Gene cloning involves inserting DNA fragments into cloning vectors, which are then transferred into host cells. Some key points:
- Plasmid vectors like pBR322 were early cloning vectors but had limitations. Improved vectors like pUC18 addressed these with features like blue-white screening and expanded multiple cloning sites.
- Lambda phage vectors can clone larger DNA fragments of 5-25kb compared to plasmid vectors. The lambda phage genome is engineered to package recombinant DNA in vitro before infecting host cells.
- Different vector types are suited to different applications based on size of insert, host range, and other factors. Gene cloning allows isolation and analysis of genes and their regulation.
Objectives:
After the end of the presentation we’ll know -
What is cloning vector?
Why cloning vector?
History
Features of a cloning vector
Types of cloning vector
Plasmid
Bacteriophage
Cosmid
Bacterial Artificial Chromosome (BAC)
Yeast Artificial Chromosome (BAC)
Human Artificial Chromosome (HAC)
Retroviral Vectors
What determines choice of vector?
Vector in molecular gene cloning
Cloning vector - The molecular analysis of DNA has been made possible by the cloning of DNA. The two molecules that are required for cloning are the DNA to be cloned and a cloning vector.
A cloning vector is a small piece of DNA taken from a virus, a plasmid or the cell of a higher organism, that can be stably maintained in an organism and into which a foreign DNA fragment can be inserted for cloning purposes.
Most vectors are genetically engineered.
The cloning vector is chosen according to the size and type of DNA to be cloned.
The vector therefore contains features that allow for the convenient insertion or removal of DNA fragment in or out of the vector, for example by treating the vector and the foreign DNA with a restriction enzyme and then ligating the fragments together.
After a DNA fragment has been cloned into a cloning vector, it may be further subcloned into another vector designed for more specific use.
Bacteriophage vectors
Bacteriophage
WHY BACTERIOPHAGE AS A VECTOR?
M13 phage
Genome of m13 phage
Life cycle and dna replication of m13
CONSTRUCTION M13 AS PHAGE VECTOR
M13 MP 2 vector
M13MP7 VECTOR
Selection of recombinants
Lambda replacement vectors
LAMBDA EMBL 4 VECTOR
P1 PHAGE
GENOME OF P1 PHAGE
P1 PHAGE AS VECTOR
P1 phage vector system
Objectives:
After the end of the presentation we’ll know -
What is cloning vector?
Why cloning vector?
History
Features of a cloning vector
Types of cloning vector
Plasmid
Bacteriophage
Cosmid
Bacterial Artificial Chromosome (BAC)
Yeast Artificial Chromosome (BAC)
Human Artificial Chromosome (HAC)
Retroviral Vectors
What determines choice of vector?
Vector in molecular gene cloning
Cloning vector - The molecular analysis of DNA has been made possible by the cloning of DNA. The two molecules that are required for cloning are the DNA to be cloned and a cloning vector.
A cloning vector is a small piece of DNA taken from a virus, a plasmid or the cell of a higher organism, that can be stably maintained in an organism and into which a foreign DNA fragment can be inserted for cloning purposes.
Most vectors are genetically engineered.
The cloning vector is chosen according to the size and type of DNA to be cloned.
The vector therefore contains features that allow for the convenient insertion or removal of DNA fragment in or out of the vector, for example by treating the vector and the foreign DNA with a restriction enzyme and then ligating the fragments together.
After a DNA fragment has been cloned into a cloning vector, it may be further subcloned into another vector designed for more specific use.
Bacteriophage vectors
Bacteriophage
WHY BACTERIOPHAGE AS A VECTOR?
M13 phage
Genome of m13 phage
Life cycle and dna replication of m13
CONSTRUCTION M13 AS PHAGE VECTOR
M13 MP 2 vector
M13MP7 VECTOR
Selection of recombinants
Lambda replacement vectors
LAMBDA EMBL 4 VECTOR
P1 PHAGE
GENOME OF P1 PHAGE
P1 PHAGE AS VECTOR
P1 phage vector system
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
Restriction Endonucleases are enzymes from bacteria that can recognize specific base sequences in DNA and cut (restrict) the DNA at that site (the restriction site). This powerpoint sllides illustrate the introduction, examples, nomenclature and types of restriction endonucleases.
molecular biology phage vector, full lifecycle and all necessary information regarding lambda phage, it contain 2 types that is insertion and replacement.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
Restriction Endonucleases are enzymes from bacteria that can recognize specific base sequences in DNA and cut (restrict) the DNA at that site (the restriction site). This powerpoint sllides illustrate the introduction, examples, nomenclature and types of restriction endonucleases.
molecular biology phage vector, full lifecycle and all necessary information regarding lambda phage, it contain 2 types that is insertion and replacement.
