73-616: See text Densovirinae is a subfamily of single-stranded DNA viruses in the family Parvoviridae . The subfamily has 11 recognized genera and 21 species. Densoviruses are known to infect members of insect orders Blattodea , Diptera , Hemiptera , Hymenoptera , Lepidoptera , and Orthoptera , while some viruses infect and multiply in crustaceans such as shrimp or crayfish , or sea stars from phylum Echinodermata . Densoviruses are small (18–26 nanometers in diameter) and non enveloped. Virions are icosahedral in shape with triangulation number (T) = 1. There are 60 copies of
146-410: A jelly roll fold folded structure in which the jelly roll (JR) fold is perpendicular to the surface of the viral capsid. Many members also share a variety of other characteristics, including a minor capsid protein that has a single JR fold, an ATPase that packages the genome during capsid assembly, and a common DNA polymerase . Two kingdoms are recognized: Helvetiavirae , whose members have MCPs with
219-694: A cell through multiple generations, but at some stage, they will exist as an independent plasmid molecule. In the context of eukaryotes, the term episome is used to mean a non-integrated extrachromosomal closed circular DNA molecule that may be replicated in the nucleus. Viruses are the most common examples of this, such as herpesviruses , adenoviruses , and polyomaviruses , but some are plasmids. Other examples include aberrant chromosomal fragments, such as double minute chromosomes , that can arise during artificial gene amplifications or in pathologic processes (e.g., cancer cell transformation). Episomes in eukaryotes behave similarly to plasmids in prokaryotes in that
292-418: 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
365-414: A consequence of replication of the viral genome. Eukaryotic ssDNA viruses are replicated in the nucleus. Most ssDNA viruses contain circular genomes that are replicated via rolling circle replication (RCR). ssDNA RCR is initiated by an endonuclease that bonds to and cleaves the positive strand, allowing a DNA polymerase to use the negative strand as a template for replication. Replication progresses in
438-1279: 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. Finally, the overall productivity could be enhanced. In contrast, plasmids used in biotechnology, such as pUC18, pBR322 and derived vectors, hardly ever contain toxin-antitoxin addiction systems, and therefore need to be kept under antibiotic pressure to avoid plasmid loss. Yeasts naturally harbour various plasmids. Notable among them are 2 μm plasmids—small circular plasmids often used for genetic engineering of yeast—and linear pGKL plasmids from Kluyveromyces lactis , that are responsible for killer phenotypes . Other types of plasmids are often related to yeast cloning vectors that include: The mitochondria of many higher plants contain self-replicating , extra-chromosomal linear or circular DNA molecules which have been considered to be plasmids. These can range from 0.7 kb to 20 kb in size. The plasmids have been generally classified into two categories- circular and linear. Circular plasmids have been isolated and found in many different plants, with those in Vicia faba and Chenopodium album being
511-467: A copy to both daughter cells. These systems, which include the parABS system and parMRC system , are often referred to as the partition system or partition function of a plasmid. Plasmids of linear form are unknown among phytopathogens with one exception, Rhodococcus fascians . Plasmids may be classified in a number of ways. Plasmids can be broadly classified into conjugative plasmids and non-conjugative plasmids. Conjugative plasmids contain
584-416: A dsDNA genome. Lastly, some dsDNA viruses are replicated as part of a process called replicative transposition whereby a viral genome in a host cell's DNA is replicated to another part of a host genome. dsDNA viruses can be subdivided between those that replicate in the cell nucleus , and as such are relatively dependent on host cell machinery for transcription and replication, and those that replicate in
657-461: A few exceptions and peculiarities exist. The family Anelloviridae is the only ssDNA family whose members have negative sense genomes, which are circular. Parvoviruses, as previously mentioned, may package either the positive or negative sense strand into virions. Lastly, bidnaviruses package both the positive and negative linear strands. The International Committee on Taxonomy of Viruses (ICTV) oversees virus taxonomy and organizes viruses at
730-655: 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 plasmids with cloned inserts. 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. Another major use of plasmids
803-420: A given size) run at different speeds in a gel during electrophoresis . The conformations are listed below in order of electrophoretic mobility (speed for a given applied voltage) from slowest to fastest: 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 continuously increasing yet different rates. Thus,
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#1732787886231876-454: A large number of commercially available cloning and expression vectors. Insertion sequences can also severely impact plasmid function and yield, by leading to deletions and rearrangements, activation, down-regulation or inactivation of neighboring gene expression . Therefore, the reduction or complete elimination of extraneous noncoding backbone sequences would pointedly reduce the propensity for such events to take place, and consequently,
