This document provides an overview of DNA cloning. It begins by defining cloning as making identical copies of DNA, genes, or cells. The basic steps of DNA cloning are described, including using a source DNA, vector, restriction enzymes to cut DNA, ligation to join DNA fragments, transformation of host bacteria, and selection of recombinant clones. Common vectors like plasmids are discussed along with selection techniques like blue-white screening. The document emphasizes that the goal is to generate multiple copies of the cloned insert DNA. Examples are given of important medical and agricultural applications of cloning genes.
DNA cloning is a technique for reproducing DNA fragments.
It can be achieved by two different approaches:
▪ cell based
▪ using polymerase chain reaction (PCR).
a vector is required to carry the DNA fragment of interest into the host cell.
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
DNA cloning is a technique for reproducing DNA fragments.
It can be achieved by two different approaches:
▪ cell based
▪ using polymerase chain reaction (PCR).
a vector is required to carry the DNA fragment of interest into the host cell.
Genomic library and shotgun sequencing. It includes the topics about genomic library,construction method, its uses and applications, shotgun sequencing, difference between random and whole genome sequencing, its advantages and disadvantages etc.
Creation of a cDNA library starts with mRNA instead of DNA. Messenger RNA carries encoded information from DNA to ribosomes for translation into protein. To create a cDNA library, these mRNA molecules are treated with the enzyme reverse transcriptase, which is used to make a DNA copy of an mRNA (i.e., cDNA). A cDNA library represents a sampling of the transcribed genes, but a genomic library includes untranscribed regions.
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
cDNA library construction using mRNA which are derived from DNA. cDNA is formed from the reverse transcription of single stranded mRNA. cDNA contains only the exons, it donot not contains introns. The mRNA consists of poly A tail in which the tRNA and rRNA donot contains poly A tail. A short oligo nucleotide of Poly T is used to isolate mRNA seperately thereby single stranded mRNA is then converted into cDNA by using reverse transcriptase enzyme.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
Scoring system is a set of values for qualifying the set of one residue being substituted by another in an alignment.
It is also known as substitution matrix.
Scoring matrix of nucleotide is relatively simple.
A positive value or a high score is given for a match & negative value or a low score is given for a mismatch.
Scoring matrices for amino acids are more complicated because scoring has to reflect the physicochemical properties of amino acid residues.
cDNA library construction using mRNA which are derived from DNA. cDNA is formed from the reverse transcription of single stranded mRNA. cDNA contains only the exons, it donot not contains introns. The mRNA consists of poly A tail in which the tRNA and rRNA donot contains poly A tail. A short oligo nucleotide of Poly T is used to isolate mRNA seperately thereby single stranded mRNA is then converted into cDNA by using reverse transcriptase enzyme.
BAC & YAC are artificially prepared chromosomes to clone DNA sequences.yeast artificial chromosome is capable of carrying upto 1000 kbp of inserted DNA sequence
DNA cloning is the process of making multiple, identical copies of a particular piece of DNA. In a typical DNA cloning procedure, the gene or other DNA fragment of interest (perhaps a gene for a medically important human protein) is first inserted into a circular piece of DNA called a plasmid.- [https://www.khanacademy.org/science/...dna.../dna-cloning.../a/overview-dna-cloning]
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DNA is ligated through DNA Ligase, problems may occur during DNA ligation are
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4. What Does It Mean: “To Clone”?
Clone: a collection of molecules or cells, all identical to an
original molecule or cell
• To "clone a gene" is to make many copies of it - for
example, by replicating it in a culture of bacteria.
• Cloned gene can be a normal copy of a gene (= “wild
type”).
• Cloned gene can be an altered version of a gene (=
“mutant”).
• Recombinant DNA technology makes manipulating
genes possible.