Gene Cloning Vectors - Plasmids, Bacteriophages and Phagemids.Ambika Prajapati
A cloning vector is a small piece of DNA that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted for cloning purposes. The cloning vector may be DNA taken from a virus, the cell of a higher organism, or it may be the plasmid of a bacterium.
They allow the exogenous DNA to be inserted, stored, and manipulated mainly at DNA level.
Types -
1.Plasmid vectors.
2.Bacteriophage vectors .
3.Phagemids.
gene cloning, secreening a library, cloning products, requrements, aqsa ijaz
Recombinant DNA molecules are only useful if they can be made to replicate and produce a large number of copies. A typical gene-cloning procedure includes the following steps (See Campbell, Figure 19.3):
Step 1: Isolation of two kinds of DNA.
Bacterial plasmids and foreign DNA containing the gene of interest are isolated.
In this example, the foreign DNA is human, and the plasmid is from E. coli and has two genes:
--> ampR that confers antibiotic resistance to ampicillin.
--> lacZ that codes for beta-galactosidase, the enzyme that catalyzes the hydrolysis of lactose
Note that the recognition sequence for the restriction enzyme used in this example is within the lacZ gene.
Step 2: Treatment of plasmid and foreign DNA with the same restriction enzyme.
The restriction enzyme cuts plasmid DNA at the restriction site, disrupting the lacZ gene.
The foreign DNA is cut into thousands of fragments by the same restriction enzyme; one of the fragments contains the gene of interest.
When the restriction enzyme cuts, it produces sticky ends on both the foreign DNA fragments and the plasmid.
Step 3: Mixture of foreign DNA with chopped plasmids.
Sticky ends of the plasmid will base pair with complementary sticky ends of foreign DNA fragments.
Step 4: Addition of DNA ligase.
DNA ligase catalyzes the formation of covalent bonds, joining the two DNA molecules and forming a new plasmid with recombinant DNA.
Step 5: Introduction of recombinant plasmid into bacterial cells.
the naked DNA is added to a bacterial culture.
Some bacteria will take up the plasmid DNA by transformation.
Step 6: Production of multiple gene copies by gene cloning and selection process for transformed cells.
Bacteria with the recombinant plasmid are allowed to reproduce, cloning the inserted gene in the process.
Recombinant plasmids can be identified by the fact that they are ampicillin resistant and will grow in the presence of ampicillin.
Step 7: Final screening for transformed cells.
X-gal, a modified sugar added to the culture medium, turns blue when hydrolyzed by beta-galactosidase. It is used as an indicator that cells have been transformed by plasmids containing the foreign insert.
Since the foreign DNA insert disrupts the lacZ gene, bacterial colonies that have successfully acquired the foreign DNA fragment will be white. Those bacterial colonies lacking the DNA insert will have a complete lacZ gene that produces beta-galactosidase and will turn blue in the presence of X-gal.
A genetically engineered DNA molecule from bacteria , phage or yeast to carry foreign DNA for the purpose of cloning and expression of the inserted DNA of interest in RDT
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
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1. Gene Cloning & Cloning Vectors
Dr Ravi Kant Agrawal, MVSc, PhD
Senior Scientist (Veterinary Microbiology)
Food Microbiology Laboratory
Division of Livestock Products Technology
ICAR-Indian Veterinary Research Institute
Izatnagar 243122 (UP) India
2. Gene Cloning - definition
• Clone: from the Greek - klon, a twig
• The production of exact copies (clones) of a particular gene or
DNA sequence using genetic engineering techniques.
• The DNA containing the target gene(s) is split into fragments
using restriction enzymes. These fragments are then inserted
into cloning vectors which transfer the recombinant DNA to
suitable host cells.
• Inside the host cell the recombinant DNA undergoes
replication; thus, a bacterial host will give rise to a colony of
cells containing the cloned target gene.
