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Recombinant DNA Technology
1. RECOMBINANT DNA TECHNOLOGY AND
ITS APPLICATIONS
Dr. Apeksha Niraula
Assistant Professor
Department of Biochemistry
BPKIHS
2.
3. Pioneers of Medicine without a
Nobel prize
Herbert Boyer and Stanley N. Cohen
First Recombinant DNA
4. OBJECTIVES
Techniques and enzymes used in manipulation of DNA
DNA Amplification and Cloning
DNA Library
Nucleotide Probes
Polymerase Chain Reaction
Blotting Techniques
Applications of Recombinant DNA Technology
5. Introduction
Recombinant DNA are the altered DNA that results from the insertion of a sequence of
deoxynucleotides not previously present into an existing molecule of DNA by enzymatic
or chemical means
Recombinant DNA Technology: Gene cloning/ Molecular cloning
Encompasses a number of experimental protocols leading to the transfer of genetic
information DNA technology (DNA) from one organism to another
Originally developed as research tools to explore and manipulate genes and to produce the
gene products (proteins)
6. Any two segments of a single-stranded DNA or RNA, having continuous
complementary sequences of 20 or more bases in common, form complementary
base pairs to form duplex structure
Duplex may be formed between DNA and DNA, RNA and RNA, or between DNA and
RNA to generate a hybrid
An application of annealing properties is construction of nucleic acid probes which
provide useful means for detecting genes and mRNAs
Annealing Properties
7.
8.
9. Enzymatic Reactions
Enzymes used in manipualtion of DNA:
I. Restriction Endonucleases
Bacterial enzymes that cleave specific palindromic sequences in double stranded DNA
Werner Arber (Nobel Prize 1978)
Most “Exquisite Scalpels”
Cleaving the double-stranded DNA very selectively at specific sites, called the
restriction sites
Each restriction site is a short sequence of 4–6 base pairs, and is palindromic
10.
11. A restriction enzyme is named according to the organism from which it was isolated
EcoRI
Escherichia (E) (Genus)
Coli (co) (Specific)
Strain Ry13 (R) (Strain)
First endonuclease (1) (Order of identification)
An additional letter indicates the type or strain (as needed), and a number (Roman
numeral) is appended to indicate the order in which the enzyme was discovered in that
particular organism
HaeIII is the third restriction endonuclease isolated from the bacterium
Haemophilus aegyptius
12. Sticky and Blunt Ends
Restriction enzymes cleave dsDNA so as to produce a 3′-hydroxyl group on one end
and a 5′-phosphate group on the other
Some restriction endonucleases, such as TaqI produce sticky or cohesive ends
HaeIII, produce fragments that have blunt ends
Using the enzyme DNA ligase sticky ends of a DNA fragment of interest can be
covalently joined with other DNA fragments that have sticky ends produced by
cleavage with the same restriction endonuclease
13.
14.
15. Some restriction enzymes can recognize the sites that are relatively small,
Four Cutters: Four nucleotides such as Hae III
Larger sites, Six Cutters: Six nucleotides in the case of Eco RI
Enzymatic digestion of a DNA molecule by different REs produces several different
fragments of varying sizes depending upon the cutting frequency of the RE
If a piece of DNA from a species is exposed to a specific RE, a characteristic array of
DNA fragments is produced; this is called RESTRICTION MAP
16.
17. Restriction Site
A DNA sequence that is recognized and cut by a restriction enzyme is called a
Restriction site
Restriction endonucleases cleave dsDNA into fragments of different sizes depending
upon the size of the sequence recognized
For example, an enzyme that recognizes a specific 4-bp sequence produces many cuts in
the DNA molecule, one every 44 bp
In contrast, an enzyme requiring a unique sequence of 6 bp produces fewer cuts (one
every 46 bp) and, therefore, longer pieces
18.
19. DNA CLONING
Introduction of a foreign DNA molecule into a replicating cell permits the cloning or,
amplification (that is, the production of many identical copies) of that DNA
Firstly, the total cellular DNA is first cleaved with a specific restriction enzyme,
creating hundreds of thousands of fragments
Each of the resulting DNA fragments is joined to a DNA vector molecule (referred to
as a cloning vector) to form a hybrid, or recombinant, DNA molecule
Each recombinant molecule carries its inserted DNA fragment into a single host cell
(for example, a bacterium), where it is replicated
20. The process of introducing foreign DNA into a cell is called Transformation for
bacteria and yeast and Transfection for higher eukaryotes
As the host cell multiplies, it forms a clone in which every bacterium contains copies
of the same inserted DNA fragment, hence the name “Cloning”
The cloned DNA can be released from its vector by cleavage (using the appropriate
restriction endonuclease) and isolated
Many identical copies of the DNA of interest can be produced
21.
