Plasmid

Plasmids are (typically) circular double-stranded DNA molecules separate from the chromosomal DNA (Fig. 1) and capable of autonomous replication. They usually occur in bacteria, sometimes in eukaryotic organisms (e.g., the 2-micrometre-ring in Saccharomyces cerevisiae). Their size varies from 1 to over 400 kilobase pairs (kbp). There are anywhere from one copy, for large plasmids, to hundreds of copies of the same plasmid present in a single cell, or even to thousands of copies for certain artificial plasmids selected for high copy number (such as the pUC series of plasmids).

Antibiotic resistance

Plasmids often contain genes or gene cassettes that confer a selective advantage to the bacterium harboring them, e.g., the ability to make the bacterium antibiotic resistant. Every plasmid contains at least one DNA sequence that serves as an origin of replication or ori (a starting point for DNA replication), which enables the plasmid DNA to be duplicated independently from the chromosomal DNA (Figure 2). The plasmid depicted Figure 2 is circular, as are the chromosomes of most bacteria, but linear plasmids are also known, which superficially resemble the chromosomes of most eukaryotes.

Episomes

Episomes are plasmids that can integrate themselves into the chromosomal DNA of the host organism (Fig. 3). For this reason, they can stay intact for a long time, be duplicated with every cell division of the host, and become a basic part of its genetic makeup. This term is no longer commonly used for plasmids, since it is now clear that a region of homology with the chromosome such as a transposon makes a plasmid into an episome. In mammalian systems, the term episome refers to a circular DNA (such as a viral genome) that is maintained by noncovalent tethering to the host cell chromosome.

Vectors

Plasmids used in genetic engineering are called vectors. They are used to transfer genes from one organism to another and typically contain a genetic marker conferring a phenotype that can be selected for or against. Most also contain a polylinker or multiple cloning site (MCS), which is a short region containing several commonly used restriction sites allowing the easy insertion of DNA fragments at this location. See also 'Applications of plasmids', below.

Types of plasmid

One way of grouping plasmids is by their ability to transfer to other bacteria. Conjugative plasmids contain so-called tra-genes, which perform the complex process of conjugation, the sexual transfer of plasmids to another bacterium (Fig. 4). Non-conjugative plasmids are incapable of initiating conjugation, hence they can only be transferred with the assistance of conjugative plasmids, by 'accident'. An intermediate class of plasmids are mobilizable, and carry only a subset of the genes required for transfer. These plasmids can 'parasitise' another plasmid, transferring at high frequency in the presence of a conjugative plasmid.

be assigned into incompatibility groups, depending on their ability to coexist in a single cell. These incompatibility groupings are due to the regulation of vital plasmid functions.

An obvious way of classifying plasmids is by function. There are five main classes:

Fertility-(F)plasmids, which contain tra-genes. They are capable of conjugation.
Resistance-(R)plasmids, which contain genes that can build a 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 (determine the production of) colicines, proteins that can kill other bacteria.
Degrative plasmids, which enable the digestion of unusual substances, e.g., toluene or salicylic acid.
Virulence plasmids, which turn the bacterium into a pathogen.

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

Plasmids that exist only as one or a few copies in each bacterium are, upon cell division, in danger of being lost in one of the segregating bacteria. Such single-copy plasmids have systems which attempt to actively distribute a copy to both daughter cells.

Some plasmids include an addiction system or "postsegregational killing system (PSK)". These plasmids produce both a long-lived poison and a short-lived antidote. Daughter cells that retain a copy of the plasmid survive, while a daughter cell that fails to inherit the plasmid dies or suffers a reduced growth-rate because of the lingering poison from the parent cell. This is an example of plasmids as selfish DNA.

