1. Fragment of DNA to be cloned is inserted into vector to produce rDNA
Vector to transport gene into host cell e.g. plasmid or bacteriophage chromosome
Multiplication of rDNA molecule together with vector
Division of host cell
After a large number of cell divisions forms a colony or clone with identical genes
Gene Cloning

2. PCR Thermal Cycler Heat to 94 oC to denature the double strand DNA
Cool to 55 oC for primers to anneal to DNA at specific position (gene of interest)
Raise to 74 oC for Taq DNA polymerase to function
Synthesis of DNA strands complementary to template DNA molecules in opposite direction
Repeat the cycle times

3. Importance of Gene Cloning and PCR
Useful in gene isolation
E.Coli contains over 4000 different genes!
PCR in a few hours, gene cloning in weeks!
Limitations of PCR:
Sequence of annealing sites must be known in order for primers to anneal to correct positions
Limit to length of DNA sequence i.e. 5 kilobases – 40 kilobases
Application of PCR:
Useful to detect or isolate gene sequences already known
eg. Test for mutation in blood using globin genes or use of primers specific for the DNA of a harmful virus

4. Plasmids
Circular molecules of DNA that lead independent existence in host
Carry genes that are responsible for a useful characteristic displayed by host bacterium
Survival in normally toxic concentrations of antibiotics – antibiotic resistance as a selectable marker
Example: ampicillin, tetracycline, kanamycin resistant gene RP4
At least one DNA sequence that can act as an origin of replication OR
Integrate into bacterial chromosome for division
< 10kb desirable for a cloning vehicle

5. Plasmid Classification
Fertility or “F” plasmids carry only tra genes and have no characteristic beyond the ability to promote conjugal plasmid transfer
Resistance or “R” plasmids confers resistance to one or more antibacterial agents
Col plasmids code for colicins, proteins that kill other bacteria
Degradative plasmids allow the host bacterium to metabolize unusual molecules e.g. toluene and Hg
Virulence plasmids confer pathogenicity on the host bacterium e.g. Ti plasmids of agrobacterium tumefaciens induce crown gall disease on plants

6. total cell DNA
pure plasmid DNA
Purification of DNA from living cells
3.1 Preparation of total cell DNA
A culture of bacteria is grown and then harvested
The cells are removed and broken to give a cell extract
The DNA is purified from the cell extract
The DNA is concentrated
3.1.1 Growing and harvesting a bacterial culture
culture bacteria in a liquid both
2 types of growth media – defined medium and undefined medium
Define media is used when the bacteria culture has to be grown under precisely controlled conditions e.g. M9
Undefined media is used when culture is grown for a source of DNA e.g. Luria-Bertani (LB) contain yeast and tryptone

7. 3.1.2 Preparation of a cell extract
Purpose is to break open bacterial cells (cell lysis) by either physical or chemical means
lysozyme digest polymeric compunds that define a cell wall’s rigidity
EDTA remove Mg2+ that is essential for the structure of cell envelope
Detergents e.g. SDS help to remove lipid molecules and cause disruption of cell membranes
Centrifugation to remove cell debris that settle at the bottom
3.1.3 Purification of DNA from a cell extract
Bacterial extract can contain a lot of protein and RNA inaddtion to desired DNA
Add phenol or 1:1 mixture of phenol and chloroform. Ppt proteins leaving behind DNA & RNA and can be seperated after centrifugation
Cell extracts that contain a large amount of proteins must be treated with Protease such as proteinase K before addition of phenol
Degrade RNA with suitable ribonuclease

8. 3.1.4 Measurement of DNA concentration
UV absorbance spectrophotometry
Absorbance at 260 nm (A260) of 1.0 == 50ug of double strand DNA/ml
UV absorbance can also check for purity of DNA preparation: A260/A280 = 1.8 for pure samples
3.1.5 Preparation of total cell DNA from non-bacteria organism
plant tissues contain large amount of carbohydrates that cannot be removed by phenol extraction
METHOD 1
Add CTAB (cetyltrimethylammonium bromide) so that CTAB complex ppt out together with the nucleic acid. Carbohydrates and proteins and other contaminants as a supernatant. Centrifuge and collect the ppt.
Nucleic acids remaining can be concentrated using ethanol precipitation and RNA remove by ribonuclease treatment

