
A cloning vector is a small piece of
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted for
cloning
Cloning is the process of producing individual organisms with identical genomes, either by natural or artificial means. In nature, some organisms produce clones through asexual reproduction; this reproduction of an organism by itself without ...
purposes. The cloning vector may be DNA taken from a
virus
A virus is a submicroscopic infectious agent that replicates only inside the living Cell (biology), cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are ...
, the
cell of a higher organism, or it may be the
plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and ...
of a bacterium. The
vector
Vector most often refers to:
* Euclidean vector, a quantity with a magnitude and a direction
* Disease vector, an agent that carries and transmits an infectious pathogen into another living organism
Vector may also refer to:
Mathematics a ...
contains features that allow for the convenient insertion of a DNA fragment into the vector or its removal from the vector, for example through the presence of
restriction site
In molecular biology, restriction sites, or restriction recognition sites, are regions of a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides; these are recognized by restriction enzymes, which cleave the DNA at ...
s. The vector and the foreign DNA may be treated with a
restriction enzyme
A restriction enzyme, restriction endonuclease, REase, ENase or'' restrictase '' is an enzyme that cleaves DNA into fragments at or near specific recognition sites within molecules known as restriction sites. Restriction enzymes are one class o ...
that cuts the DNA, and DNA fragments thus generated contain either blunt ends or overhangs known as sticky ends, and vector DNA and foreign DNA with compatible ends can then be joined by
molecular ligation. After a DNA fragment has been cloned into a cloning vector, it may be further
subcloned into another vector designed for more specific use.
There are many types of cloning vectors, but the most commonly used ones are genetically engineered
plasmid
A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and ...
s. Cloning is generally first performed using ''
Escherichia coli
''Escherichia coli'' ( )Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. is a gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Escherichia'' that is commonly fo ...
'', and cloning vectors in ''E. coli'' include plasmids,
bacteriophage
A bacteriophage (), also known informally as a phage (), is a virus that infects and replicates within bacteria. The term is derived . Bacteriophages are composed of proteins that Capsid, encapsulate a DNA or RNA genome, and may have structu ...
s (such as
phage λ),
cosmids, and
bacterial artificial chromosome
A bacterial artificial chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually '' E. coli''. F-plasmids play a crucial role because they contain partiti ...
s (BACs). Some DNA, however, cannot be stably maintained in ''E. coli'', for example very large DNA fragments, and other organisms such as yeast may be used. Cloning vectors in yeast include
yeast artificial chromosomes (YACs).
Features of a cloning vector
All commonly used cloning vectors in
molecular biology
Molecular biology is a branch of biology that seeks to understand the molecule, molecular basis of biological activity in and between Cell (biology), cells, including biomolecule, biomolecular synthesis, modification, mechanisms, and interactio ...
have key features necessary for their function, such as a suitable cloning site and selectable marker. Others may have additional features specific to their use. For reason of ease and convenience, cloning is often performed using ''
E. coli''. Thus, the cloning vectors used often have elements necessary for their propagation and maintenance in ''E. coli'', such as a functional
origin of replication (ori). The
ColE1 origin of replication is found in many plasmids. Some vectors also include elements that allow them to be maintained in another organism in addition to ''E. coli'', and these vectors are called
shuttle vector.
Cloning site
All cloning vectors have features that allow a gene to be conveniently inserted into the vector or removed from it. This may be a
multiple cloning site (MCS) or polylinker, which contains many unique
restriction sites. The restriction sites in the MCS are first cleaved by restriction enzymes, then a
PCR-amplified target gene also digested with the same enzymes is ligated into the vectors using
DNA ligase. The target DNA sequence can be inserted into the vector in a specific direction if so desired. The restriction sites may be further used for
sub-cloning into another vector if necessary.
Other cloning vectors may use
topoisomerase instead of ligase and cloning may be done more rapidly without the need for restriction digest of the vector or insert. In this
TOPO cloning method a linearized vector is activated by attaching topoisomerase I to its ends, and this "TOPO-activated" vector may then accept a PCR product by ligating both the 5' ends of the PCR product, releasing the topoisomerase and forming a circular vector in the process. Another method of cloning without the use of DNA digest and ligase is by
DNA recombination, for example as used in the
Gateway cloning system. The gene, once cloned into the cloning vector (called entry clone in this method), may be conveniently introduced into a variety of expression vectors by recombination.
Selectable marker
A
selectable marker
A selectable marker is a gene introduced into cell (biology), cells, especially bacteria or cells in cell culture, culture, which confers one or more traits suitable for artificial selection. They are a type of reporter gene used in laboratory micr ...
is carried by the vector to allow the selection of positively
transformed cells.
Antibiotic
An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting pathogenic bacteria, bacterial infections, and antibiotic medications are widely used in the therapy ...
resistance is often used as marker, an example being the
beta-lactamase gene, which confers resistance to the
penicillin
Penicillins (P, PCN or PEN) are a group of beta-lactam antibiotic, β-lactam antibiotics originally obtained from ''Penicillium'' Mold (fungus), moulds, principally ''Penicillium chrysogenum, P. chrysogenum'' and ''Penicillium rubens, P. ru ...
group of
beta-lactam antibiotics like
ampicillin
Ampicillin is an antibiotic belonging to the aminopenicillin class of the penicillin family. The drug is used to prevent and treat several bacterial infections, such as respiratory tract infections, urinary tract infections, meningitis, s ...