949-527: A loop around the genome by means of extending the 3'-end of the positive strand, displacing the prior positive strand, and the endonuclease cleaves the positive strand again to create a standalone genome that is ligated into a circular loop. The new ssDNA may be packaged into virions or replicated by a DNA polymerase to form a double-stranded form for transcription or continuation of the replication cycle. Parvoviruses contain linear ssDNA genomes that are replicated via rolling hairpin replication (RHR), which
1022-534: A major capsid protein (MCP) that has the HK97 fold. Viruses in the realm also share a number of other characteristics involving the capsid and capsid assembly, including an icosahedral capsid shape and a terminase enzyme that packages viral DNA into the capsid during assembly. Two groups of viruses are included in the realm: tailed bacteriophages, which infect prokaryotes and are assigned to the order Caudovirales , and herpesviruses, which infect animals and are assigned to
1095-646: A particular nutrient, including the ability to degrade recalcitrant or toxic organic compounds. Plasmids can also provide bacteria with the ability to fix nitrogen . Some plasmids, called cryptic plasmids , play a crucial role in horizontal genes transfer , since they carry antibiotic-resistance genes. Thus they are important factors in spreading resistance, which can result in antibiotic treatment failures. Naturally occurring plasmids vary greatly in their physical properties. Their size can range from very small mini-plasmids of less than 1-kilobase pairs (kbp) to very large megaplasmids of several megabase pairs (Mbp). At
1168-500: A plasmid containing the insulin gene leads to a large production of insulin. Plasmids may also be used for gene transfer as a potential treatment in gene therapy so that it may express the protein that is lacking in the cells. Some forms of gene therapy require the insertion of therapeutic genes at pre-selected chromosomal target sites within the human genome . Plasmid vectors are one of many approaches that could be used for this purpose. Zinc finger nucleases (ZFNs) offer
1241-411: A process called transformation . These plasmids contain a selectable marker , usually an antibiotic resistance gene, which confers 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
1314-596: A realm: ssDNA viruses are classified into one realm and include several families that are unassigned to a realm: 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 ; however, plasmids are sometimes present in archaea and eukaryotic organisms . Plasmids often carry useful genes, such as antibiotic resistance and virulence . While chromosomes are large and contain all
1387-565: A relation to a group of proteins that contain SJR folds, including the Cupin superfamily and nucleoplasmins . Marine viruses in Varidnaviria are ubiquitous worldwide and, like tailed bacteriophages, play an important role in marine ecology. Most identified eukaryotic DNA viruses belong to the realm. Notable disease-causing viruses in Varidnaviria include adenoviruses , poxviruses , and
1460-418: A replication origin site and move in opposite directions of each other, is widely used. A rolling circle mechanism that produces linear strands while progressing in a loop around the circular genome is also common. Some dsDNA viruses use a strand displacement method whereby one strand is synthesized from a template strand, and a complementary strand is then synthesized from the prior synthesized strand, forming
1533-519: A series of spontaneous events that culminate in an unforeseen rearrangement, loss, or gain of genetic material. Such events are frequently triggered by the transposition of mobile elements or by the presence of unstable elements such as non-canonical (non-B) structures. Accessory regions pertaining to the bacterial backbone may engage in a wide range of structural instability phenomena. Well-known catalysts of genetic instability include direct, inverted, and tandem repeats, which are known to be conspicuous in
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#17327878862311606-464: A set of transfer genes which promote sexual conjugation between different cells. In the complex process of conjugation , plasmids may be transferred from one bacterium to another via sex pili encoded by some of the transfer genes (see figure). 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
1679-439: A single cell is called the plasmid copy number , and is determined by how the replication initiation is regulated and the size of the molecule. Larger plasmids tend to have lower copy numbers. Low-copy-number 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 that attempt to actively distribute
1752-460: A single vertical JR fold, and Bamfordvirae , whose members have MCPs with two vertical JR folds. Varidnaviria is either monophyletic or polyphyletic and may predate the LUCA. The kingdom Bamfordvirae is likely derived from the other kingdom Helvetiavirae via fusion of two MCPs to have an MCP with two jelly roll folds instead of one. The single jelly roll (SJR) fold MCPs of Helvetiavirae show