9. METHOD 2
Add guanidinium thiocyanate to dissolve all biochemical other than nucleic acids
Pass the sample through a chromatography column with silica particles inside. DNA in presence of guanidinium thiocyanate bind more strongly to silica
DNA is recovered by adding water which destabilizes interaction between DNA and silica
3.2.1 Plasmid Separation
Separation by size work on the principle that cells are lysed under very carefully controlled conditions
very little breakage of DNA chromosome. Hence DNA is much larger than plasmid and can be removed together with cell debris in centrifugation
Chromosomal DNA also attached to cell envelope and settle at bottom

10. Method 1
For E. Coli and related species under controlled lysis
Add EDTA and lysozyme in the presence of 25% sucrose – prevent cell from bursting immediately
Cell lysis is induced by adding non-ionic detergent (Triton X-100) because ionic detergent cause chromosomal breakage
Centrifugation leaves a cleared lysate consisting of only plasmid DNA
Method 2
Separation by conformation using alkaline denaturation.
Plasmid is circular DNA but also often supercoiled
A narrow pH range at which non-supercoiled DNA is denatured while supercoiled plasmid will not. pH range between 12.0 – 12.5 (using NaOH)
After non supercoiled DNA’s H bonding is broken to form linear strand DNA, add acid to reach pH 7.0
Denatured bacteria DNA strands entangle into a mass and can be centrifuged, leaving pure plasmid DNA in supernatant

11. 3.2.2 Plasmid Amplification
To increase the copy number of plasmid
some multicopy plasmid can replicate in the absence of protein synthesis, whereas main bacteria chromosome cannot replicate
After a satisfactory cell density is reached, add inhibitor of protein synthesis e.g. chloramphenicol and incubate for another 12 hrs
Plasmid copy of , hence an efficient way of increasing yield of multicopy plasmid

12. Chapter 4: manipulation of purified DNA
DNA manipulative enzymes
Nuclease – cut or degrade nucleic acid
exonuclease remove nucleotides one at a time from end of DNA
endonuclease break internal phosphodiester bonds within DNA
Ligase – join nucleic acid
Polymerase – make copies of molecules
Modifying enzymes – remove or add chemical grp
alkaline phosphatase remove phosphate grp at 5’ end of DNA
Polynucleotide kinase reverse effect to alkaline phosphatase
Terminal deoxynucleotidyl transferase add deoxyribonucleotides to 3’ end of DNA
Topoisomerase – introduce or remove supercoils from covalently closed circular DNA

13. Chapter 5: Introduction of DNA into living cells
5.1.1 Transformation - Uptake of foreign DNA molecule by a cell
Most cell take only limited amounts of DNA normally, must increase efficiency of intake by physical or chemical enhancement
E.coli cells soaked in ice cold salt solution more efficient at DNA uptake. A solution of 50mM CaCl2 is used
Next heat shock the solution to 42 oC for 2 min to facilitate uptake of plasmid by cell
5.1.2 Selection for transformed cells
using selectable marker e.g. amipicillin resistance gene or tetracycline resistance gene
LacZ’ gene codes for beta galactosidase, breaks lactose to glucose + galactose
e.g. PUC8 plasmid with both AmpR and LacZ’ genes
some strains of E.coli have modified lacZ gene that lack the segment LacZ’

14. These mutants can only synthesize beta galactosidase if it has PUC8 plasmid that carries the missing LacZ’ gene segment
Add X-gal (5-bromo-4-chloro-3-indoyl-B-D-galactopyra-lactose) which is broken down by B galactosidase to form a blue product
Add IPTG (inducer of the beta galactosidase)
Xgal + IPTG + agar plate to select cells between white and blue colonies
Cloning vectors for E.Coli
pBR322 – ori, ampR, tetR
pBR327 – ori, ampR, tetR
pUC8 – ori, ampR, lacZ’
Nomenclature of plasmid cloning vectors
pBR322
p – plasmid
BR – identifies the laboratory in which vector was discovered (BR for Bolivar and Rodriguez, the 2 researchers that developed it)
322 – distinguishes this plasmid from others developed in the same laboratory (pBR325, pBR327 etc..)