It has been suggested that this article or section be merged with short tandem repeat. (Discuss)

Microsatellites, or Simple Sequence Repeats (SSRs), are polymorphic loci present in nuclear DNA and organellar DNA that consist of repeating units of 1-4 base pairs in length.^[1] They are typically neutral, co-dominant and are used as molecular markers which have wide-ranging applications in the field of genetics, including kinship and population studies. Microsatellites can also be used to study gene dosage (looking for duplications or deletions of a particular genetic region). Miniaturized satellites are recent artificial satellites of unusually low weights and small sizes. ... Image File history File links Merge-arrows. ... A short tandem repeat (STR) in DNA is a class of polymorphisms that occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. ... In biology, polymorphism can be defined as the occurrence in the same habitat of two or more forms of a trait in such frequencies that the rarer cannot be maintained by recurrent mutation alone. ... Nuclear DNA is DNA contained within a nucleus of eukaryotic organisms. ... Base pairs, of a DNA molecule. ... It has been suggested that dominant gene be merged into this article or section. ... Molecular markers are DNA sequences that can be identified by a simple assay, allowing the presence or absence of neighbouring stretches of the genome to be inferred. ... This article is about the general scientific term. ... Kinship is the most basic principle of organizing individuals into social groups, roles, and categories. ... Schematic of a region of a chromosome before and after a duplication event Gene duplication occurs when an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome leads to the duplication of a region of DNA containing a gene [1]. The significance of this process for... A genetic deletion is a genetic aberration in which part of a chromosome is missing. ...

Introduction

One common example of a microsatellite is a (CA)n repeat, where n is variable between alleles. These markers often present high levels of inter- and intra-specific polymorphism, particularly when tandem repeats number ten or greater.^[2] The repeated sequence is often simple, consisting of two, three or four nucleotides (di-, tri-, and tetranucleotide repeats respectively), and can be repeated 10 to 100 times. CA nucleotide repeats are very frequent in human and other genomes, and are present every few thousand base pairs. As there are often many alleles present at a microsatellite locus, genotypes within pedigrees are often fully informative, in that the progenitor of a particular allele can often be identified. In this way, microsatellites are ideal for determining paternity, population genetic studies and recombination mapping. It is also the only molecular marker to provide clues about which alleles are more closely related.^[3] An allele is any one of a number of alternative forms of the same gene occupying a given locus (position) on a chromosome. ... A nucleotide is an organic molecule consisting of a heterocyclic nucleobase (a purine or a pyrimidine), a pentose sugar (deoxyribose in DNA or ribose in RNA), and a phosphate or polyphosphate group. ... This article is about modern humans. ... In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... This article does not cite any references or sources. ... A pedigree chart is a chart which tells one all of the known phenotypes for an organism and its ancestors, most commonly humans, show dogs, and race horses. ... An ancestor is a parent or (recursively) the parent of an ancestor. ...

Microsatellites owe their variability to an increased rate of mutation compared to other neutral regions of DNA. These high rates of mutation can be explained most frequently by slipped strand mispairing (slippage) during DNA replication on a single DNA double helix. Mutation may also occur during recombination during meiosis.^[4] Some errors in slippage are rectified by proofreading mechanisms within the nucleus, but some mutations can escape repair. The size of the repeat unit, the number of repeats and the presence of variant repeats are all factors, as well as the frequency of transcription in the area of the DNA repeat. Interruption of microsatellites, perhaps due to mutation, can result in reduced polymorphism. However, this same mechanism can occasionally lead to incorrect amplification of microsatellites; if slippage occurs early on during PCR, microsatellites of incorrect lengths can be amplified. For linguistic mutation, see Apophony. ... Mutation process which occurs during DNA replication. ... DNA replication. ... The Double-Helix are an alien race in the Wing Commander science fiction series. ... Recombination usually refers to the biological process of genetic recombination and meiosis, a genetic event that occurs during the formation of sperm and egg cells. ... For the figure of speech, see meiosis (figure of speech). ... Proofreading means reading a proof copy of a text in order to detect and correct any errors. ... HeLa cells stained for DNA with the Blue Hoechst dye. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... Generally, amplification is a basic process sometimes seen in nature, and often used in processes which involve a signal which must be made stronger. ...