1825-401: A single-stranded DNA genome. ssDNA viruses have the same manner of transcription as dsDNA viruses. However, because the genome is single-stranded, it is first made into a double-stranded form by a DNA polymerase upon entering a host cell. mRNA is then synthesized from the double-stranded form. The double-stranded form of ssDNA viruses may be produced either directly after entry into a cell or as
1898-441: 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, ranging from the plasmid extraction kits ( miniprep to the maxiprep or bulkprep) , alkaline lysis , enzymatic lysis, and mechanical lysis . The former can be used to quickly find out whether
1971-425: 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 groups. A microbe can harbour different types of plasmids, but 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
2044-525: A way to cause a site-specific double-strand break to the DNA genome and cause homologous recombination . Plasmids encoding ZFN could help deliver a therapeutic gene to a specific site so that cell damage , cancer-causing mutations, or an immune response is avoided. Plasmids were historically used to genetically engineer the embryonic stem cells of rats to create rat genetic disease models. The limited efficiency of plasmid-based techniques precluded their use in
2117-433: Is chiefly based on transcription of mRNA, viruses in each Baltimore group also typically share their manner of replication. Viruses in a Baltimore group do not necessarily share genetic relation or morphology. The first Baltimore group of DNA viruses are those that have a double-stranded DNA genome. All dsDNA viruses have their mRNA synthesized in a three-step process. First, a transcription preinitiation complex binds to
2190-435: Is demonstrated by using a suitable host that can mass produce specialized metabolites, some of these molecules are able to control microbial population. Plasmids can contain and express several BGCs with a few plasmids known to be exclusive for transferring BGCs. BGC's can also be transfers to the host organism's chromosome, utilizing a plasmid vector, which allows for studies in gene knockout experiments. By using plasmids for
2263-438: 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 (referred to as a multiple cloning site ). DNA structural instability can be defined as
Densovirinae - Misplaced Pages Continue
2336-436: Is not fully understood. The relation between caudoviruses and herpesviruses is also uncertain: they may share a common ancestor or herpesviruses may be a divergent clade from the realm Caudovirales . A common trait among duplodnaviruses is that they cause latent infections without replication while still being able to replicate in the future. Tailed bacteriophages are ubiquitous worldwide, important in marine ecology, and
2409-475: Is one mechanism of horizontal gene transfer , and plasmids are considered part of the mobilome . Unlike viruses, which encase their genetic material in a protective protein coat called a capsid , plasmids are "naked" DNA and do not encode genes necessary to encase the genetic material for transfer to a new host; however, some classes of plasmids encode the conjugative "sex" pilus necessary for their own transfer. Plasmids vary in size from 1 to over 400 k bp , and
2482-552: Is similar to RCR. Parvovirus genomes have hairpin loops at each end of the genome that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the genome, producing numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the viral endonuclease. For parvoviruses, either the positive or negative sense strand may be packaged into capsids, varying from virus to virus. Nearly all ssDNA viruses have positive sense genomes, but
2555-609: Is supported by bioinformatics software . These programs record the DNA sequence of plasmid vectors, help to predict cut sites of restriction enzymes , and to plan manipulations. Examples of software packages that handle plasmid maps are ApE, Clone Manager , GeneConstructionKit, Geneious, Genome Compiler , LabGenius, Lasergene, MacVector , pDraw32, Serial Cloner, UGENE , VectorFriends, Vector NTI , and WebDSV. These pieces of software help conduct entire experiments in silico before doing wet experiments. Many plasmids have been created over
2628-412: Is to make large amounts of proteins. In this case, researchers grow bacteria containing a plasmid harboring the gene of interest. Just as the bacterium 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 the protein, for example, utilizing the rapid reproduction of E.coli with
2701-489: The African swine fever virus . Poxviruses have been highly prominent in the history of modern medicine, especially Variola virus , which caused smallpox . Many varidnaviruses can become endogenized in their host's genome; a peculiar example are virophages , which after infecting a host, can protect the host against giant viruses . dsDNA viruses are classified into three realms and include many taxa that are unassigned to
2774-441: The cytoplasm , in which case they have evolved or acquired their own means of executing transcription and replication. dsDNA viruses are also commonly divided between tailed dsDNA viruses, referring to members of the realm Duplodnaviria , usually the tailed bacteriophages of the order Caudovirales , and tailless or non-tailed dsDNA viruses of the realm Varidnaviria . The second Baltimore group of DNA viruses are those that have
