This document discusses various types of cloning vectors including plasmids, bacteriophages, cosmids, phagemids, and artificial chromosomes that are used to clone DNA fragments. It provides details on commonly used plasmid vectors like pBR322 and pUC, lambda phage vectors, properties of cosmids, phagemids and artificial chromosomes like BACs, YACs, and MACs. Components, applications, and limitations of these different vector types are summarized.

1. CLONING VECTORS
Dr. Mayank Chaudhary
Assistant Professor
Department of Biotechnology
Maharishi Markandeshwar (Deemed to be University)
Mullana-Ambala, Haryana, INDIA

2. PLASMIDS
• These are extra-chromosomal, double-stranded, circular DNA molecules
capable of autonomous replication within bacterial cells.
• Size of plasmids range from 1kb-250kb.
• Episomes/Integrative Plasmids: Plasmids that replicate by integration into
bacterial chromosomal DNA.
• Copy number: Number of molecules of individual plasmid that is found in
single bacterial cell. On the basis of copy no.:
1) Stringent: Have low copy no. per cell (1 or 2)
2) Relaxed: Present in multiple copies per cell.

4. • Plasmid Classification:
1) Fertility or F Plasmids: Conjugative plasmid carrying transfer gene (tra) and having
the ability to form conjugation bridge (F pilus) with F- bacterium. Eg. F plasmid of
E.coli.
2) Resistance or R Plasmids: Carry genes which give resistance to bacteria from one
or more antibacterial agents. Eg. RP4 plasmid found in Pseudomonas.
3) Col Plasmids: Have genes that code for colicins (proteins that kill other bacteria).
Eg. ColE1 of E.coli.
4) Degradative Plasmids: Allows host bacterium to metabolize unwanted molecules
such as toluene and salicylic acid. Eg. TOL of Pseudomonas putida.
5) Virulence Plasmids: Confers pathogenicity to host bacteria. Eg. Ti plasmid of
Agrobacterium tumefaciens.
6) Cryptic Plasmids: Do not have any effect on the phenotype of the cell carrying
them.

5. pBR322
• Plasmids can have insert size of ≤15kb.
• Nomenclature:
• P: indicates that it is a plasmid
• BR: identifies laboratory where it was constructed (stands for Bolivar and
Rodriguez who investigated it)
• 322: distinguishes it from other vectors developed in the same laboratory.
• Useful Properties:
 Suitable size (4363 bp ‹ 10kb)- To avoid problems such as DNA breakage
during purification.
 2 marker genes (ampicillin and tetracycline resistant genes)
 High copy number

7. pUC
• Nomenclature:
• p: indicates plasmid
• UC: University of California
• Useful Properties:
• Small size (2686 bp)
• High copy numer
• Contain lacZ sequence (easy identification through blue/white screening)
• Ampicillin resistant marker gene

8. Bacteriophages
• Viruses that infect bacteria.
• Simple structure: Nucleic acid surrounded by protein coat (capsid).
• Phage infection cycle: lytic or lysogenic

11. • Typical insert size for phage is 5-20kb.
• Features of lambda DNA molecule:
1) Size of lambda DNA molecules is 49kb.
2) Gene clustering (genes performing related functions are grouped that
allows switching on/off of genes as a group rather than individually.
3) DNA conformation: Linear DNA has two free ends with 12nt single-
stranded stretch on either side. These single strands are complementary
and can base pair to form circular, double-stranded molecule.
Complementary single strands are called as sticky ends/cohesive ends. Also
known as Cos sites.
Function of Cos sites: 1) Allows circularization of linear DNA molecule
injected into bacterial cell. 2) Acts as recognition sites for RE to separate out
large number of DNA molecules formed through rolling circle mechanism.

13. • Types of vectors developed using Lambda genome:
1) Insertion Vectors
2) Replacement Vectors
Insertion vectors: Foreign DNA is inserted into lambda genome without
significant change of wild-type genome resulting int small insert size (upto
10kb).

14. • Replacement vectors: Stuffer fragment is replaced by foreign DNA
resulting in insert size of 10-23kb.

16. Cosmid
• Hybrid plasmid with bacterial ori sequence and cos sequences derived from
lambda phage.
• Within a cell, Cosmid replicates as a plasmid (Recombinant DNA is
therefore obtained from colonies rather than plaques).
• Contains gene for selection.
• Insert size: 35-50 kb.
• Widely used for synthesis of genomic libraries.
• Example of Cosmids: pJB8
• Limitations of Cosmid vector:
1) Slower replication
2) Higher frequency of recombination
3) Unstability inside host (E.coli)

17. Phagemid
• Cloning vectors that are hybrid of filamentous phage M13 and plasmids.
• Components of Phagemid vector:
1) Origin of replication of plasmid
2) Intergenic region (IG) containing packaging signal for phage particle
3) Gene encoding phage coat protein
4) Selection marker
5) Restriction enzyme recognition sites
• Commonly used for phage display technology (proteins are expressed as
fusions to phage coat proteins and displayed on the viral surface)
• Example: pEMBL
• Advantages of Phagemids over Phage vectors: Higher carrying capacity,
higher transformation efficiency and more stability.

19. Artificial chromosomes
• These are DNA molecules assembled in-vitro that can function as
natural chromosomes. Types:
• BACs: Bacterial artificial chromosomes
• YACs: Yeast artificial chromosomes
• MACs: Mammalian artificial chromosomes
• PACs: P1-derived artificial chromosomes

20. BACs
Insert size: 100-300 kb
• Components of BACs:
1) oriS, repE-F: for plasmid replication and regulation of copy number
2) parA and parB: To maintain low copy number and to avoid two F
plasmids in single cell
3) Antibiotic resistance marker gene
4) lacZ gene for blue/white selection
5) T7 and Sp6 promoters for transcription of inserted genes
Example: pBeloBAC11

21. YACs
Insert size: 100-500 kb
• YAC has sequences to exist as circular plasmid inside bacteria and as linear
nuclear chromosome in yeast.
• Components of YAC vectors:
1) E.coli origin of replication
2) Yeast origin of replication
3) Elements of eukaryotic yeast chromosome (centromere and telomere)
4) Selection markers for both the host
• Can be used to express eukaryotic proteins that require post-translational
modifications.

22. MACs
Insert size: 100 kb-1 Mb
• MACs also depend upon presence of centromeric, telomeric sequences and
origin of DNA replication.
• Two procedures for generation of MACs:
1) Telomere directed fragmentation of natural chromosomes. (eg. HAC from
chromosome 21)
2) De novo assembly of cloned centromeric, telomeric and replication origins
in-vitro.
• MACs have application in gene therapy and eukaryotic protein expression.

23. REFERENCES
1) T.A. Brown. Gene Cloning and DNAAnalysis-An Introduction. Seventh
Edition.
2) NPTEL notes (Module 1).