22. A vector is a molecule of DNA to which the fragment of DNA to be cloned is joined
Essential properties of a vector:
Capacity for autonomous replication within a host cell
Presence of at least one specific nucleotide sequence recognized by a restriction
endonuclease
Presence of at least one gene (such as an antibiotic resistance gene) that confers the
ability to select for the vector
Commonly used vectors include plasmids and viruses
Vectors
23. Prokaryotic organisms typically contain single, large, circular chromosomes
Most species of bacteria also normally contain small, circular, extrachromosomal DNA
molecules called plasmids
Plasmids may carry genes that convey antibiotic resistance to the host bacterium and
may facilitate the transfer of genetic information from one bacterium to another
Can be readily isolated from bacterial cells, their circular DNA cleaved at specific sites by
restriction endonucleases, and up to 15 kb (kilobases) of foreign DNA (cut with the
same restriction enzyme) inserted
Prokaryotic plasmids
24.
25. Improved vectors that can more efficiently accommodate larger DNA
segments, or express the passenger genes in different cell types
Bacteriophage λ : Naturally occurring viruses that infect bacteria
Retroviruses
Artificial constructs:
Cosmid
BAC, YAC, Human artifical chromosomes
BAC and YAC can accept DNA inserts of 100–300 kb and 250–1,000 kb,
respectively
Other Vectors
26. A DNA library is a collection of cloned restriction fragments of the DNA of an organism
Two kinds of libraries are commonly used:
Genomic libraries
Complementary DNA (cDNA) libraries
Genomic libraries: Contain a copy of every DNA nucleotide sequence in the genome
cDNA libraries: Contain those DNA sequences that only appear as processed
messenger RNA (mRNA) molecules, and these differ according to cell type and
environmental conditions
DNA libraries
28. POLYMERASE CHAIN REACTION
PCR is an in vitro method for amplifying a selected DNA sequence that does not rely on
the biologic (in vivo) cloning method
PCR permits the synthesis of millions of copies of a specific nucleotide sequence in a few
hours
Can amplify the sequence, even when the targeted sequence makes up less than one part
in a million of the total initial sample
Can be used to amplify DNA sequences from any source, including viral, bacterial, plant,
or animal
30. A genomic library is created by digestion of the total DNA of an organism with a
restriction endonuclease and subsequent ligation to an appropriate vector
Recombinant DNA molecules replicate within host bacteria
Amplified DNA fragments collectively represent the entire genome of the organism and
are called a Genomic Library
Genomic DNA libraries:
31. cDNA lacks introns and the control regions of the genes
High level of expression of protein coding gene in a particular tissue allows the
mRNA transcribed from that gene is likely also present at high concentrations in the
cells of that tissue
For example, reticulocyte mRNA is composed largely of molecules that code for the
α-globin and β-globin chains of hemoglobin A (HbA)
Complementary DNA libraries:
32. Synthesis of complementary DNA (cDNA)
from messenger RNA (mRNA) using
reverse transcriptase.
Ligation of double-stranded (ds) DNA
sequences containing a restriction site to
each end allows biologic cloning of cDNA
**DNA is resistant to alkaline hydrolysis
dATP, dCTP, dGTP, dTTP =
deoxyadenosine, deoxycytidine,
deoxyguanosine, and deoxythymidine
triphosphates
33.
34. Sequencing cloned DNA fragments
The base sequence of DNA fragments that have been cloned can be determined
Sanger dideoxy chain termination method :Original Method
In this method, the single-stranded DNA (ssDNA) to be sequenced is used as the
template for DNA synthesis by DNA polymerase (DNA pol)
A radiolabeled primer complementary to the 3′-end of the target DNA is added, along
with the four deoxyribonucleoside triphosphates (dNTP)
The sample is divided into four reaction tubes, and a small amount of one of the four
dideoxyribonucleoside triphosphates (ddNTP) is added to each tube
35.
36.
37. PROBES
Cleavage of large DNA molecules by restriction enzymes produces an enormous array
of fragments
How can the DNA sequence of interest be picked out of such a mixture?