2847-476: The hok/sok (host killing/suppressor of killing) system of plasmid R1 in Escherichia coli . This variant produces both a long-lived poison and a short-lived antidote . Several types of plasmid addiction systems (toxin/ antitoxin, metabolism-based, ORT systems) were described in the literature and used in biotechnical (fermentation) or biomedical (vaccine therapy) applications. Daughter cells that retain
2920-498: The 3' open reading frame encodes two or three capsid proteins (VP1, VP2, VP3). Both the 5' and 3' termini have hairpin loops. If a third open reading frame is present (depends on the genus) it encodes a second non structural protein. The genome is ambisense, encoding proteins on both the positive sense and negative sense directions. Transcriptional regulation and post-transcriptional modification are used to produce different nonstructural proteins and structural proteins. Virions enter
2993-416: 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 to release the DNA fragments. Because of its tight conformation, supercoiled DNA migrates faster through a gel than linear or open-circular DNA. The use of plasmids as a technique in molecular biology
Densovirinae - Misplaced Pages Continue
3066-624: The DNA is stably maintained and replicated with the host cell. Cytoplasmic viral episomes (as in poxvirus infections) can also occur. Some episomes, such as herpesviruses, replicate in a rolling circle mechanism, similar to bacteriophages (bacterial phage viruses). Others replicate through a bidirectional replication mechanism ( Theta type plasmids). In either case, episomes remain physically separate from host cell chromosomes. Several cancer viruses, including Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus , are maintained as latent, chromosomally distinct episomes in cancer cells, where
3139-553: The DNA upstream of the site where transcription begins, allowing for the recruitment of a host RNA polymerase . Second, once the RNA polymerase is recruited, it uses the negative strand as a template for synthesizing mRNA strands. Third, the RNA polymerase terminates transcription upon reaching a specific signal, such as a polyadenylation site. dsDNA viruses make use of several mechanisms to replicate their genome. Bidirectional replication, in which two replication forks are established at
3212-611: The basal level at the rank of realm. Virus realms correspond to the rank of domain used for cellular life but differ in that viruses within a realm do not necessarily share common ancestry , nor do the realms share common ancestry with each other. As such, each virus realm represents at least one instance of viruses coming into existence. Within each realm, viruses are grouped together based on shared characteristics that are highly conserved over time. Three DNA virus realms are recognized: Duplodnaviria , Monodnaviria , and Varidnaviria . Duplodnaviria contains dsDNA viruses that encode
3285-412: The boundary between a chromosome and a plasmid, found in about 10% of bacterial species sequenced by 2009. These elements carry core genes and have codon usage similar to the chromosome, yet use a plasmid-type replication mechanism such as the low copy number RepABC. As a result, they have been variously classified as minichromosomes or megaplasmids in the past. In Vibrio , the bacterium synchronizes
3358-973: The cell. Different plasmids may therefore be assigned to different incompatibility groups depending on whether they can coexist together. Incompatible plasmids (belonging to the same incompatibility group) normally share the same replication or partition mechanisms and can thus not be kept together in a single cell. Another way to classify plasmids is by function. There are five main classes: Plasmids can belong to more than one of these functional groups. Although most plasmids are double-stranded DNA molecules, some consist of single-stranded DNA , or predominantly double-stranded RNA . RNA plasmids are non-infectious extrachromosomal linear RNA replicons, both encapsidated and unencapsidated, which have been found in fungi and various plants, from algae to land plants. In many cases, however, it may be difficult or impossible to clearly distinguish RNA plasmids from RNA viruses and other infectious RNAs. Chromids are elements that exist at
3431-562: The circular plasmids share a common ancestor, some genes in the mitochondrial plasmid have counterparts in the nuclear DNA suggesting inter-compartment exchange. Meanwhile, the linear plasmids share structural similarities such as invertrons with viral DNA and fungal plasmids, like fungal plasmids they also have low GC content, these observations have led to some hypothesizing that these linear plasmids have viral origins, or have ended up in plant mitochondria through horizontal gene transfer from pathogenic fungi. Plasmids are often used to purify
3504-416: The coat protein in the virion. Each copy has a shape described as a "quadrilateral 'kite-shaped' wedge", and the appearance of the surface is rough with many small projections. Virions do not appear to contain lipids . Genomes are non-segmented, about 4–6 kilobases in length and usually contain two or three open reading frames . The 5' open reading frame encodes two nonstructural proteins (NS-1 and NS-2) and