• To work directly with specific genes, scientists prepare
gene-sized pieces of DNA in identical copies, a process
called DNA cloning
5. Fig. 20-2
Cell containing gene
of interest
Bacterium
1 Gene inserted into
plasmid
Bacterial
Plasmid
chromosome
Recombinant
DNA (plasmid)
Gene of
interest
DNA of
chromosome
2 Plasmid put into
bacterial cell
Recombinant
bacterium
3 Host cell grown in culture
to form a clone of cells
containing the “cloned”
gene of interest
Gene of
Interest
Protein expressed
by gene of interest
Copies of gene
Basic
Protein harvested
4 Basic research and
various applications
research
on gene
Gene for pest
resistance inserted
into plants
Gene used to alter
bacteria for cleaning
up toxic waste
Protein dissolves
blood clots in heart
attack therapy
Basic
research
on protein
Human growth hormone treats stunted
growth
6. • A preview of gene cloning and some uses of cloned genes
• Most methods for cloning pieces of DNA in the laboratory share
general features, such as the use of bacteria and their plasmids
• Plasmids
are small circular DNA molecules that replicate separately from the
bacterial chromosome
•
•
•
•
•
Cloned genes are useful for making copies of a particular gene
and producing a protein product
Gene cloning involves using bacteria to make multiple copies of a
gene
Foreign DNA is inserted into a plasmid, and the recombinant
plasmid is inserted into a bacterial cell
Reproduction in the bacterial cell results in cloning of the plasmid
including the foreign DNA
This results in the production of multiple copies of a single gene
7. Gene cloning, genetic engineering,
recombinant DNA technology
They‟re more or less the same
It basically means :
joining together DNA from
different sources/organisms,
forming a recombinant DNA
molecule
Then put this recombinant DNA
into a host cell, usually bacteria
The host cell will then replicate
many copies of this recombinant
DNA molecule
Sometimes, we might want to
ask the host cell to use the
genetic information in the
recombinant DNA to make
proteins
8. Why genetic engineering ?
Medical & health
applications
Production of novel and
important proteins
13. The basics of cloning
You need :
1) Source of DNA - to be cloned
2) Choice of vectors – to carry,
maintain and replicate cloned gene in host
cell
3) Restriction enzymes - to cut DNA
4) DNA ligase - to join foreign and
vector DNA recombinant DNA
5) Host cell – in which the recombinant
DNA can replicate
14. 1) Source of DNA
• Genomic DNA
– DNA extracted from cells and purified
• cDNA
– by reverse transcription of mRNA
• Amplified DNA
– using Polymerase Chain Reaction
• Synthetic DNA
– DNA made artificially using a machine
15. 2) Vector
• to carry the ligated foreign gene into the host cell
• maintain the foreign gene in the host cell
• Replicate
• pass into new cells during cell division
• Expressed the cloned foreign gene to make a
protein
16. Different types of cloning vectors
•plasmids
•bacteriophage l, M13
•Cosmids, phagemids
•Artificial chromosomes
BAC, YAC, MAC etc.
17. Plasmid
• Extrachromosomal DNA found in
bacteria & fungi
• Close circular DNA molecules,
supercoiled
• Can replicate autonomously,
independent of chromosome
• Can be transfer to other cells by
conjugation
• Can be integrated into the
chromosome
• In nature, plasmids carry genes that are not essential under normal conditions
• But confers a survival advantage under extreme conditions eg. resistance to
antibiotics, metabolism of unusual substrates
• Number of plasmid per cell - controlled by plasmid itself
High copy number > 100 /cell; low copy number < 20 /cell
• Plasmid incompatibility – the presence of one plasmid in a cell excludes other
plasmids
18. pBR322 – a high copy number plasmid
Important DNA elements :
1. The rop (or sometimes ori)
origin of replication, so that the
plasmid can be maintained &
replicated in the host cell
2. Antibiotic resistance marker
genes (ApR for ampicillin
resistance and TcR for
tetracycline) so that we can
select
3. Unique restrcition sites (EcoRI,
PvuI etc) so that we can cut the
plasmid in one place only.
and insert the foreign gene we
want to clone
19. 3) Restriction enzyme
> Type II Restriction endonuclease
• Enzymes found in some microorganisms
• Natural role to destroy invading foreign DNA
– eg. bacteriophage DNA
• Recognizes very specific short sequences of DNA
– Each enzyme has its own recognition sequence/ site
– Sometimes two different enzymes have the same recognition
sites, in which case they are known as isoschizomers
• Cuts DNA in very specific manner
• Technically – one Unit of RE will completely digest 1 ug
of substrate DNA in a 50 ul reaction volume in 60 minutes
20. Restriction enzymes cut DNA at very specific sequences
• HindIII
PstI
•
EcoRI
FatI
•
SexAI
SspI
Recognition sites – always palindromic
-Formation of hairpin loops
21. How REs cut DNA
Sticky ends can re-anneal by base-pairing
22. Sticky ends has complementary overhangs
- allows for proper reannealing and joining of DNA molecules
27. Inserting the recombinant DNA molecule into a Competent E.coli cell
The cells must be made competent be treating with CaCl2 or very little
DNA will be taken up.