3. Significance
• A particular gene can be isolated and its nucleotide sequence
determined
• Control sequences of DNA can be identified & analyzed
• Protein/enzyme/RNA function can be investigated
• Mutations can be identified, e.g. gene defects related to
specific diseases
• Organisms can be ‘engineered’ for specific purposes
4. History
• G. Mendel, in the middle of the 19th
century coined the term gene
for the factor controlling the inheritance of biological
characteristics of an organism.
• In 1903, W. Sutton proposed that genes reside on chromosomes.
• In 1922 Gene mapping by T H Morgan and he analyzed the
relative positions of 2000 genes on 4 chromosomes of the
fruitfly, Drosophila melanogaster.
• In 1944 Avery, Macleod and McCarty and in 1952 Hershey and
Chase explained the molecular nature of the gene to be
Deoxyribonucleic acid.
• 1952 to 1966: The Structure of DNA, genetic code and the
process of transcription and translation.
• 1971-1973: New technology like recombinant DNA technology or
genetic engineering or the process of Gene cloning developed.
This technology helped in studying the regulation of genes,
aberrations in the genes and then used genes for production of
desired proteins.
• In 1985, Kary Mullis invented the Polymerase Chain reaction
6. Cloning Vector
• It is the central
component of a
gene cloning
process.
• A small piece of DNA
into which a foreign
DNA fragment can
be inserted.
• The insertion of the
fragment is carried
out by treating the
vector and the
foreign DNA with a
restriction enzyme
that creates the
same overhang, then
ligating the
fragments together.
7. Characteristics of a cloning vector
• Ori (Origin of replication) is a specific sequence of nucleotide
from where replication starts
• It should have selectable marker gene
• It should have restriction sites: a synthetic multiple cloning site
(MCS) can be inserted into the vector
• Replicate inside the host cell to form multiple copies of the
recombinant DNA molecule.
• Less than 10kb in size.
8. Contd….
Origin of Replication: Allow
the vector as well as the
foreign DNA to amplify in
the host cell
Selectable Marker:
Antibiotic resistance genes-
Allow the host to grow on
selective media; Can
selectively amplify this
specific vector in the host
cell
Multiple Cloning Sites:
Allow insertion of foreign
DNA
9. Types of Cloning Vectors
• They allow the exogenous DNA to be inserted, stored, and
manipulated mainly at DNA level.
• Types
1. Plasmid vectors
2. Bacteriophage vectors
3. Cosmids
4. Phagemids
5. Fosmids
6. BACs & YACs
10. Plasmid Vector
• Plasmid vectors are double-stranded, extra-chromosomal DNA
molecules, circular, self-replicating.
• Advantages:
– Small, easy to handle
– Easy purification
– Straightforward selection strategies
– Useful for cloning small DNA fragments (< 10kbp)
• Disadvantages:
– Less useful for cloning large DNA fragments (> 10kbp)
11. 1. Contains an origin of replication, allowing for replication
independent of host’s genome.
2. Contains Selective markers: Selection of cells containing a
plasmid
twin antibiotic resistance
blue-white screening
3. Contains a multiple cloning site (MCS)
4. Easy to be isolated from the host cell.
5. Plasmids range in size from 1.0kb to 250kb e.g. pUC8 is 2.1 kb
and TOL is 117 kb in size.
A plasmid vector for cloning
12. pBR322
• It was one of the first vectors to be developed in 1977.
• The ‘p’ indicates that it is plasmid, ‘BR’ indicates Bolivar and
Rodriguez
• ‘322’ distinguishes it from the other plasmids produced in the
same laboratory e.g. pBR325, pBR327, pBR328.
• It is 4363bp in size i.e. less than 10kb
• It carries two sets of antibiotic resistance genes i.e. either
ampicillin or tetracycline can be used as a selectable marker.
• Each of the marker genes carries unique restriction sites and
insertion of DNA into these sites inactivates the specific marker
site. e.g. insertion of new DNA with Pst1, Puv1, Ppa1 or Sca1
inactivates the ampR
gene.
• It has a high copy number. They are about 15 molecules present
in transformed cells but it can be increased to 1000 to 3000 by
plasmid amplification in the presence of protein synthesis
inhibitor i.e. chloramphenicol.
• The vector comprises DNA derived from three different
naturally occurring plasmids: the ampR
gene is from R1 plasmid,
tetR
from R6-5 plasmid and the ori gene from pMB1 plasmid.