Amplification of microsatellites

Microsatellites can be amplified for identification using Polymerase Chain Reaction (PCR), using templates of flanking regions (primers). DNA is repeatedly denatured at a high temperature to separate the double strand, then cooled to allow annealing of primers and the extension of nucleotide sequences along opposite strands. This process results in production of enough DNA to be visible on agarose or acrylamide gels; only small amounts of DNA are needed for amplification as thermocycling in this manner creates an exponential increase in the replicated segment.^[5] With the abundance of PCR technology, primers that flank microsatellite loci are simple and quick to use, but the development of correctly functioning primers is often a tedious and costly process. “PCR” redirects here. ... Wikipedia does not yet have an article with this exact name. ... Look up primer in Wiktionary, the free dictionary. ... An agarose is a polysaccharide polymer material, generally extracted from seaweed. ... R-phrases , , , , , , , S-phrases , Flash point 138 °C Autoignition temperature 424 °C Except where noted otherwise, data are given for materials in their standard state (at 25 Â°C, 100 kPa) Infobox disclaimer and references The chemical compound acrylamide (acrylic amide) has the chemical formula C3H5NO. Its IUPAC name is 2...

Development of microsatellite primers

If searching for microsatellite markers in specific regions of a genome; for example within a particular exon of a gene, primers can be designed manually. This involves searching the genomic DNA sequence for microsatellite repeats, which can be done by eye or by using automated tools such as repeat masker. Once the potentially useful microsatellites are determined (removing non-useful ones such as those with random inserts within the repeat region), the flanking sequences can be used to design oligonucleotide primers which will amplify the specific microsatellite repeat in a PCR reaction. Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. ...

Random microsatellite primers can be developed by cloning random segments of DNA from the focal species. These are inserted into a plasmid or phage vector, which is in turn implanted into Escherichia coli bacteria. Colonies are then developed, and screened with fluorescently–labelled oligonucleotide sequences that will hybridise to a microsatellite repeat, if present on the DNA segment. If positive clones can be obtained from this procedure, the DNA is sequenced and PCR primers are chosen from sequences flanking such regions to determine a specific locus. This process involves significant trial and error on the part of researchers, as microsatellite repeat sequences must be predicted and primers that are randomly isolated may not display significant polymorphism.^[2][6] Microsatellite loci are widely distributed throughout the genome and can be isolated from semi-degraded DNA of older specimens, as all that is needed is a suitable substrate for amplification through PCR. For the cloning of human beings, see human cloning. ... Figure 1: Illustration of a bacterium with plasmids enclosed showing chromosomal DNA and plasmids. ... E. coli redirects here. ... Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. ... Short and long arms Chromosome. ...

ISSR-PCR

ISSR (for inter-simple sequence repeat) is a general term for a genome region between microsatellite loci. The complementary sequences to two neighboring microsatelites are used as PCR primers; the variable region between them gets amplified. The limited length of amplification cycles during PCR prevents excessive replication of overly long contiguous DNA sequences, so the result will be a mix of a variety of amplified DNA strands which are generally short but vary much in length.

Sequences amplified by ISSR-PCR can be used for DNA fingerprinting. Since an ISSR may be a conserved or nonconserved region, this technique is not useful for distinguishing individuals, but rather for phylogeography analyses or maybe delimiting species; sequence diversity is lower than in SSR-PCR, but still higher than in actual gene sequences. In addition, microsatellite sequencing and ISSR sequencing are mutually assisting, as one produces primers for the other. Phylogeography is the attempt to take into account the geographic distribution of species in establishing their phylogeny, and to understand the geographic patterns that may result from divergence, ultimately leading to speciation. ... For other uses, see Species (disambiguation). ...

