. CRISPR is another mechanism employed
by the microbes which provide acquired immunity
against viruses and plasmids.
In the case of bacteria, the spacers are taken from the viruses that
previously attacked the organism. They serve as a memories,
which enables bacteria to recognize the viruses and fight off
future attacks. With CRISPR, it is now possible to modify,
delete, insert, activate or inactivate any gene. CRISPR can be
combined with gene therapy so that the modified gene can be
delivered anywhere in the body.
CRISPR-Cas9

41. A great leap in medical science has taken place on the
14th September 1990.
Event: The first gene
therapy trial for an
inherited disorder was
initiated on
The patient:
Ashanthi DeSilva, 4 year
old
Disorder treated:
Adenosine deaminase
(ADA) deficiency.
GENE THERAPY

42. It is intracellular delivery of genes to generate a
therapeutic effect by correcting an existing abnormality.
Only somatic gene therapy, by inserting the new gene into
somatic cell of the patient is under trials. Germ line therapy is
considered as unethical.
What is Gene Therapy?

43. 1. Isolate the healthy gene.
2. Incorporate this gene on a carrier or vector as an
expression cassette.
3. Deliver the vector to the target cells.
Summary of the Procedure

44. a) Ex vivo strategy – when the cells are cultured , where the new
genes are infused into patient’s cells; and modified cells are
injected back to the patient.
b) In situ strategy when the expression cassette is injected to the
patient either intravenously or directly to the tissue.
c) In vivo strategy, where the vector is administered directly to
the cell.
How the Genes are Introduced?

45. Ex vivo gene therapy.

46. Disease Gene transferred by
1. Severe combined
immunodeficiency (SCID)
Adenosine deaminase enzyme into
lymphocytes by retrovirus
2. Duchenne muscular dystrophy
(DMD)
Dystrophin gene on short arm of X chromosome; by retrovirus
3. Cystic fibrosis (CF) CFTR gene to bronchial epithelium; adenovirus
4. Familial hyper-cholesterolemia LDL receptor gene on chromosome 19 to hepatocytes; retrovirus
5. Hemophilia A and B genes for factor VIII and IX into fibroblasts
6. Cancer Activation of p53 (tumor suppressor gene)
7. Leber’s Hereditary Optic
Neuropathy
Introducing the gene for the enzyme (isomero hydrolase) using an
adeno viral vector
Success Stories of Gene Therapy

47. The following limitations are encountered for gene therapy:
(a) Inconsistent results.
(b) Lack of ideal vector.
(c) Lack of targeting ability in the nonviral vectors.
(d) Death of the patient during the course of gene therapy for OTC
(ornithine transcarbamoylase) deficiency was reported.
(e) Reactivation of retroviral vector due to illegitimate combination
of the inserted gene leading to leukemia in the patient
At present trials are on, but restricted with stringent protocols and
follow up.
Obstacles to Success

48. Stem cells have the ability to divide for an indefinite period. They
can give rise to a variety of specialized cell types. This
phenomenon is known as developmental plasticity. Stem cells can
be isolated from embryos, umbilical cord as well as from any other adult tissues.
Plasticity is more for embryonic stem cells.
Stem cells have the unique capacity to produce unaltered daughter cells (renewal) and
also to generate specialized cells (potency). Stem cells may be capable of producing
all types of cells of the organism (totipotent), or able to generate cells of the three
germ layers (pluripotent), or able to produce only closely related cell types
(multipotent), or may produce only one cell type (unipotent).
Stem cells are widely being used in the treatment of the diseases like stroke, brain
injury, Alzheimer’s disease, Parkinsonism, wound healing, myocardial infarction,
muscular dystrophy, spinal cord injury, diabetes, and cancers.
Stem Cells

49. Differentiation of stem cells.