14. Ampicillin resistant? yes yes
Tetracycline resistant? No yes
B X B
B
B
X
Ampr
ori
Ampr
Tcr
ori
pBR322
Ampr Tcr
ori
Screening by insertional inactivation of a resistance gene
15. Replica plating: transfer of the colonies from one
plate to another using absorbent pad or Velvet
transfer of colonies
+ampicillin + ampicillin
+ tetracycline
these colonies have bacteria with
recombinant plasmid
17. pBR327
• It was produced by removing a 1089bp segment from pBR322.
• The ampR
and tetR
genes are intact.
• It has high copy number than pBR322 i.e. 30-45 molecules per E.
coli cell. Thus, more the copies of the cloned genes more will be
the effect of the cloned gene on the host cell detectable.
• The deletion destroys the conjugative ability of the vector
which is important for biological containment.
18. FROM pBR322 to pUC
• pBR322 requires
double screening
• pBR322 has limited
number of restriction
site
For these reasons
pUC (on the left)
was engineered
19. pUC8- Lac selection plasmid
• It is 2750bp in size and is one of the most popular E. coli cloning
vectors.
• Derived from pBR322 in which only the ori and the ampR
genes
remain.
• The nucleotide sequence of ampR
gene has been changed so that
it no longer contains the unique restriction sites.
• The restriction sites are clustered into the lac Z’ gene.
• It has a high copy number of 500-700 molecules per cell even
before amplification.
• The identification of the recombinant cells can be achieved by a
single step process i.e. by plating onto agar medium containing
ampicillin and X-gal.
20. Conti-
• The clustering of the restriction sites allows a DNA fragment
with two different sticky ends to be cloned without resorting
to additional manipulations.
• pUC18/pUC19 is a vector having different combinations of
restriction sites and provide greater flexibility for the DNA to
be cloned.
• The restriction site clusters in these vectors are the same as the
clusters in M13mp series of vectors. Thus, the DNA cloned in
pUC vectors can be transferred directly to its M13mp
counterpart enabling the cloned gene to be obtained as a single
stranded DNA.
23. Next Major Advance in Plasmid(ology)
The inclusion of polylinkers
into plasmid vectors
Polylinker is a tandem array of
restriction endonuclease sites
in a very short expanse of
DNA
For example, pUC18’s
polylinker
Sites for 13 RE’s
Region spans the
equivalent of 20 amino
acids or 60 nucleotides
24. The Polylinker Advantage
Unique sites (usually)
Insert excision facilitated
Restriction endonuclease mapping and Subcloning made easier
Directional cloning
25. Blue-White screening for pUC18
• Colonies with recombinant plasmids
are white, and colonies with
nonrecombinant plasmids are blue.
• Resistant to ampicillin, has (ampr
gene)
• Contains portion of the lac operon
which codes for beta-galactosidase.
• X-gal is a substrate of beta-
galactosidase and turns blue in the
presence of functional beta-
galactosidase is added to the medium.
• Insertion of foreign DNA into the
polylinker disrupts the lac operon,
beta-galactosidase becomes non-
functional and the colonies fail to turn
blue, but appear white.
27. Alpha complementation
LacZ Beta galactosidase
(Homotetramer)
• 1021aa 3,1 kbp
• Bacteria carry mutant allele
(LacZΔM15) lacking N-
terminal domain inactive
protein
• Alpha peptide carried by
vector plasmid
• MCS inserted into LacZ alpha
peptide
With insert = white colonies
Without insert = blue
colonies
• Exploits X-Gal (5-bromo-4-
cloro-3-indonyl-
Betagalactoside), a
chromogenic substrate
analog to galactose
28.
29. What are advantages of pUC over pBR322?
• Single step
screening
• MCS increases the
number of
potential cloning
strategies available
X-gal (also abbreviated BCIG for bromo-chloro-indolyl-galactopyranoside)
is an organic compound consisting of galactoside linked to indole.
X-gal is cleaved by β-galactosidase yielding galactose and 5-bromo-4-
chloro-3-hydroxyindole.
The latter is then oxidized into 5,5'-dibromo-4,4'-dichloro-indigo, an
insoluble blue product.