28. Selecting for transformants carrying recombinant DNA
No vector or recombinant DNA
– will not grow on media + ampicillin
Vector only
– will grow on media + ampicillin
Recombinant DNA (vector + insert) –
will grow on ampicillin
This is the one we want !
The goal of any cloning experiment is to obtain transformants carrying
cloned insert DNA. There are several strategies to maximise these
29. The goal of any cloning experiment is to obtain transformants carrying
cloned insert DNA.
There are several strategies to maximise these
1.
Directional cloning
Use two different restriction enzymes to cut each end of the vector
(and also the foreign DNA you want to clone)
- Generate different sticky ends – cannot self ligate
EcoRI
BamHI
EcoRI
BamHI
30. 3. Dephosphorylation of
vector
-both the 3‟OH group and
5‟PO4 group are required for
ligation
-if the 5‟PO4 groups on the
vector ends are removed –
cannot self-ligate
-Using a phosphatase
enzyme
-e.g calf intestinal
phosphatase etc.
P
P
31. Blue white selection – lacZ complementation
The vector contains a portion of the E.coli LacZ gene.
A multiple cloning site (MCS) sequence is inserted into the LacZ‟ fragment
32. The LacZ gene codes for the b-galactosidase enzyme
The b-gal enzyme
hydrolyses lactose into
glucose and galactose
33. The LacZ gene can be broken into two parts, a and b
- each part encoding a fragment of the b-galactosidase enzyme
LacZb’
Inserted into
plasmid vector
LacZa
b- fragment
34. A fully active enzyme can be reconstituted from both fragments
LacZb’
Inserted into
plasmid vector
LacZa
b- fragment
The b-gal enzyme can
also hydrolyse a colorless
substance called X-Gal
into glucose and a blue
color pigment
35. To do blue white selection, the gene of interest is cloned into the MCS
Gene you
want to clone
Transformants are plated onto a medium containing :
o Antibiotic for selection
o IPTG to induce expression of the LacZ’
o X-Gal to detect the presence of b-galactosidase
36. Transformants with vector only :
o LacZ is expressed a fragment is produced
o Complements b-fragment to form fully active enzyme
o Hydrolyses X-Gal Blue color colonies
37. Transformants with recombinant DNA:
o LacZ is destroyed by insertion of foreign gene no a fragment
o Cannot form fully active enzyme
o No hydrolysis of X-Gal White color colonies
40. Sometimes, a simple cloning vector is not good enough
We might want to ask the bacteria cell to make proteins using
information on the cloned gene
We need to use an expression vector
41. Expression vector
- clone foreign gene AND make foreign
protein
- requires extra DNA elements
Promoter – to initiate transcription –
synthesis of mRNA
Terminator – to stop transcription
Fusion tags – for making fusion proteins
e.g. Histidinex6, c-myc, HA, GFP
In frame MCS
Other things – e.g. Poly-A sites
45. Production of recombinant insulin – „Humulin‟ in E.coli
DNA for peptide A and Peptide B – synthesized chemically
Peptide A – 21 amino acids – 63 nucleotides + ATG + stop codon
Peptide B – 30 amino acids – 90nucleotides +ATG +stop codon
Clone into a different plasmid vector s– into the gene for B-galactosidase
Both DNA‟s were cloned in frame with the b-gal gene
Expressed as fusion proteins – Peptide (A or B) + part of b-gal
This is necessary – otherwise the small peptides will be quickly degraded
Fusion with b-gal stabilises the peptides
46. Expression driven by the LacZ promoter
Fusion proteins are purified from the cells
The B-gal part is then cleaved off by reacting with cyanogen bromide
which cleaves methionine
The peptide and then purified and chemically reacted to form disulfide bonds
What is the problem of this approach ?