Applications of plasmids

Plasmids serve as important tools in genetics and biochemistry labs, where they are commonly used to multiply (make many copies of) or express particular genes. There are many plasmids that are commercially available for such uses. Initially, the gene to be replicated is inserted in a plasmid. These plasmids contain, in addition to the inserted gene, one or more genes capable of providing antibiotic resistance to the bacterium that harbors them. The plasmids are next inserted into bacteria by a process called transformation, which are then grown on specific antibiotic(s). Bacteria which took up one or more copies of the plasmid then express (make protein from) the gene that confers antibiotic resistance. This is typically a protein which can break down any antibiotics that would otherwise kill the cell. As a result, only the bacteria with antibiotic resistance can survive, the very same bacteria containing the genes to be replicated. The antibiotic(s) will, however, kill those bacteria that did not receive a plasmid, because they have no antibiotic resistance genes. In this way the antibiotic(s) acts as a filter selecting out only the modified bacteria. Now these bacteria can be grown in large amounts, harvested and lysed to isolate the plasmid of interest.

Another major use of plasmids is to make large amounts of proteins. In this case you grow the bacteria containing a plasmid harboring the gene of interest. Just as the bacteria produces proteins to confer its antibiotic resistance, it can also be induced to produce large amounts of proteins from the inserted gene. This is a cheap and easy way of mass-producing a gene or the protein it then codes for — for example, insulin or even antibiotics.

Plasmid DNA extraction

As alluded to above, plasmids are often used to purify a specific sequence, since they can easily be purified away from the rest of the genome. For their use as vectors, and for molecular cloning, plasmids often need to be isolated.

There are several methods to isolate plasmid DNA from bacteria, the archaetypes of which are the miniprep and the maxiprep. The former can be used to quickly find out whether the plasmid is correct in any of several bacterial clones. The yield is a small amount of impure plasmid DNA, which is sufficient for analysis by restriction digest and for some cloning techniques.

In the latter, much larger volumes of bacterial suspension are grown from which a maxi-prep can be performed. Essentially this is a scaled-up miniprep followed by additional purification. This results in relatively large amounts (several ug) of very pure plasmid DNA.

In recent times many commercial kits have been created to perform plasmid extraction at various scales, purity and levels of automation.

Conformations

When performing DNA electrophoresis, plasmid DNA may appear in the following five conformations, which (for a given size) run at different speeds in a gel during electrophoresis. These are listed below in order of electrophoretic mobility (speed for a given applied voltage) from slowest to fastest:

"Nicked Open-Circular" DNA has one strand cut.
"Linear" DNA has free ends, either because both strands have been cut, or because the DNA was linear in vivo. You can model this with an extension cord that is not tied to itself.
"Relaxed Circular" DNA is fully intact with both strands uncut, but has been enzymatically "relaxed" (supercoils removed). You can model this by letting an extension cord relax and then plugging it into itself.
"Supercoiled Denatured" DNA is like supercoiled DNA (see below), but has unpaired regions that make it slightly less compact; this can result from excessive alkalinity during plasmid preparation. You can model this by twisting a badly frayed extension cord and then plugging it into itself.
"Supercoiled" (or "Covalently Closed-Circular") DNA is fully intact with both strands uncut, and with a twist built in, resulting in a compact form. You can model this by twisting an extension cord in good condition and then plugging it into itself.

The rate of migration for small linear fragments is directly proportional to the voltage applied at low voltages. At higher voltages, larger fragments migrate at continually increasing yet different rates. Therefore the resolution of a gel decreases with increased voltage.

At a specified, low voltage, the migration rate of small linear DNA fragments is a function of their length. Large linear fragments (over 20kb or so) migrate at a certain fixed rate regardless of length. This is because the molecules 'reptate', with the bulk of the molecule following the leading end through the gel matrix. Restriction digests are frequently used to analyse purified plasmids. These enzymes specifically break the DNA at certain short sequences. The resulting linear fragments form 'bands' after gel electrophoresis. It is possible to purify certain fragments by cutting the bands out of the gel and dissolving the gel in the fragments.

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