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A plasmid is a small DNA molecule within a cell that is physically separated

from a chromosomal DNA and can replicate independently. They are most
commonly found in bacteria as small, circular, double-stranded DNA
molecules; however, plasmids are sometimes present in archaea and
eukaryotic organisms. In nature, plasmids often carry genes that may benefit
the survival of the organism, for example antibiotic resistance. While the
chromosomes are big and contain all the essential information for living,
plasmids usually are very small and contain only additional information.
Artificial plasmids are widely used as vectors in molecular cloning, serving to
drive the replication of recombinant DNA sequences within host organism.

Properties

and

characteristics
There are two types of plasmid integration into a host bacteria: Non-integrating plasmids
replicate as with the top instance, whereas episomes, the lower example, can integrate into the
host chromosome.
The term plasmid was first introduced by the American molecular biologist Joshua Lederberg in
1952, originally to describe any bacterial genetic material that exists in an extrachromosomal
state for at least part of its replication cycle. Later, to distinguish it from viruses, the definition
was narrowed to genetic elements that exist exclusively or predominantly outside of the
chromosome and can replicate autonomously.
In order for the plasmids to replicate independently within a cell, they must possess a stretch of
DNA that can act as an origin of replication. The self-replicating unit, in this case the plasmid, is
called a replicon. A typical bacterial replicon may consist of a number of elements, such as the
gene for plasmid-specific replication initiation protein (Rep), repeating units called iterons,

DnaA boxes, and an adjacent AT-rich region. Smaller plasmids make use of the host replicative
enzymes to make copies of themselves, while larger plasmids may carry genes specific for the
replication of those plasmids. A few types of plasmids are also capable of inserting into the host
chromosome, and these integrative plasmids are sometimes referred to as episomes in
prokaryotes.

Plasmids may be classified in a number of ways. Plasmids can be broadly classified into
conjugative plasmids and non-conjugative plasmids. Conjugative plasmids contain a set of
transfer or tra genes which promote sexual conjugation between different cells. [7] In the complex
process of conjugation, plasmid may be transferred from one bacterium to another via sex pili
encoded by some of the tra genes (see figure).[9] Non-conjugative plasmids are incapable of
initiating conjugation, hence they can be transferred only with the assistance of conjugative
plasmids. An intermediate class of plasmids are mobilizable, and carry only a subset of the genes
required for transfer. They can parasitize a conjugative plasmid, transferring at high frequency
only in its presence.
Plasmids can also be classified into incompatibility group. A microbe can harbour different types
of plasmids, however, different plasmids can only exist in a single bacterial cell if they are
compatible. If two plasmids are not compatible, one or the other will be rapidly lost from the
cell. Different plasmids may therefore be assigned to different incompatibility group depending
on whether they can coexist together. Incompatible plasmids normally share the same replication
or partition mechanisms.

Another way to classify plasmids is by function. There are five main classes:

Fertility F-plasmids, which contain tra genes. They are capable of conjugation and result
in the expression of sex pilli.

Resistance (R) plasmids, which contain genes that provide resistance against antibiotics
or poisons. Historically known as R-factors, before the nature of plasmids was
understood.

Col plasmids, which contain genes that code for bacteriocins, proteins that can kill other
bacteria.

Degradative plasmids, which enable the digestion of unusual substances, e.g. toluene and
salicylic acid.

Virulence plasmids, which turn the bacterium into a pathogen.

Plasmids can belong to more than one of these functional groups.

Vectors
Further information: Vector (molecular biology)
Artificially constructed plasmids may be used as vectors in genetic engineering. These plasmids
serve as important tools in genetics and biotechnology labs, where they are commonly used to
clone and amplify (make many copies of) or express particular genes. A wide variety of plasmids
are commercially available for such uses. The gene to be replicated is normally inserted into a
plasmid that typically contains a number of features for their use. These include a gene that
confers resistance to particular antibiotics (ampicillin is most frequently used for bacterial
strains), an origin of replication to allow the bacterial cells to replicate the plasmid DNA, and a
suitable site for cloning. A schematic representation of the pBR322 plasmid, one of the first
plasmids to be used widely as a cloning vector. Shown on the plasmid diagram are the genes
encoded (amp and tet for ampicillin and tetracycline resistance respectively), its origin of
replication (ori), and various restriction sites (indicated in blue).
Cloning
Plasmids are the most-commonly used bacterial cloning vectors. These cloning vectors contains
a site that allows DNA fragments to be inserted, for example a multiple cloning site or polylinker
which has several commonly-used restriction sites to which DNA fragments may be ligated.
After the gene of interest is inserted, the plasmids are introduced into bacteria by a process called
transformation. These plasmids contain a selectable marker, usually an antibiotic resistance gene,
which confer on the bacteria an ability to survive and proliferate in a selective growth medium
containing the particular antibiotics. The cells after transformation are exposed to the selective
media, and only cells containing the plasmid may survive. In this way, the antibiotics act as a
filter to select only the bacteria containing the plasmid DNA. The vector may also contain other

marker genes or reporter genes to facilitate selection of plasmid with cloned insert. Bacteria
containing the plasmid can then be grown in large amounts, harvested, and the plasmid of
interest may then be isolated using various methods of plasmid preparation.
A plasmid cloning vector is typically used to clone DNA fragments of up to 15 kbp. To clone
longer lengths of DNA, lambda phage with lysogeny genes deleted, cosmids, bacterial artificial
chromosomes, or yeast artificial chromosomes are used.