Answer: Use of a probe, a short piece of ssDNA or RNA, labeled with a radioisotope,
such as 32P, or with a nonradioactive molecule, such as biotin or a fluorescent dye
Sequence of a probe is complementary to a sequence in the DNA of interest, called the
Target DNA
Probes are used to identify which band on a gel or which clone in a library contains the
target DNA, a process called screening
40. Disposal of radioactive waste is becoming increasingly expensive, nonradiolabeled
probes have been developed
Most successful: Based on the vitamin biotin, which can be chemically linked to the
nucleotides used to synthesize the probe
Biotin was chosen: Binds very tenaciously to avidin
Avidin can be attached to a fluorescent dye detectable optically with great
sensitivity
Thus, a DNA fragment that hybridizes with the biotinylated probe can be made visible
by immersing the gel in a solution of dye-coupled avidin
Biotinylated probes
41. After washing away the excess avidin, the DNA fragment that binds the probe is
fluorescent
Labeled probes can allow detection and localization of DNA or RNA sequences in cell or
tissue preparations, a process called in situ hybridization (ISH)
If the probe is fluorescent (F), the technique is called FISH
42. Blotting Techniques
Southern Blotting: Edward Southern
Combines the use of restriction enzymes, electrophoresis, and DNA probes to
generate, separate, and detect pieces of DNA
Northern Blotting: For detection of mRNA
Western Blotting: For detection of Proteins
46. For understanding the molecular basis of a number of diseases (Familial
hypercholesterolemia, sickle cell disease, thalassemia, cystic fibrosis and muscular dystrophy)
Human proteins can be produced in abundance for therapy (e.g. Insulin, Growth hormone,
Tissue plasminogen activator)
Proteins for vaccines (e.g. Hepatitis B) and for diagnostic testing (e.g. AIDS tests) can be
obtained
Can be used to diagnose existing diseases and predict the risk of developing a given disease
Gene therapy for Sickle cell disease, Thalassemias, Adenosine deaminase deficiency and
other diseases
Applications
Herbert Boyer and Stanley N. Cohen develop recombinant DNA technology, showing that genetically engineered DNA molecules may be cloned in foreign cells
Recombinant DNA technology is a controlled mixing of genes rather than relying on natural mixing of whole genomes, single genes can be altered, replaced, deleted, or moved into new genomes
This directed diversity can produce organisms with predictable traits, as natural purebreds, but with single gene differences. The ability to manipulate single traits has implications not only in the laboratory but also in treatment and prevention of disease; for example, through gene therapy
Hence, named as Restriction Endonucleases (RE), or simply restriction enzymes
More than 800 types of REs are known; and more than 400 of them are available commercially
Sticky ends: The resulting DNA fragments have single-stranded regions that are complementary to each other)
Blunt ends: that are entirely double stranded and, therefore, do not form hydrogen bonds with each other
A ligase encoded by bacteriophage T4 can covalently join blunt-ended fragments
Each RE cuts DNA into different fragment sizes, which is not necessarily the same size as those cut by another enzyme
Hundreds of these enzymes, each having different cleavage specificities (varying in both nucleotide sequences and length of recognition sites), are commercially available
The recombinant plasmid vector can be introduced into a bacterium, producing large numbers of copies of the plasmid
The bacteria are grown in the presence of antibiotics, thus selecting for cells containing the hybrid plasmids, which provide antibiotic resistance
Artificial plasmids are routinely constructed
Example is the classic pBR322, which contains an origin of replication, two antibiotic resistance genes, and >40 unique restriction sites
Use of plasmids is limited by the size of the DNA that can be inserted
Fragment of phage lambda DNA including COS site + plasmid = Cosmid
cDNA lacks introns and the control regions of the genes, whereas these are present in genomic DNA
PCR was discovered by Kary Mullis in 1984
Regardless of the restriction enzyme used, the chances are good that the gene of interest contains more than one restriction site recognized by that enzyme
If this is the case, and if the digestion is allowed to go to completion, the gene of interest is fragmented (that is, it is not contained in any one clone in the library)
To avoid this usually undesirable result, a partial digestion is performed in which either the amount or the time of action of the enzyme is limited
This results in cleavage occurring at only a fraction of the restriction sites on any one DNA molecule, thus producing fragments of ~20 kb
Enzymes that cut very frequently (that is, those that recognize 4-bp sequences) are generally used for this purpose so that the result is an almost random collection of fragments
This insures a high degree of probability that the gene of interest is contained, intact, in some fragment
Because it contains no 3′-hydroxyl group, incorporation of a ddNMP terminates elongation at that point. The products of this reaction, then, consist of a mixture of DNA strands of different lengths, each terminating at a specific base
Separation of the various DNA products by size in an electric field using polyacrylamide gel electrophoresis, followed by autoradiography, yields a pattern of bands from which the DNA base sequence can be read. [Note: The shorter the fragment, the farther it travels on the gel, with the shortest fragment representing that which was made first (that is, the 5′-end).]
In place of a labeled primer, a mixture of the four ddNTP linked to different fluorescent dyes and in a single reaction tube is now commonly used\
The mixture is separated by capillary electrophoresis, the fluorescent labels are detected, and a color readout of the sequence is generated
[Note: The Human Genome Project used variations of this technique to sequence the human genome.]
Advances in sequencing technology, so-called next generation, or high-throughput sequencing, now allow the rapid sequencing of an entire genome with increased fidelity and decreased cost through the simultaneous (parallel) sequencing of many DNA pieces. [Note: Sequencing of the exome, that portion of the genome that encodes proteins, is now possible.]