Limitations of microsatellites

Microsatellites have proved to be versatile molecular markers, particularly for population analysis, but they are not without limitations. Microsatellites developed for particular species can often be applied to closely related species, but the percentage of loci that successfully amplify may decrease with increasing genetic distance.^[6] Point mutation in the primer annealing sites in such species may lead to the occurrence of ‘null alleles’, where microsatellites fail to amplify in PCR assays.^[6][7] Null alleles can be attributed to several phenomena. Sequence divergence in flanking regions can lead to poor primer annealing, especially at the 3’ section, where extension commences; preferential amplification of particular size alleles due to the competitive nature of PCR can lead to heterozygous individuals being scored for homozygosity (partial null). PCR failure may result when particular loci fail to amplify, whereas others amplify more efficiently and may appear homozygous on a gel assay, when they are in reality heterozygous in the genome. Null alleles complicate the interpretation of microsatellite allele frequencies and thus make estimates of relatedness faulty. Furthermore, stochastic effects of sampling that occurs during mating may change allele frequencies in a way that is very similar to the effect of null alleles; an excessive frequency of homozygotes causing deviations from Hardy-Weinberg equilibrium expectations. Since null alleles are a technical problem and sampling effects that occur during mating are a real biological property of a population, it is often very important to distinguish between them if excess homozygotes are observed. Genetic distance is a measure of the disimilarity of genetic material between different species or individuals of the same species. ... A null allele is an allele with the effect of either absence of the gene product at the molecular level, or the absence of function at the phenotypic level. ... In vector calculus, the divergence is an operator that measures a vector fields tendency to originate from or converge upon a given point. ... Heterozygote cells are diploid or polyploid and have different alleles at a locus (position) on homologous chromosomes. ... Homozygote cells are diploid or polyploid and have the same alleles at a locus (position) on homologous chromosomes. ... Stochastic, from the Greek stochos or goal, means of, relating to, or characterized by conjecture; conjectural; random. ...

When using microsatellites to compare species, homologous loci may be easily amplified in related species, but the number of loci that amplify successfully during PCR may decrease with increased genetic distance between the species in question. Mutation in microsatellite alleles is biased in the sense that larger alleles contain more bases, and are therefore likely to be mistranslated in DNA replication. Smaller alleles also tend to increase in size, whereas larger alleles tend to decrease in size, as they may be subject to an upper size limit; this constraint has been determined but possible values have not yet been specified. If there is a large size difference between individual alleles, then there may be increased instability during recombination at meiosis.^[6] In tumour cells, where controls on replication may be damaged, microsatellites may be gained or lost at an especially high frequency during each round of mitosis. Hence a tumour cell line might show a different genetic fingerprint from that of the host tissue. Tumor (American English) or tumour (British English) originally means swelling, and is sometimes still used with that meaning. ... Mitosis divides genetic information during cell division. ... Genetic fingerprinting or DNA testing is a technique to distinguish between individuals of the same species using only samples of their DNA. Its invention by Sir Alec Jeffreys at the University of Leicester was announced in 1985. ...

See also

• minisatellite
• genetic marker
• mobile element
• transposon
• short interspersed repetitive elements
• long interspersed repetitive element
• junk DNA
• variable number tandem repeats
• short tandem repeats
• Trinucleotide repeat disorders
• microsatellite instability

A minisatellite is a section of DNA that consists of a short series of bases 10-100bp, these occur at more than 1000 locations in the Genome. ... A genetic marker is a known DNA sequences (e. ... A DNA composite transposon. ... Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... Retrotransposons are genetic elements than can amplify themselves in a genome and are ubiquitous components of the DNA of many eukaryotic organisms. ... In molecular biology, junk DNA is a collective label for the portions of the DNA sequence of a chromosome or a genome for which no function has yet been identified. ... A variable number tandem repeats (VNTR) is a short nucleotide sequence ranging from 14 to 100 nucleotides long that is organized into clusters of tandem repeats, usually repeated in the range of between 4 and 40 times per occurrence. ... A short tandem repeat (STR) in DNA is a class of polymorphisms that occurs when a pattern of two or more nucleotides are repeated and the repeated sequences are directly adjacent to each other. ... Trinucleotide repeat disorders (also known as trinucleotide repeat expansion disorders, expansion disorders or codon reiteration disorders) are due to stretches of DNA in a gene that contain the same trinucleotide sequence repeated many times. ... Microsatellites are repeated sequences of DNA. Although the length of these microsatellites is highly variable from person to person, each individual has microsatellites of a set length. ...

External links

• About microsatellites:
  • Microsatellite DNA Methodology
• Search tools :
  • Tandem Repeats Finder
  • Mreps
  • STAR
  • TRED
  • TandemSWAN
  • Microsatellite repeats finder
  • JSTRING - Java Search for Tandem Repeats in genomes
  • Phobos - a tandem repeat search tool for perfect and imperfect repeats - the maximum pattern size depends only on computational power
  • sputnik - a simple microsatellite search program
  • MISA - MIcroSAtellite identification tool

References