. Some vectors contain two selectable markers, for example the plasmid pACYC177 has both ampicillin and
kanamycin
Kanamycin A, often referred to simply as kanamycin, is an antibiotic used to treat severe bacterial infections and tuberculosis. It is not a first line treatment. It is used by mouth, injection into a vein, or injection into a muscle. Kanamy ...
resistance gene.
Shuttle vector which is designed to be maintained in two different organisms may also require two selectable markers, although some selectable markers such as resistance to
zeocin and
hygromycin B are effective in different cell types.
Auxotrophic selection markers that allow an auxotrophic organism to grow in
minimal growth medium may also be used; examples of these are ''
LEU2'' and ''
URA3'' which are used with their corresponding auxotrophic strains of yeast.
Another kind of selectable marker allows for the positive selection of plasmid with cloned gene. This may involve the use of a gene lethal to the host cells, such as
barnase,
Ccda, and the
parD/parE toxins. This typically works by disrupting or removing the lethal gene during the cloning process, and unsuccessful clones where the lethal gene still remains intact would kill the host cells, therefore only successful clones are selected.
Reporter gene
Reporter genes are used in some cloning vectors to facilitate the screening of successful clones by using features of these genes that allow successful clone to be easily identified. Such features present in cloning vectors may be the
''lacZ''α fragment for α complementation in
blue-white selection, and/or
marker gene or
reporter genes in frame with and flanking the
MCS to facilitate the production of
fusion proteins. Examples of fusion partners that may be used for screening are the
green fluorescent protein (GFP) and
luciferase.
Elements for expression
A cloning vector need not contain suitable elements for the
expression of a cloned target gene, such as a
promoter and
ribosomal binding site (RBS), many however do, and may then work as an
expression vector
An expression vector, otherwise known as an expression construct, is usually a plasmid or virus designed for gene expression in cells. The vector (molecular biology), vector is used to introduce a specific gene into a target cell, and can command ...
. The target
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
may be inserted into a site that is under the control of a particular promoter necessary for the expression of the target gene in the chosen host. Where the promoter is present, the expression of the gene is preferably tightly controlled and
inducible so that proteins are only produced when required. Some commonly used promoters are the
T7 and
''lac'' promoters. The presence of a promoter is necessary when screening techniques such as
blue-white selection are used.
Cloning vectors without promoter and RBS for the cloned DNA sequence are sometimes used, for example when cloning genes whose products are toxic to ''
E. coli'' cells. Promoter and RBS for the cloned DNA sequence are also unnecessary when first making a
genomic or
cDNA library of clones since the cloned genes are normally subcloned into a more appropriate expression vector if their expression is required.
Some vectors are designed for transcription only with no heterologous protein expressed, for example for ''in vitro'' mRNA production. These vectors are called transcription vectors. They may lack the sequences necessary for polyadenylation and termination, therefore may not be used for protein production.
Types of cloning vectors
A large number of cloning vectors are available, and choosing the vector may depend upon a number of factors, such as the size of the insert, copy number and cloning method. Large insert may not be stably maintained in a general cloning vector, especially for those with a high copy number, therefore cloning large fragments may require more specialised cloning vector.
Plasmid
Plasmids are autonomously replicating circular extra-chromosomal DNA. They are the standard cloning vectors and the ones most commonly used. Most general plasmids may be used to clone DNA inserts of up to 15 kb in size. One of the earliest commonly used cloning vectors is the
pBR322 plasmid. Other cloning vectors include the
pUC series of plasmids, and a large number of different cloning plasmid vectors are available. Many plasmids have high copy numbers, for example,
pUC19 has a copy number of 500-700 copies per cell,
and high copy number is useful as it produces greater yield of recombinant plasmid for subsequent manipulation. However low-copy-number plasmids may be preferably used in certain circumstances, for example, when the protein from the cloned gene is toxic to the cells.
Some plasmids contain an
M13 bacteriophage origin of replication and may be used to generate single-stranded DNA. These are called
phagemids, and examples are the
pBluescript series of cloning vectors.
Bacteriophage
The bacteriophages used for cloning are the
λ phage
Lambda phage (coliphage λ, scientific name ''Lambdavirus lambda'') is a bacterial virus, or bacteriophage, that infects the bacterial species ''Escherichia coli'' (''E. coli''). It was discovered by Esther Lederberg in 1950. The wild type of ...
and
M13 phage. There is an upper limit on the amount of DNA that can be packed into a phage (a maximum of 53 kb), therefore to allow foreign DNA to be inserted into phage DNA, phage cloning vectors may need to have some non-essential genes deleted, for example the genes for
lysogeny since using phage λ as a cloning vector involves only the lytic cycle. There are two kinds of λ phage vectors - insertion vector and replacement vector. Insertion vectors contain a unique cleavage site whereby foreign DNA with size of 5–11 kb may be inserted. In replacement vectors, the cleavage sites flank a region containing genes not essential for the lytic cycle, and this region may be deleted and replaced by the DNA insert in the cloning process, and a larger sized DNA of 8–24 kb may be inserted.
