User:Jfitz1974/sandbox

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Extrachromosomal DNA Article Work Area
Extrachromosomal DNA is any DNA that is found outside of the nucleus of a cell. It is also referred to as extranuclear DNA or cytoplasmic DNA. Most DNA in an individual genome is found in chromosomes but DNA found outside of the chromosomes also serve important biological functions.

In prokaryotes, nonviral extrachromosomal DNA is primarily found in plasmids whereas in eukaryotes extrachromosomal DNA is primarily found in organelles. Mitochondrial DNA is a main source of extrachromosomal DNA. Extrachromosomal DNA is often used in research of replication because it is easy to identify and isolate.

Extrachromosomal DNA in Viruses
Viral DNA is an example of extrachromosomal DNA. Understanding viral genomes is very important for understanding the evolution and mutation of the virus. Viruses are made up of a nucleic acid core surrounded by a protein coat. They are parasitic and require a host to replicate. Viruses utilize the host cells resources to replicate. Some viruses, such as HIV and oncogenetic viruses, incorporate their own DNA into the genome of the host cell. Viral genomes can be made up of ssDNA, dsDNA, ssRNA, or dsRNA. Viruses can also be found in both linear and circular form

Influenza is a well-known virus. There are three main types of Influenze differentiated by proteins, Influenza A, B, and C. The viral genomes of A and B consist of ssRNA. The high mutation rates, caused by high error rates in ssRNA replication, is one reason these viruses have high evolutionary success.

Extrachromosomal DNA in Prokaryotes
Extrachromosomal DNA exists in prokaryotes as circular or linear plasmids. Bacterial plasmids are typically short sequences, consisting of 1 kb to a few hundred kb segments, and contain an origin of replication which allows the plasmid to replicate independently of the bacterial chromosome. The total number of a particular plasmid within a cell is referred to as the copy number and can be as few as two copies per cell up to several hundred copies per cell. Circular bacterial plasmids are classified according to the special functions that the genes encoded on the plasmid provide. Fertility  plasmids allow for conjugation to occur, resistance plasmids contain genes that convey resistance to a variety of different antibiotics such as ampicillin and tetracycline, virulence plasmids contain the genetic elements necessary for the bacterium to become pathogenic, and degradative plasmids harbor the genes that allow the bacterium to degrade a variety of substances such as aromatic compounds and xenobiotics. Bacterial plasmids can also function in pigment production, nitrogen fixation and the resistance to heavy metals in those bacteria that possess them.

Naturally occurring spherical plasmids can be modified to contain multiple resistance genes and several unique restriction sites, making them valuable tools as cloning vectors in biotechnology applications.

Linear bacterial plasmids were first identified in Streptomyces bacteria, but have since been identified in a number of other bacterial species. Antibiotic resistance genes have been found on linear plasmids as well as on circular plasmids.

Extrachromosomal Circular DNA
Extrachromosomal circular DNA (eccDNA) is present in all eukaryotic cells, is usually derived from genomic DNA, and consists of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 base pairs to more than 20,000 base pairs. In plants, eccDNA contains repeated sequences similar to those that are found in the centromeric regions of the chromosomes and in repetitive satellite DNA. In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA. Certain organisms, such as yeast, rely on DNA replication to produce eccDNA whereas eccDNA formation can occur in other organisms, such as mammals, independently of the replication process. The function of eccDNA has not been widely studied, but it has been proposede that the production of eccDNA elements from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes.

Extrachromosomal DNA in Medicine and Disease
Sometimes called EEs, extrachromosomal elements, has been associated with genomic instability in eukaryotes. Small polydispersed DNAs (spcDNAs) are commonly found in conjunction with genome instability. SpcDNAs are derived from repetitive sequences sucah as satellite DNA, retrovirus-like DNA elements, and transposable elements in the genome. They are thought to be the products of gene rearrangements. Double Minute Chromosomes (DMs) are also extrachromosomal elements that are associated with genome instability. DMs are commonly seen in cancer cells. DMs are thought to be produced through breakages in chromosomes or overreplication of DNA in an organism. Studies show that in cases of cancer and other genomic instability, higher levels of EEs can be observed.

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