Tandem repeats occur in
DNA when a pattern of one or more nucleotides is repeated and the repetitions are directly adjacent to each other. Several protein domains also form
tandem repeats within their amino acid primary structure, such as
armadillo repeats. However, in proteins, perfect tandem repeats are unlikely in most ''in vivo'' proteins, and most known repeats are in proteins which have been designed.
An example would be:
: ATTCG ATTCG ATTCG
in which the sequence ATTCG is repeated three times.
Terminology
When between 10 and 60 nucleotides are repeated, it is called a
minisatellite. Those with fewer are known as
microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
s or
short tandem repeats.
When exactly two nucleotides are repeated, it is called a ''dinucleotide repeat'' (for example: ACACACAC...). The
microsatellite instability in
hereditary nonpolyposis colon cancer most commonly affects such regions.
When three nucleotides are repeated, it is called a ''trinucleotide repeat'' (for example: CAGCAGCAGCAG...), and abnormalities in such regions can give rise to
trinucleotide repeat disorders.
When the repeat unit copy number is variable in the population being considered, it is called a
variable number tandem repeat (VNTR).
MeSH classifies variable number tandem repeats under minisatellites.
Mechanism
Tandem repeats can occur through different mechanisms. For example, slipped strand mispairing (SSM), (also known as
replication slippage
Replication may refer to:
Science
* Replication (scientific method), one of the main principles of the scientific method, a.k.a. reproducibility
** Replication (statistics), the repetition of a test or complete experiment
** Replication crisis
* ...
), is a mutation process which occurs during DNA replication. It involves denaturation and displacement of the DNA strands, resulting in mispairing of the complementary bases. Slipped strand mispairing is one explanation for the origin and evolution of repetitive DNA sequences.
Other mechanisms include
unequal crossover
Unequal crossing over is a type of gene duplication or deletion event that deletes a sequence in one strand and replaces it with a duplication from its sister chromatid in mitosis or from its homologous chromosome during meiosis. It is a type of ...
and
gene conversion.
Uses
Tandem repeat describes a pattern that helps determine an individual's inherited traits.
Tandem repeats can be very useful in determining
parentage
A parent is a caregiver of the offspring in their own species. In humans, a parent is the caretaker of a child (where "child" refers to offspring, not necessarily age). A ''biological parent'' is a person whose gamete resulted in a child, a male ...
.
Short tandem repeats are used for certain
genealogical DNA test
A genealogical DNA test is a DNA-based test used in genetic genealogy that looks at specific locations of a person's genome in order to find or verify ancestral genealogical relationships, or (with lower reliability) to estimate the ethnic m ...
s.
DNA is examined from ''
microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
s'' within the chromosomal DNA. Parentage can be determined through the similarity in these regions.
Polymorphic tandem repeats (alias VNTRs) are also present in microorganisms and can be used to trace the origin of an outbreak. The corresponding assay in which a collection of VNTRs is typed to characterize a strain is most often called
MLVA (Multiple Loci VNTR Analysis).
In the field of
computer science
Computer science is the study of computation, automation, and information. Computer science spans theoretical disciplines (such as algorithms, theory of computation, information theory, and automation) to practical disciplines (includin ...
, tandem repeats in strings (e.g., DNA sequences) can be efficiently detected using
suffix trees or
suffix arrays.
Studies in 2004 linked the unusual genetic plasticity of
dogs to mutations in tandem repeats.
See also
*
Microsatellite
A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome. ...
*
Minisatellite
*
ProRepeat
*
Satellite DNA
*
Tandem Repeats Database
*
Tandem repeat locus
*
Variable number tandem repeats
References
External links
*Examples:
*
VNTRs- info and animated example
*Databases:
*
TRDB - The Tandem Repeats Database *
The Microorganisms Tandem Repeats Database*
Short Tandem Repeats Database*
Tandem Repeats in major genomes *Search tools:
TAPO: A combined method for the identification of tandem repeats in protein structures*
*
Mreps*
STAR*
Splinter*
TRED - Tandem Repeats over the Edit Distance*
*
Microsatellite repeats finder*
JSTRING - Java Search for Tandem Repeats in genomes*
**
ttps://web.archive.org/web/20140606101328/http://ugene.unipro.ru/documentation/manual/plugins/repeat_finder.html#tandem-repeats UGENE - an ultra fast and memory efficient open-source tandem repeats finder implementation.
TRAL: Tandem Repeat Annotation Library - a meta-predictor tool with statistical filtering, with a range of functions for repeat annotation and analyses
{{Organisms et al.
Repetitive DNA sequences
de:Tandemwiederholung