Thus, if X-gal and an inducer of β-galactosidase (usually IPTG) is contained
within an agar medium on a culture plate, colonies which have a
functional lacZ gene can easily be distinguished.
30. pGEM3Z
• It is very similar to pUC vector and is of same size (2750bp).
• It carries the ampR
and Lac Z gene. The cluster of restriction sites
is present in the Lac Z gene.
• It has two promoter sequences i.e. T7 promoter (RNA
polymerase of T7 bacteriophage) and SP6 (RNA polymerase of
SP6 phage) promoter sequences that lie on the either side of
the cluster of restriction sites.
• These promoters act as the sites for the attachment of RNA
polymerase. Thus if a recombinant pGEM3Z is mixed with RNA
polymerase in a test tube, transcription occurs and RNA copies
of the cloned fragment are synthesized.
31. Bacteriophage
• These are the viruses that specifically infect bacteria and during
infection inject the phage DNA into the host cell where it
undergoes replication.
• The phages are simple in structure and consist of DNA molecule
having several genes for phage replication which is surrounded
by a capsid made up of proteins.
32. Types of Phages
• On the basis of structure
Head and Tail phages: e.g. λ phage
Filamentous phages: e.g. M13
• On the basis of phage infection cycle
Lytic Phage:
The infection cycle is completed very quickly and the release of
new phage particles is associated with the lysis of the host cell
Lysogenic phage:
The phage DNA gets integrated into the bacterial DNA known as
PROPHAGE and after many cell divisions released by the lysis of
the host cell e.g. λ phage.
Some phages do not form prophages and the new phage
particles are continuously assembled and released from the
host cell without the lysis of the host cell e.g. M13 phage.
33. λ Phage
• It is 49kb in size and is used as a
cloning vector because:
The genes related in terms of
function are clustered together in the
genome and allows the genes to be
switched on and off as a group rather
than individually.
The linear double stranded DNA
molecule has a stretch of 12
nucleotides at its either ends which
act as sticky ends or cohesive ends
(cos sites)
They can base pair to form a circular
DNA molecule which is important for
insertion into the bacterial genome.
Another role of cos sites is in the
formation of large number of λ DNA
molecules by rolling circle mechanism
of replication (Catenane).
34. λ Phage Cloning Vector
• “Head and Tail” phage, very well-studied
• Large, linear genome of ~49.0 kb
• Two lifestyle modes
– Lytic: replicative mode
– Lysogenic: latent mode
• It has a large size genome (49kb) and only 3kb new DNA can be
inserted because if the size of the molecule is more than 52kb
then it can not be packaged into the head of the phage.
• The phage has more than one recognition sequence for almost
all the restriction endonucleases. So the use of any restriction
enzyme will break the phage DNA into number of small
fragments.
• Despite these disadvantages, λ phages are used to clone large
DNA (5kb to 25kb) molecules.
37. Recombination and Lysogeny
Cos site: At the ends short (12bp) ss- complementary region
“cohesive or sticky” ends--- circulation after infection
Left Arm: Structural genes for head and tail
Central Region: genes for lysogenic growth and
recombination/insertion of genome into baterial genome
Right Arm: genes involved in DNA replication and lytic growth
Only 30 kb is required for lytic growth.
Thus, one could clone 19 kb of “foreign” DNA.
Packaging efficiency 78%-105% of the lambda genome.
38. Engineered version of bacteriophage λ (infects E. coli).
Central region of the λ chromosome (linear) is cut with a
restriction enzyme and digested DNA is inserted.
DNA is packaged in phage heads to form virus particles.
Phages with both ends of the λ chormosome and a 37-52 kb
insert replicate by infecting E. coli.
Phages replicate using E. coli and the lytic cycle.
Produces large quantities of 37-52 kb cloned DNA.
Like plasmid vectors, large number of restriction sites available;
phage λ cloning vectors are useful for larger DNA fragments
than pUC19 plasmid vectors.
Phage λ cloning vectors:
42. The infection process is about
thousand times more efficienct
than transformation with
plasmid vectors.
106
tansformed colonies per
microgram of plasmid vector
109
plaques per microgram of
recombinant Lambda vector
43. Strategies
• For the construction of the cloning vector, the non-essential
region (between positions 20 and 35) in the genome of the
phage was removed which decreased the size of the molecule
by 15kb. Thus, upto 18kb of new DNA can be inserted
• By in vitro mutagenesis and by natural selection one or two
restriction sites are removed e.g. EcoR1.