3577-489: The creation of more accurate human cell models. However, developments in adeno-associated virus recombination techniques, and zinc finger nucleases , have enabled the creation of a new generation of isogenic human disease models . Plasmids assist in transporting biogenetic gene clusters - a set of gene that contain all the necessary enzymes that lead to the production of special metabolites (formally known as secondary metabolite) . A benefit of using plasmids to transfer BGC
3650-456: The essential genetic information for living under normal conditions, plasmids are usually very small and contain additional genes for special circumstances. Artificial plasmids are widely used as vectors in molecular cloning , serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation . Synthetic plasmids are available for procurement over
3723-438: The host cell is achieved by attachment to host receptors, which may be mediated by clathrin-mediated endocytosis or clathrin -independent dynamin -dependent endocytosis . The NS-1 protein has a superfamily 3 DNA helicase and an HuH endonuclease motif. These motifs are common in small DNA viruses. The proteins that contain these motifs bind to the viral origins of replication and unwind and nick these origins, allowing access by
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#17327878862313796-416: The host cells, for example: enabling the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. Some of these genes encode traits for antibiotic resistance or resistance to heavy metal, while others may produce virulence factors that enable a bacterium to colonize a host and overcome its defences or have specific metabolic functions that allow the bacterium to utilize
3869-410: 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 can also insert into the host chromosome, and these integrative plasmids are sometimes referred to as episomes in prokaryotes . Plasmids almost always carry at least one gene. Many of the genes carried by a plasmid are beneficial for
3942-407: The host's proteins to the viral genome for replication and transcription . The genome is replicated by a unique rolling hairpin mechanism. DNA-templated transcription, with some alternative splicing mechanism is the manner of transcription. Eleven genera are currently recognized, containing a combined 21 species: Ambidensovirus was previously recognized as a genus, but in 2019 it was split into
4015-527: The internet by various vendors using submitted sequences typically designed with software, if a design does not work the vendor may make additional edits from the submission. Plasmids are considered replicons , units of DNA capable of replicating autonomously within a suitable host. However, plasmids, like viruses , are not generally classified as life . Plasmids are transmitted from one bacterium to another (even of another species) mostly through conjugation . This host-to-host transfer of genetic material
4088-530: The most studied and whose mechanism of replication is known. The circular plasmids can replicate using the θ model of replication (as in Vicia faba ) and through rolling circle replication (as in C.album ). Linear plasmids have been identified in some plant species such as Beta vulgaris , Brassica napus , Zea mays , etc. but are rarer than their circular counterparts. The function and origin of these plasmids remains largely unknown. It has been suggested that
4161-538: The notion of plasmid was refined over time to refer to genetic elements that reproduce autonomously. Later in 1968, it was decided that the term plasmid should be adopted as the term for extrachromosomal genetic element, and to distinguish it from viruses, the definition was narrowed to genetic elements that exist exclusively or predominantly outside of the chromosome, can replicate autonomously, and contribute to transferring mobile elements between unrelated bacteria. In order for plasmids to replicate independently within
4234-496: The number of identical plasmids in a single cell can range from one up to thousands. The term plasmid was coined in 1952 by the American molecular biologist Joshua Lederberg to refer to "any extrachromosomal hereditary determinant." The term's early usage included any bacterial genetic material that exists extrachromosomally for at least part of its replication cycle, but because that description includes bacterial viruses,
4307-519: The order Herpesvirales . Duplodnaviria is a very ancient realm, perhaps predating the last universal common ancestor (LUCA) of cellular life. Its origins not known, nor whether it is monophyletic or polyphyletic. A characteristic feature is the HK97-fold found in the MCP of all members, which is found outside the realm only in encapsulins , a type of nanocompartment found in bacteria: this relation
4380-550: The origins of Duplodnaviria and Varidnaviria are less clear. Prominent disease-causing DNA viruses include herpesviruses , papillomaviruses , and poxviruses . The Baltimore classification system is used to group viruses together based on their manner of messenger RNA (mRNA) synthesis and is often used alongside standard virus taxonomy, which is based on evolutionary history. DNA viruses constitute two Baltimore groups: Group I: double-stranded DNA viruses, and Group II: single-stranded DNA viruses. While Baltimore classification
4453-429: The overall recombinogenic potential of the plasmid. Plasmids are the most-commonly used bacterial cloning vectors. These cloning vectors contain 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
