© 2014 pearson education, inc. introduction: how to clone a gene? manipulation of dna sequences in...
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© 2014 Pearson Education, Inc.
Introduction: How to Clone a gene? Manipulation of DNA sequences in organisms – Is known as genetic engineering
Techniques used to engineer genes –Are called recombinant DNA
technology
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© 2014 Pearson Education, Inc.
Using Plasmids in Cloning
Plasmids– Are small, circular DNA molecules – Are often found in bacteria– Replicate independently of the
chromosome
Plasmids can serve as a vector– A vehicle for transferring recombinant
genes to a new host
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What makes Plasmids good vectors?1. Contain DNA replication initiation
site (ori)
2. Contain a promoter sequence for initiating transcription of the inserted gene
3. Contain antibiotic resistance gene which allows for identification of bacteria that carry the plasmid
4. Contain restriction enzymes recognition sites for gene insertion
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ApplicationsRecombinant Plasmids are extremely useful because it allows manufacturing mass quantity of biological molecules. For example:
Protein used to dissolve blood clots in heart attack therapy (tissue plasminogen activator)
InsulinHepatitis B surface antigen, to
vaccinate against the Hep B virusGene for pest resistance that is
inserted into plantsGene used to alter bacteria for
cleaning up toxic waste
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Cloning Genes in Recombinant PlasmidsIn order for recombinant DNA to be useful it must be made in vast amounts.
HOW?1. Isolate 2 different DNA = bacterial plasmid
that serves as vector, and human DNA of interest
2. Treats both DNA with same RESTRICTION ENZYME
3. Sticky ends of the DNA joins by DNA ligase. Result : Recombinant DNA plasmid containing gene of interest.
4. Plasmids is inserted into bacterial cells by transformation
5. Gene Cloning – Bacteria reproduces = mass production of the recombinant DNA
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Restriction Endonucleases
• 1962: “molecular scissors” discovered in bacteria. Also called restriction enzymes
• E. coli bacteria have an enzymatic immune system that recognizes and destroys foreign DNA
• 3,000 enzymes have been identified, around 200 have unique properties, many are purified and available commercially
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Origins of Restriction Enzymes
Discovered in bacteria. They restrict the growth of bacteriophage by cutting the viral DNA and rendering them harmless.
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Restriction EndonucleasesWhy don’t bacteria destroy their own DNA with their restriction enzymes?
DNA Modification
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Restriction Endonucleases
Named for bacterial genus, species, strain, and type
Example: EcoR1Genus: EscherichiaSpecies: coliStrain: ROrder discovered: 1
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Restriction Endonucleases
Recognition sites have symmetry (palindromic)
“Hannah”
Bam H1 site:5’-GGATCC-3’3’-CCTAGG-5’
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Restriction EndonucleasesEnzymes recognize specific 4-8 bp
sequencesSome enzymes cut in a staggered
fashion - “sticky ends” EcoRI 5’…GAATTC…3’ 3’…CTTAAG…5’
Some enzymes cut in a direct fashion – “blunt ends”
PvuII 5’…CAGCTG…3’ 3’…GTCGAC…5’
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Restriction Enzyme in Action
Sticky Ends
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Human Insulin gene cut with EcoRI Plasmid cut with EcoRI
5’-C-G-G-T-A-C-T-A-G-OH3’-G-C-C-A-T-G-A-T-C-T-T-A-A-PO4
PO4-A-A-T-T-C-A-G-C-T-A-C-G-3’ HO-G-T-C-G-A-T-G-C-5’
+
5’-A-C-G-G-T-A-C-T-A-G A-A-T-T-C-A-G-C-T-A-C-G-3’3’-T-G-C-C-A-T-G-A-T-C-T-T-A-A G-T-C-G-A-T-G-C-5’
Complementary base pairing
+ DNA Ligase, + rATP
recombinant DNA molecule
5’-A-C-G-G-T-A-C-T-A-G-A-A-T-T-C-A-G-C-T-A-C-G-3’3’-T-G-C-C-A-T-G-A-T-C-T-T-A-A-G-T-C-G-A-T-G-C-5’
Restriction Enzymes for Cloning
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Lab 2 (Tab B): Clone That Gene
Students will prepare a recombinant plasmid by
using restriction enzymes
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Goals of Activity
• Know the characteristics of plasmids
• Explain how plasmids are used in cloning a gene
• Understand the function of restriction enzymes and how they are used in creating a recombinant plasmid
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Students will …..
Lab 2: use restriction enzymes to digest the 2 plasmids
OR
Lab 2a: digest a plasmid with 2 restriction enzymes.
Good to do a visual to help students see what they are doing: paper
plasmids
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The New Plasmids
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The Recombinant Plasmids
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RFP expression
araC gene rfp genePBAD
Transcription
mRNA
Translation
araC protein
Bruce Wallace
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RFP expression
rfp genePBAD
araC protein
araC gene
araC protein prevents RFP transcription by causinga loop to form in the region of the fp gener
Bruce Wallace
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RFP expression
araC protein
arabinose
araC gene rfp genePBAD
arabinose – araC proteincomplex
RNA polymerase
Arabinose – araC protein complex prevents DNA loopingand helps to align RNA polymerase
on the promoter site (PBAD).
mRNA
Transcription
Translation
RFP(red fluorescent
protein)
Bruce Wallace
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RFP
Bruce Wallace
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Running Digested DNA Through Gel Electrophoresis
Lab 4: Verification of recombinant plasmid creation
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How does it work?
• DNA is cut into smaller fragments.
• Loading dye is used to sink the DNA into the wells in the gel and to track the movements of DNA
•The negative DNA molecule is attracted to the positive (RED) electrode.
•DNA moves based on size and structure; with the smallest fragments move fastest
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Different Structural Forms
circle
“nicked-circle”
“multimer”
Different structural forms produce different bands.
Nicked Circle
SupercoiledLinear
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Goals of this Hands-On Lab
• Compare cut vs uncut plasmid DNA by running them through a gel.
• Look for different banding patterns and understand how to read them.
• Predict what kind of banding pattern a plasmid will make based on: 1.The restriction enzyme used.2.The plasmid’s structural shape.
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Restriction analysis of pKAN-R and pARA
M K+ K- A+ A-
500
1000
1500
20003000400050008000
10000
Confirmation of restriction and ligation
L M K+ K- A+ A- L
Bruce Wallace
807 bp
4705 bp 4495 bp
377 bp
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Lonza Flash Gel System
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Lab 5: Transformation
Plasmid vectors can be introduced into bacteria by transformation: the process of taking up DNA from the environment
Why? If a recombinant plasmid can be inserted
into a bacterial or yeast cell – The foreign DNA will be copied and
transmitted to new cells as the host cell multiplies
– Produces millions of identical copies of specific genes
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preparing competent cells for transformation
Lipid bilayer(inner)
Lipid bilayer(outer)
Peptidoglycanlayer
Adhesion zone
Calcium ions
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Transforming Escherichia coli with pARA-R
Recombinant Plasmids
Competent Cells
pARA-R
Bruce Wallace
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Calcium ions
pARA-R
transforming Escherichia coli with pARA-R
Adhesion zone
Lipid bilayer(inner)
Lipid bilayer(outer)
Peptidoglycanlayer
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Transgenic Colony Allowed to Grow in Selective Media
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growth of transformed bacteria on various plates
P+ plates
P- plates
LB LB/amp LB/amp/ara
LB LB/amp
No growth