44. Insertion Vectors
• In these vectors the non-essential region is deleted and the two
arms ligated together. The vector possesses one unique
restriction site.
• λgt10: It can clone up to 8kb of new DNA inserted in the EcoR1
site located in the c1 gene.
• λZAP11: In this vector up to 10kb of DNA can be inserted in to
any of the 6 restriction sites within the polylinker. This
inactivates the lac Z gene of the vector
45. Replacement Vectors
• This vector has two recognition sites for the restriction
endonuclease used for cloning.
• These sites replace the segment of DNA (Stuffer fragment)
from the vector genome by the DNA to be cloned.
• These vectors can carry large pieces of DNA than insertion
vectors.
• λEMBL4: This vector can be used to insert up to 20kb of DNA.
46. λ Replacement vectors
• Left arm:
– head & tail proteins
• Right arm:
– DNA synthesis
– regulation
– host lysis
• Deleted central
region:
– integration &
excision
– regulation
47. M13 Phage
• It is 6407 nucleotides in length, circular and consists of a single
stranded DNA molecule and is used as a cloning vector because
It is less than 10kb in size.
The double stranded replicative form of the genome acts like a
plasmid.
Genes cloned can be obtained in the form of single stranded
DNA which is helpful in gene sequencing and in vitro
mutagenesis.
It is easily prepared from the culture of infected E. coli cells.
Single-stranded, circular genome, 6.4 kb
Infect only F+ bacteria, using pilus F- coded
Can clone pieces of DNA up to 6X the M13 genome size (36 kb) --
but the larger the DNA, the less stable the clone is…..
• Drawback: foreign DNA can be unstable (slows down host cell
growth, so deletions confer a selective advantage)
48. M13 Phage Cloning Vector
• The M13 genome is 6.4kb in length
• Consists of ten closely packed genes for replication of the
phage.
• There is a single 507 nucleotide intergenic sequence (IS) into
which new DNA can be inserted
• This region includes the ori gene
Useful for
– Sequencing
– Site-directed mutagenesis (later)
– Any other technique that requires single stranded DNA
51. M13 doesn’t lyse cells, but it does slow them down
M13 infections form plaques, but they are “turbid”
“lawn” of
E. coli
52. M13 Vectors
• M13mp1-The lac Z gene was introduced in the IS and it does not
have any unique restriction site in the gene.
• M13mp2- This vector was constructed by including the EcoR1
site in the lac Z gene. This was done by a single nucleotide
change in GGATTC near the start of the lac Z gene to GAATTC by
in vitro mutagenesis. The β-galactosidase enzyme remains
functional in the vector.
• M13mp7- It was formed by inserting a polylinker into the EcoR1
site of lac Z gene of M13mp2. A polylinker is a short nucleotide
sequence that consists of number of restriction sites (EcoR1,
BamH1, Sal1 and Pst1) and has a EcoR1 sticky ends. This
polylinker does not disrupt the function of Lac Z gene.
55. Bacteriophage vectors
Advantages:
– Useful for cloning large DNA fragments (10 - 23 kb)
– Inherent size selection for large inserts
Disadvantages:
– Less easy to handle
Uses of Bacteriophages:
Lambda phage cloning vectors:
• For gene cloning of large DNA fragments (eukaryotic genes)
• Excellent selection capability (stuffer stuff)
• Clone lots of precisely-sized DNA fragments for library
construction
M13 based cloning vectors:
• Single-stranded DNA
• Sequencing
• Site-directed mutagenesis
56. Phagemids/Phasmids: plasmid/F1M13
hybrids A phagemid or phasmid is a plasmid that contains an f1
origin of replication from an f1 phage.
It can be used as a type of cloning vector in combination with
filamentous phage M13.
A phagemid can be replicated as a plasmid, and also be packaged as single
stranded DNA in viral particles.
Phagemids contain an origin of replication (ori) for double stranded
replication, as well as an f1 ori to enable single stranded replication and
packaging into phage particles.
Many commonly used plasmids contain an f1 ori and are thus phagemids.
Similarly to a plasmid, a phagemid can be used to clone DNA fragments
and be introduced into a bacterial host by a range of techniques, such as
transformation and electroporation.