There is also a lower size limit for DNA that can be packed into a phage, and vector DNA that is too small cannot be properly packaged into the phage. This property can be used for selection - vector without insert may be too small, therefore only vectors with insert may be selected for propagation.
Cosmid
Cosmids are plasmids that incorporate a segment of bacteriophage λ DNA that has the cohesive end site (''cos'') which contains elements required for packaging DNA into λ particles. Under apt origin of replication (ori), it can replicate as a plasmid. It is normally used to clone large DNA fragments between 28 and 45 Kb.
Bacterial artificial chromosome
Insert size of up to 350 kb can be cloned in
bacterial artificial chromosome
A bacterial artificial chromosome (BAC) is a DNA construct, based on a functional fertility plasmid (or F-plasmid), used for transforming and cloning in bacteria, usually '' E. coli''. F-plasmids play a crucial role because they contain partiti ...
(BAC). BACs are maintained in ''E. coli'' with a copy number of only 1 per cell.
BACs are based on
F plasmid, another artificial chromosome called the
PAC is based on the
P1 phage.
Yeast artificial chromosome
Yeast artificial chromosome are used as vectors to clone DNA fragments of more than 1 mega base (1Mb=1000kb) in size. They are useful in cloning larger DNA fragments as required in mapping genomes such as in the
Human Genome Project. It contains a telomeric sequence, an autonomously replicating sequence (features required to replicate linear chromosomes in yeast cells). These vectors also contain suitable restriction sites to clone foreign DNA as well as genes to be used as selectable markers.
Human artificial chromosome
Human artificial chromosome may be potentially useful as a gene transfer vectors for gene delivery into human cells, and a tool for expression studies and determining human chromosome function. It can carry very large DNA fragment (there is no upper limit on size for practical purposes), therefore it does not have the problem of limited cloning capacity of other vectors, and it also avoids possible insertional mutagenesis caused by integration into host chromosomes by viral vector.
Animal and plant viral vectors
Viruses that infect plant and animal cells have also been manipulated to introduce foreign genes into plant and animal cells. The natural ability of viruses to adsorb to cells, introduce their DNA and replicate have made them ideal vehicles to transfer foreign DNA into eukaryotic cells in culture. A vector based on
Simian virus 40 (SV40) was used in first cloning experiment involving mammalian cells. A number of vectors based on other type of viruses like
Adenoviruses and
Papilloma virus have been used to clone genes in mammals. At present, retroviral vectors are popular for cloning genes in mammalian cells. In case of plants like
Cauliflower mosaic virus,
Tobacco mosaic virus
Tobacco mosaic virus (TMV) is a positive-sense single-stranded RNA virus species in the genus '' Tobamovirus'' that infects a wide range of plants, especially tobacco and other members of the family Solanaceae. The infection causes characteris ...
and
Gemini viruses have been used with limited success.
Contemporary uses and versatility
Cloning vectors today are essential not only for routine gene isolation and subcloning, but also as the basis fo
advanced molecular biology tools They are engineered for specialized tasks—such as phage- or cosmid-based systems to carry larger inserts, shuttle vectors to enable cloning across different host species, and viral vectors tailored for gene therapy and recombinant protein production. Modern vectors streamline workflows by combining multiple functions—efficient DNA delivery, stable replication, effective selection, and expression control—in a single construct designed for diverse research and biotechnological applications.
Screening: example of the blue/white screen
Many general purpose vectors such as
pUC19 usually include a system for detecting the presence of a cloned DNA fragment, based on the loss of an easily scored phenotype. The most widely used is the gene coding for ''E. coli''
β-galactosidase, whose activity can easily be detected by the ability of the enzyme it encodes to hydrolyze the soluble, colourless substrate
X-gal (5-bromo-4-chloro-3-indolyl-beta-d-galactoside) into an insoluble, blue product (5,5'-dibromo-4,4'-dichloro indigo). Cloning a fragment of DNA within the vector-based ''lacZα'' sequence of the β-galactosidase prevents the production of an active enzyme. If X-gal is included in the selective agar plates, transformant colonies are generally blue in the case of a vector with no inserted DNA and white in the case of a vector containing a fragment of cloned DNA.
See also
*
Vector (molecular biology)
In molecular cloning, a vector is any particle (e.g., plasmids, cosmids, Lambda phages) used as a vehicle to artificially carry a foreign nucleic acid sequence, nucleic sequence – usually DNA – into another Cell (biology), cell, where it can D ...
*
Plant transformation vector
*
IMAGE cDNA clones
*
fosmid
*
Golden Gate Cloning
References
{{Reflist, 2
external links
https://entechonline.com/cloning-vector-definition-types-and-applications/
Genetics techniques
Molecular biology
Cloning
Plasmids