Microsatellite

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Microsatellites (synonymous with Simple Sequence Repeats , SSR , short tandem repeats , STR ) are short, mostly non-coding DNA sequences of two to six base pairs in length, which are often repeated in the genome of an organism . Often times, many repetitions are concentrated at the same locus (position of a sequence). They occur more frequently in eukaryotes . The STR include not only the VNTR ( variable number of tandem repeats, variable number of tandem repeats ' ) to the group of SSLP ( Simple sequence length polymorphism , simple Sequenzlängenpolymorphismus' ).

properties

Palindromic microsatellites can hairpins form

The repeated sequence in a microsatellite is very simple. It consists of two to four nucleotides and can recur 10 to 100 times. Microsatellites occur over a million times in the human genome , depending on how they are counted . Sequencing at the locus of a microsatellite results in sequences like “DAY DAY DAY DAY DAY DAY…”. Microsatellites are the most common form of repetitive DNA. Most common are the dinucleotide repeats of type (CA) n. These make up about 0.5% of the genome.

Microsatellites can be used for genetic analysis ( STR analysis ), since the number of repetitions also differs in different individuals of a species . In this way, polymorphisms in the DNA can be detected.

An analysis of the length of the two microsatellite at a specific location ( locus ) in the genome is carried out by the PCR analysis. Short synthetic oligonucleotides (so-called primers ) are used that are complementary to the DNA sequences that flank the microsatellite of interest. The two (mostly different) products of the PCR can be separated by gel electrophoresis and their length can thus be determined. The result is often two numbers that correspond to the number of repetitions of the motif (e.g. TH01 6.9 means that the STR marker TH01 has 6 repetitions on the first and 9 repetitions on the second allele of the person examined).

Programs for the search of microsatellites

program algorithm perfect imperfect Motif sizes, perfect Motif sizes, imperfect needs motif library recognizes alternative alignments finds partially or fully overlapping microsatellites particularities
MISA exactly Yes No 1 to length of the sequence - No ? Yes
Phobos exactly Yes Yes 1 -> 5000 1 -> 50 No Yes Yes
REPuter
SciRoKo exactly Yes Yes 1-6 1-6 No ? ? interactive analysis of the results
sputnik exactly Yes Yes 1-5 1-5 No No No
Tandem repeat finder probabilistic Yes Yes 1-2000 1-2000 No Yes Yes
Troll exactly Yes No 1-6 - Yes No ?

See also

Individual evidence

  1. ↑ John M. Butler: Forensic DNA Typing. Academic Press, 2005, ISBN 978-0-080-47061-0 , p. 85.
  2. ^ A b John M. Butler: Fundamentals of Forensic DNA Typing. Academic Press, 2009, ISBN 978-0-080-96176-7 , p. 148.