However, infection of a bacterial host containing a phagemid with a
'helper' phage, for example VCSM13 or M13K07, provides the necessary
viral components to enable single stranded DNA replication and
packaging of the phagemid DNA into phage particles.
The 'helper' phage infects the bacterial host by first attaching to the host
cell's pilus and then, after attachment, transporting the phage genome
into the cytoplasm of the host cell.
Inside the cell, the phage genome triggers production of single stranded
phagemid DNA in the cytoplasm. This phagemid DNA is then packaged
into phage particles.
57. Phagemids/Phasmids: plasmid/M13
hybrids The phage particles containing
ssDNA are released from the
bacterial host cell into the
extracellular environment.
Filamentous phages retard
bacterial growth but,
contrasting with the
lambda phage and the T7 phage,
are not generally lytic.
Helper phages are usually
engineered to package less
efficiently (via a defective phage
origin of replication)
than the
phagemid so that the resultant
phage particles contain
predominantly phagemid DNA.
F1 Filamentous phage infection
requires the presence of a pilus
so only bacterial hosts
containing the F-plasmid or its
derivatives can be used to
generate phage particles.
58.
59. A cosmid is a type of hybrid plasmid that contains a Lambda phage
cos sequence.
Cosmids (cos sites + plasmid = cosmids) DNA sequences are originally from
the lambda phage.
They are often used as a cloning vector in genetic engineering.
Cosmids can be used to build genomic libraries.
They were first described by Collins and Hohn in 1978.
Cosmids can contain 37 to 52 (normally 45) kb of DNA, limits based on the
normal bacteriophage packaging size.
They can replicate as plasmids if they have a suitable origin of replication: for
example SV40 ori in mammalian cells, ColE1 ori for double-stranded DNA
replication or f1 ori for single-stranded DNA replication in prokaryotes.
They frequently also contain a gene for selection such as antibiotic resistance
, so that the transformed cells can be identified by plating on a medium
containing the antibiotic. Those cells which did not take up the cosmid would
be unable to grow.[3]
Unlike plasmids, they can also be packaged in phage capsids, which allows
the foreign genes to be transferred into or between cells by transduction.
Plasmids become unstable after a certain amount of DNA has been inserted
into them, because their increased size is more conducive to recombination.
To circumvent this, phage transduction is used instead. This is made possible
by the cohesive ends, also known as cos sites. In this way, they are similar to
using the lambda phage as a vector, except all the lambda genes have been
deleted with the exception of the cos sequence.
Cosmids
60. Features of both plasmid and
lambda phage cloning vectors.
Circular.
Do not occur naturally
Origin (ori) sequence for E. coli.
Selectable marker, e.g. ampR
.
Restriction sites (for cloning).
Contain Phage λ (lambda) cos sites
which permits packaging into λ
phage heads and therefore
introduction to E. coli cells.
Packaging only occurs with 37-52 kb
fragments - selection for large
fragments
Useful for 37-52 kb.
Packaged DNA is inserted into cells
and then replicates as a very large
plasmid
Cosmids
61. Cloning in a cosmid
Desired
ligation
Products--
these are
packaged
62. Cloning in a cosmid
Instead of transformation,
desired ligation products are
packaged and then transfected
into cells
Selection for colonies, not
screening of plaques (not
infectious)
63. 1. Based on the E. coli
bacterial F-plasmid.
2. Can insert 40 kb
fragment of DNA.
3. Low copy number in the
host (e.g., 1 fosmid).
4.Fosmids offer higher
stability than comparable
high copy number
cosmids.
5. Contain other features
similar to
plasmids/cosmids such as
origin sequence and
polylinker.
Fosmid:
64. Vectors that enable artificial chromosomes to be created and
cloned into E. coli.
Features:
Useful for cloning up to 200-300 kb, but can be handled like
regular bacterial plasmid vectors.
Useful for sequencing large stretches of chromosomal DNA;
frequently used in genome sequencing projects.
Like other vectors, BACs contain:
Origin (ori) sequence derived from an E. coli plasmid called the
F factor.
Multiple cloning sites (restriction sites).
Selectable markers (antibiotic resistance).
