1. 基因工程與原理 GENE CLONING AND DNA ANALYSIS Chapter 2
Vectors for Gene Cloning: Plasmids and Bacteriophage

2. 2 Vectors for Gene Cloning: Plasmids and Bacteriophages
2.1.1 Size and copy number
2.1.2 Conjugation and compatibility
2.1.3 Plasmid classification
2.1.4 Plasmids in organisms other than bacteria
2.2 Bacteriophages
2.2.1 The phage infection cycle
2.2.2 Lysogenic phages
Gene organization in the  DNA molecule
The linear and circular forms of  DNA
M13—a filamentous phage
2.2.3 Viruses as cloning vectors for other organisms

3. 2.1 Plasmids
Figure 2.1
Plasmids: independent genetic elements found in bacterial cells.

4. Figure 2.2
The use of antibiotic resistance as a selectable marker for a plasmid. RP4 (top) carries genes for resistance to ampicillin, tetracycline and kanamycin. Only those E. coli cells that contain RP4 (or a related plasmid) are able to survive and grow in a medium that contains toxic amounts of one or more of these antibiotics.

5. origin of replication
Figure 2.3
Replication strategies for (a) a non-integrative plasmid, and (b) an episome.

6. 2.1.1 Size and copy number
The factors that control copy number are not well understood.
Stringent v.s. Relaxed

7. Several different kinds of plasmid may be found in a single cell.
2.1.2 Conjugation and compatibility
Figure 2.4
Plasmid transfer by conjugation between bacterial cells. The donor and recipient cells attach to each other by a pilus, a hollow appendage present on the surface of the donor cell. A copy of the plasmid is then passed to the recipient cell. Transfer is thought to occur through the pilus, but this has not been proven and transfer by some other means (e.g. directly across the bacterial cell walls) remains a possibility.

8. 2.1.3 Plasmid classification
Fertility or F plasmids carry the tra genes.
Resistance or R plasmid carry genes conferring on the host bacterium resistance to one or more antibacterial agents.
Col plasmids code for colicin, proteins that kill other bacteria.
Degradative plasmids allow the host bacterium to metabloize unusual molecules. (TOL of Pseudomonas putida 戀臭假單胞菌)
Virulence plasmids confer pathogenicity on the host bacterium. (Ti plasmid of Agrobacterium tumefaciens農桿菌)
2.1.4 Plasmids in organisms other than bacteria
The eukaryotic plasmid, 2 mm circle, occurs in many strains of the yeast Saccharomyces cerevisiae.

9. 2.2 Bacteriophages
Figure 2.5
The two main types of phage structure: (a) head-and-tail (e.g. λ); (b) filamentous (e.g. M13).

10. 2.2.1 The phage infection cycle
lytic cycle
Figure 2.6
The general pattern of infection of a bacterial cell by a bacteriophage.

11. 2.2.2 Lysogenic phages
The prophage is quiescent.
The bacterium referred as a lysogen.
Figure 2.7
The lysogenic infection cycle of bacteriophage lambda (λ).

12. Figure 2.8
The infection cycle of bacteriophage M13.

13. Clustering of related genes/ switched on and off as a group
Figure 2.9
The λ genetic map, showing the positions of the important genes and the functions of the gene clusters.

14. Sticky ends or cohesive ends
Circularized/ insertion into bacterial genome.
Rolling circle replication
Figure 2.10
The linear and circular forms of λ DNA. (a) The linear form, showing the left and right cohesive ends. (b) Base pairing between the cohesive ends results in the circular form of the molecule. (c) Rolling circle replication produces a catenane of new linear λ DNA molecules, which are individually packaged into phage heads as new λ particles are assembled.

15. RF: 100 copies/ cell
1000 new phages being produced during each generation of infected cell
Figure 2.11
The M13 infection cycle, showing the different types of DNA replication that occur. (a) After infection the single-stranded M13 DNA molecule is converted into the double-stranded replicative form (RF). (b) The RF replicates to produce multiple copies of itself. (c) Single-stranded molecules are synthesized by rolling circle replication and used in the assembly of new M13 particles.

16. Several features of M13 make this phage attractive as a cloning vector:
Less than 10 kb in size.
The double-stranded replicative form (RF)
Can be obtained in the form of single-stranded DNA
Useful for the DNA sequencing and in vitro mutagenesis.
Phage display: identify the proteins interaction.
2.2.3 Viruses as cloning vectors for other organisms
Adenoviruses for human
Baculoviruses for insect cells
Caulimoviruses and geminviruses for plants.