1. Biotechnology
Chapter 17

2. DNA Manipulation
The molecular biology revolution started with the discovery of restriction endonucleases
-Enzymes that cleave DNA at specific sites
These enzymes are significant in two ways
1. Allow a form of physical mapping that was previously impossible
2. Allow the creation of recombinant DNA molecules (from two different sources)

3. DNA Manipulation
Restriction enzymes recognize DNA sequences termed restriction sites
There are two types of restriction enzymes:
-Type I = Cut near the restriction site
-Type II = Cut at the restriction site
-The sites are palindromes
-Both strands have same sequence when read 5’ to 3’

4. DNA Manipulation
Type II enzymes produce staggered cuts that generate “sticky ends” -Overhanging complementary ends
Therefore, fragments cut by the same enzyme can be paired
DNA ligase can join the two fragments forming a stable DNA molecule

6. Gel Electrophoresis
A technique used to separate DNA fragments by size;
The gel (agarose or polyacrylamide) is subjected to an electrical field;
The DNA, which is negatively-charged, migrates towards the positive pole
-The larger the DNA fragment, the slower it will move through the gel matrix;
DNA is visualized using fluorescent dyes

8. Transformation
Transformation is the introduction of DNA from an outside source into a cell.
Natural transformation occurs in many species
-However, not in E. coli, which is used routinely in molecular biology labs
-Artificial transformation techniques have been developed to introduce foreign DNA into it

9. Molecular Cloning A clone refers to a genetically identical copy;
Molecular cloning is the isolation of a specific DNA sequence (usually protein-encoding)
-Sometimes called gene cloning
The most flexible and common host for cloning is E. coli
Propagation of DNA in a host cell requires a vector

10. Vectors Plasmids are small, circular extrachromosomal DNA molecules
-Used for cloning small pieces of DNA
-Have three important components
1. Origin of replication
2. Selectable marker
3. Multiple cloning site (MCS)

11. Vectors

12. Vectors Phage vectors are modified bacterial viruses
-Most based on phage lambda (l) of E. coli
-Used to clone inserts up to 40 Kbp
-Have two features not shared with plasmid vectors
-They kill their host cells
-They have linear genomes
-Middle replaced with inserted DNA

13. Vectors

14. DNA Libraries
A collection of DNA fragments from a specific source that has been inserted into host cells;
A genomic library represents the entire genome;
A cDNA library represents only the expressed part of the genome
-Complementary DNA (cDNA) is synthesized from isolated mRNA using the enzyme reverse transcriptase

16. DNA Libraries
Molecular hybridization is a technique used to identify specific DNAs in complex mixtures
-A known single-stranded DNA or RNA is labeled
-It is then used as a probe to identify its complement via specific base-pairing
-Also termed annealing
Molecular hybridization is the most common way of identifying a clone in a DNA library

17. DNA Analysis Restriction maps
-Molecular biologists need maps to analyze and compare cloned DNAs;
-The first maps were restriction maps
-Initially, they were created by enzyme digestion & analysis of resulting patterns
-Many are now generated by computer searches for cleavage sites

18. DNA Analysis Southern blotting
-A sample DNA is digested by restriction enzymes & separated by gel electrophoresis;
-Gel is transferred (“blotted”) onto a nitrocellulose filter
-Then hybridized with a cloned, radioactively-labeled DNA probe
-Complementary sequences are revealed by autoradiography

20. DNA Analysis DNA fingerprinting
-An identification technique used to detect differences in the DNA of individuals;
-Makes use of a variety of molecular procedures;
-First used in a US criminal trial in 1987
-Tommie Lee Andrews was found guilty of rape

21. DNA Analysis DNA sequencing -A set of nested fragments is generated
-End with known base
-Separated by high-resolution gel electrophoresis, resulting in a “ladder”
-Sequence is read from the bottom up

22. DNA Analysis DNA sequencing
-The enzymatic technique develop by Frederick Sanger is powerful but is labor intensive and time-consuming
-The development of automated techniques made sequencing faster and more practical
-Fluorescent dyes are used instead of radioactive labels
-Reaction is done in one tube
-Data are assembled by a computer

23. DNA Analysis Polymerase chain reaction (PCR) -Developed by Kary Mullis
-Allows the amplification of a small DNA fragment using primers that flank the region
-Each PCR cycle involves three steps:
1. Denaturation (high temperature)
2. Annealing of primers (low temperature)
3. DNA synthesis (intermediate temperature)
-Taq polymerase

25. DNA Analysis Polymerase chain reaction (PCR)
-Has revolutionized science and medicine because it allows the investigation of minute samples of DNA
-Forensics
-Detection of genetic defects in embryos
-Analysis of mitochondrial DNA from early human species

26. Genetic Engineering Has generated excitement and controversy.
Expression vectors contain the sequences necessary to express inserted DNA in a specific cell type.
Transgenic animals contain genes that have been inserted without the use of conventional breeding.

27. Genetic Engineering In vitro mutagenesis
-Ability to create mutations at any site in a cloned gene
-Has been used to produce knockout mice, in which a known gene is inactivated
-The effect of loss of this function is then assessed on the entire organism
-An example of reverse genetics

29. Medical Applications Human proteins
-Medically important proteins can be produced in bacteria
-Human insulin
-Interferon
-Atrial peptides
-Tissue plasminogen activator
-Human growth hormone

30. Medical Applications

31. Medical Applications Vaccines
-Subunit vaccines: Genes encoding a part of the protein coat are spliced into a fragment of the vaccinia (cowpox) genome
-DNA vaccines: Depend on the cellular immune response (not antibodies)

32. Medical Applications

33. Medical Applications Gene therapy
-Adding a functional copy of a gene to correct a hereditary disorder
-Severe combined immunodeficiency disease (SCID) illustrates both the potential and the problems
-Successful at first, but then patients developed a rare leukemia

34. Agricultural Applications
Herbicide resistance
-Broadleaf plants have been engineered to be resistant to the herbicide glyphosate
-This allows for no-till planting

35. Agricultural Applications
Pest resistance
-Insecticidal proteins have been transferred into crop plants to make them pest-resistant
-Bt toxin from Bacillus thuringiensis
Golden rice
-Rice that has been genetically modified to produce b-carotene (provitamin A)
-Converted in the body to vitamin A

36. Agricultural Applications
Daffodil
phytoene
synthase
gene (psy)
psy
crtI
lcy
Phytoene
Carotene
desaturase
-Cyclase
Genes introduced
into rice genome
Expression
in endosperm
GGPP
Lycopene
-Carotene
(Provitamin A)
Bacterial
carotene
gene (crtI)
lycopene
-cyclase
gene (lcy)
Rice
chromosome

37. Agricultural Applications