Bacterial Artificial Chromosomes (BACs):
65. BACs: Bacterial Artificial Chromosomes
Based on the F factor of E. coli:
100 kb plasmid, propagates through conjugation
low copy number (1-2 copies per cell)
2 genes (parA and parB): accurate partitioning during cell
division
BACs: just have par genes, replication ori, cloning sites,
selectable marker
Can propagate very large pieces of DNA: up to 300 kb
Relatively easy to manipulate: move into cells by
transformation (electroporation)
67. • Vectors that enable artificial chromosomes to be
created and cloned into yeast.
• Based on the chromosome of Yeast
Features:
• CEN1, centromere sequencesegregation
• TEL, telomere sequencesextremity protection
• ARS1, autonomous replicating sequencereplication
• Selectable marker (amino acid dependence, etc.) on
each arm.
• Amp
• ori, origin of replication for propagation in an E. coli
host.
• Restriction sites (for DNA ligation).
• Acquiring 150kbp it acquires chromosome like features
• SUP4 gene, a suppressor tRNA gene which overcomes
the effect of the ade-2 ochre mutation and restores
wild-type activity, resulting in colorless colonies.
• The host cells are also designed to have recessive trp1
and ura3 alleles which can be complemented by the
corresponding TRP1 and URA3 alleles in the vector,
providing a selection system for identifying cells
containing the YAC vector.
• Useful for cloning very large DNA fragments up to 500
kb; useful for very large DNA fragments.
YACs: Yeast Artificial Chromosomes
68.
69.
70. DESADVANTAGES OF YAC
• Very fragile and prone to breakage,
• Unstable, with their foreign DNA inserts often being deleted
• Loss of the entire YAC during mitotic growth
• Difficult to separate the YAC from the other host chromosomes
• The yield of DNA is not high
• Chimaerism
73. What determines the choice of vector
• insert size
vector sizevector size
restriction sitesrestriction sites
copy numbercopy number
cloning efficiencycloning efficiency
ability to screen for insertsability to screen for inserts
74. Not all vectors permit
the identification of the desired
clones by simple selection or
color based strategies.
In the majority of cases we
need alternative approaches!!!!
75. Thanks
Acknowledgement: All the material/presentations available online on the subject
are duly acknowledged.
Disclaimer: The author bear no responsibility with regard to the source and
authenticity of the content.
Questions???
Editor's Notes
In molecular biology and microbiology, replica plating is a technique in which one or more secondary Petri plates containing different solid (agar-based) selective growth media (lacking nutrients or containing chemical growth inhibitors such as antibiotics) are inoculated with the same colonies of microorganisms from a primary plate (or master dish), reproducing the original spatial pattern of colonies. The technique involves pressing a velvet-covered disk to a primary plate, and then imprinting secondary plates with cells in colonies removed by the velvet from the original plate. Generally, large numbers of colonies (roughly 30-300) are replica plated due to the difficulty in streaking each out individually onto a separate plate.
The purpose of replica plating is to be able to compare the master plate and any secondary plates to screen for a selectable phenotype. For example, a colony which appeared on the master plate but failed to appear at the same location on a secondary plate shows that the colony was sensitive to a substance on that particular secondary plate. Common screenable phenotypes include auxotrophy and antibiotic resistance.
Replica plating is especially useful for negative selection. For example, if one wanted to select colonies that were sensitive to ampicillin, the primary plate could be replica plated on a secondary Amp+ agar plate . The sensitive colonies on the secondary plate would die but the colonies could still be deduced from the primary plate since the two have the same spatial patterns from ampicillin resistant colonies. The sensitive colonies could then be picked off from the primary plate.
By increasing the variety of secondary plates with different selective growth media, it is possible to rapidly screen a large number of individual isolated colonies for as many phenotypes as there are secondary plates.
This technique was first described in the context of the Luria-Delbruck experiment in 1943.
Retrieved from &quot;http://en.wikipedia.org/wiki/Replica_plating&quot;
X-gal (also abbreviated BCIG for bromo-chloro-indolyl-galactopyranoside) is an organic compound consisting of galactoside linked to indole.
X-gal is cleaved by β-galactosidase yielding galactose and 5-bromo-4-chloro-3-hydroxyindole.
The latter is then oxidized into 5,5&apos;-dibromo-4,4&apos;-dichloro-indigo, an insoluble blue product. Thus, if X-gal and an inducer of β-galactosidase (usually IPTG) is contained within an agar medium on a culture plate, colonies which have a functional lacZ gene can easily be distinguished.