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#17327878862314526-675: 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. In essence, this is a scaled-up miniprep followed by additional purification. This results in relatively large amounts (several hundred micrograms) of very pure plasmid DNA. Many commercial kits have been created to perform plasmid extraction at various scales, purity, and levels of automation. Plasmid DNA may appear in one of five conformations, which (for
4599-496: The preferred term for autonomously replicating extrachromosomal DNA. At a 1968 symposium in London some participants suggested that the term episome be abandoned, although others continued to use the term with a shift in meaning. Today, some authors use episome in the context of prokaryotes to refer to a plasmid that is capable of integrating into the chromosome. The integrative plasmids may be replicated and stably maintained in
4672-734: The realm Monodnaviria , which also includes some dsDNA viruses. Additionally, many DNA viruses are unassigned to higher taxa. Reverse transcribing viruses, which have a DNA genome that is replicated through an RNA intermediate by a reverse transcriptase , are classified into the kingdom Pararnavirae in the realm Riboviria . DNA viruses are ubiquitous worldwide, especially in marine environments where they form an important part of marine ecosystems, and infect both prokaryotes and eukaryotes . They appear to have multiple origins, as viruses in Monodnaviria appear to have emerged from archaeal and bacterial plasmids on multiple occasions, though
4745-447: The realm are called CRESS-DNA viruses and have circular ssDNA genomes. ssDNA viruses with linear genomes are descended from them, and in turn some dsDNA viruses with circular genomes are descended from linear ssDNA viruses. Viruses in Monodnaviria appear to have emerged on multiple occasions from archaeal and bacterial plasmids , a type of extra-chromosomal DNA molecule that self-replicates inside its host. The kingdom Shotokuvirae in
4818-673: The realm likely emerged from recombination events that merged the DNA of these plasmids and complementary DNA encoding the capsid proteins of RNA viruses. CRESS-DNA viruses include three kingdoms that infect prokaryotes: Loebvirae , Sangervirae , and Trapavirae . The kingdom Shotokuvirae contains eukaryotic CRESS-DNA viruses and the atypical members of Monodnaviria . Eukaryotic monodnaviruses are associated with many diseases, and they include papillomaviruses and polyomaviruses , which cause many cancers, and geminiviruses , which infect many economically important crops. Varidnaviria contains DNA viruses that encode MCPs that have
4891-443: The replication of the chromosome and chromid by a conserved genome size ratio. 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
4964-493: 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 20 kb or so) migrate at a certain fixed rate regardless of length. This is because the molecules 'respirate', 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
5037-602: The six genera prefixed with Aqu -, Blatt -, Hemi -, Pefu -, Proto -, and Scindo -. DNA virus A DNA virus is a virus that has a genome made of deoxyribonucleic acid (DNA) that is replicated by a DNA polymerase . They can be divided between those that have two strands of DNA in their genome, called double-stranded DNA (dsDNA) viruses, and those that have one strand of DNA in their genome, called single-stranded DNA (ssDNA) viruses. dsDNA viruses primarily belong to two realms : Duplodnaviria and Varidnaviria , and ssDNA viruses are almost exclusively assigned to
5110-448: The subject of much research. Herpesviruses are known to cause a variety of epithelial diseases, including herpes simplex , chickenpox and shingles , and Kaposi's sarcoma . Monodnaviria contains ssDNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication and all other viruses descended from such viruses. The prototypical members of
5183-402: The upper end, little differs between a megaplasmid and a minichromosome . Plasmids are generally circular, but examples of linear plasmids are also known. These linear plasmids require specialized mechanisms to replicate their ends. Plasmids may be present in an individual cell in varying number, ranging from one to several hundreds. The normal number of copies of plasmid that may be found in
5256-463: The uptake of BGCs, microorganisms can gain an advantage as production is not limited to antibiotic resistant biosynthesis genes but the production of toxin s/antitoxins. The term episome was introduced by François Jacob and Élie Wollman in 1958 to refer to extra-chromosomal genetic material that may replicate autonomously or become integrated into the chromosome. Since the term was introduced, however, its use has changed, as plasmid has become
5329-478: The viruses express oncogenes that promote cancer cell proliferation. In cancers, these episomes passively replicate together with host chromosomes when the cell divides. When these viral episomes initiate lytic replication to generate multiple virus particles, they generally activate cellular innate immunity defense mechanisms that kill the host cell. Some plasmids or microbial hosts include an addiction system or postsegregational killing system (PSK), such as
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