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Recombinant DNA Technology
Dates in the Development of Gene Cloning:
1965 - plasmids
1967 - ligase
1970 - restriction endonucleases
1972 - first experiments in gene splicing
1974 - worldwide moratorium declared
1975 - Asilomar Conference to determine how to proceed
1979 - guidelines relaxed
Overview of Basic Cloning Experiment
Properties of Vectors for Transferring Genes
1. able to enter host
2. replicate in host (ori for DNA replication)
3. selectable marker genes to identify it, ie. sugar metabolism, antibiotic resistance
Types of Vectors:
1. Phages (λ or M13)
lambda (λ) - accept large DNA fragments (40 kb)
M13 - (10 KB fragments) unique promoters that aid in DNA sequencing.
2. Plasmids (pBR322) - ideal vectors to carry foreign DNA transferred to host cell
-small, antibiotic-resistance genes
-often contain polylinkers - multiple unique RE sites
-ORI
-some have a eukaryotic transcriptional promoter
3. YAC – yeast artificial chromosome, ORI, centromere for segregation,
telomeres for stability
Shuttle vectors – used in more than one type of host, plasmids that can move between
prokaryotic and eukaryotic cells, ex. must have marker genes for E. coli and S.
cerevisiae
- eukaryotic transcriptional promoter in prokaryotic vector
Expression vectors –
- examine the regulation of a gene (how initiation of transcription is controlled by
promoter)
How - promoter and translational start sequence placed next to insertion site,
connect the promoter to a reporter gene (GFP is used) - gene that can be easily
assayed
-use inducible promoter
Restriction Endonucleases
1. restriction - modification system; defense against foreign DNA
- methylation of RE target sequences
1 2. several classes - Type II that cut in target sequence; recognize palindromes
3. Types of cuts
a. cohesive or sticky ends - reanneal with ligase
b. blunt ends - can be ligated with T4 ligase
4. Other considerations
type of cut, cleavage site, parameters for the reaction to occur
5. Typical number of RE cuts:
- bacteria 2 x 106 bp - 100-1000 fragments
- euk cells 3 x 109 bp - 106 fragments
- plasmid, phage - 1-10 fragments
6. Isoschizomers - different MO and enzyme --> same cut site,
but may generate different type of cut
For recombinant DNA work - develop plasmids that have a single RE site.
Restriction Mapping
Method to determine where a RE cuts DNA relative to other RE
Reasons for Isolating Random Genomic DNA fragment (blunt end fragments)
- RE may cut inside the gene
- Methods - hydrodynamic shearing – vortexing, syringe needle
Joining of DNA Molecules/With Blunt Ends
A. Homopolymer tailing
-terminal nucleotidyl transferase, adds nucleotides to 3'-0H on SS-DNA,
requires no template
-results in poly A and poly T tails
B. Blunt End ligation
T4 Ligase - will joint blunt ends, requires 3'-OH and 5'P
DNA and ligase must be in high conc.
C. Linkers - short synthetic DNA fragments
contains a RE site --> attached with T4 ligase – often changes end to RE sticky end
when digested with appropriate RE
Generate DNA Sequences (genes) that are hard to isolate:
1. Isolation of cDNA using Reverse Transcriptase (RT)
a. eukaryotic DNA cannot be put into prokaryotic cells --> mRNA will not be edited
b. find eukaryotic cells that produce abundance of mRNA
c. isolate mRNA (already edited)
d. use RT isolated from cancer viruses (retroviruses - HIV) to make a DNA copy
(termed cDNA)
2 2. Amino acid sequencing of protein to be manufactured
produce synthetic DNA (preferred codon program)
clone/express sDNA
3. Formation of cDNA library
mRNA with exons removed
library composed of coding regions
search for genes (proteins) of interest
Detection of Recombinant Molecules
Possible products of ligation (cloning) reaction:
1. re-ligated vector
2. vector with one or more foreign DNA fragments
3. foreign DNA with no vector
Methods must address or differentiate between:
1. vector contains foreign DNA
2. foreign DNA contains gene of interest
a. easy if gene is a selectable marker
b. difficult if eukaryotic gene does not change phenotype
Common Methods used to Detect Clones/Transformed Cells
1. Insertional Inactivation
2 or more antibiotic resistant genes (pBR322)
Cycloserine enrichment technique - removes 1 step in the detection procedure
2. Cohesive ends, join 3'-OH and 5'P
-treat vector with alkaline phosphatase to remove 5'-P
-prevent re-circularization of vector
-foreign DNA then supplies the 5'-P
3. Cosmids - plasmids that carry the COS site from λ phage
uses cos site-cutting system --> package DNA into phage head.
System only works on DNA if:
1. DNA must have 2 cos sites
2. cos sites separated by 38 kb to 54 kb
packages DNA in vitro
-results in cloned DNA inserted between 2 cos sites
-when cosmid is inserted into a cell - acts like a plasmid
4. α- complementation (lac Z method)
inactivation of lac Z gene codes for β-galactosidase
x-gal --> spread on plate surface, when metabolized results in a blue color
Lac+ --> blue colonies
Lac- --> white colonies
system used in original automated DNA sequencing methods, cloning kits
Ways to get DNA into Target Cells
1. Transformation, Electroporation, Transduction
2. Liposomes
3 -small spheres made from artificial membranes
-fuse with plasma membranes
-release contents into the cell
3. Microinjection
-very fine needle to puncture cell wall/membrane
-even directly into the nucleus (egg)
4. “Gene gun” – thick cell wall of plants
-particle of gold/nanosphere of silicon coated with DNA
Identifying Clones/Products after the DNA has Been Inserted into the Cell
1. Identify Recombinants by size
-isolate plasmids and run a gel
-select cultures with larger plasmids
2. Colony or In situ hybridization assay
need a probe - mRNA etc
3. Radioactive Antibody Test - test for protein production
4. Immunoprecipitation Test - test for protein production
temperature sensitive autolysis - cells lysed --> released protein
protein reacts with antibody in agar plate
5. Epitope tags
-short DNA sequences fused in the ORF to be expressed
-code for peptide recognized by commercial antibody
-allow to identify/purify product
PCR - Polymerase Chain Reaction
Kary Mullis - history of discovery (Scientific American, April 1990)
Requirements:
1. thermal cycler
2. primers
-complimentary to 3' end of DNA on either end of gene of interest
-their 5' ends serve as primers for Tag polymerase
3. dNTPs
4. Taq Pol - not inactivated by denaturing temperature of cycler
Uses;
1. identify rare genes
2. recover genes in samples that are in low concentration
viral DNA sequences → detection of food poisoning MO (dead)
3. Site directed mutagenesis (change base in primer to induce mutation)
4. environmental surveys – non-culturable MO, metagenomics
5. used in DNA sequencing technology
6. make copies of specific genes for sequencing (16S rRNA genes)
Forensic Genetics using VNTR’S - Variable Number Tandem Repeats
cut w/RE
4 gel w/fragments
probe
autoradiography
“DNA” fingerprint
STR’s - microsatellite repeats
microsatellite repeats - 30-35bp
Other Uses of Recombinant DNA Technology
exponential leap → prokaryotic system to eukaryotic system
- cloning Euk genes in Prok cells
Pharming - transgenic animals
- attach to gene to casein or hemoglobulin
Reverse genetics - (protein → RNA → gene)
Gene Therapy - replacement of “bad” genes
Antisense RNA therapy
Human Genome Project
goals - prenatal diagnosis
- carrier screening
Gene screening → single gene defects (BRAC)
Genetic Profiling
Release of Recombinant MO
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