Short tandem repeats STRs

Biomolecular MS and in particular MALDI-TOF-MS (see Sections 2.1.22 and 2.2.1) permit the routine analysis of oligonucleotides up to 70-mers, intact nucleic acids, and the direct detection of DNA products with no primer labels with an increase in analysis speed and mass accuracy especially in contrast to traditional DNA separation techniques such as slab gels or capillary electrophoresis. Applications focus on the characterization of single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs). Precise and accurate gene expression measurements show relative and absolute numbers of target molecules determined independently of the number of PCR cycles. DNA methylation can be studied quantitatively. 

The initial VNTRs were several hundred nucleotide units long requiring extended laboratory periods for the various segments to separate on the gel. Today, most tests employ shorter, 3 5 nucleotides long, VNTRs that allow for more rapid movement on the gel, resulting in faster and less costly results. It also allows for the production of a greater number of sequences that are looked at, and hence a greater ability to match or not match the results. These shorter sequences are called short tandem repeats (STRs). 

DNA fingerprinting is currently based on the analysis of autosomal short tandem repeats (STRs). STRs are DNA segments that are typically found in noncoding regions of genome and are composed of repeating units of 3-5 nucleotides sequence patterns. Because of their high mutation rate. 

In 1984, it was discovered that human genes contain short, repeating sequence of noncoding DNA, called short tandem repeats (STRs). The STR loci are slightly different for every individual except identical twins. By sequencing these loci, a unique pattern for each individual can be obtained. On the basis of this fundamental discovery, the technique of DNA fingerprinting was developed. 

A multiplex genetic analysis of short tandem repeats (STR) was carried out in a glass chip [543,983,984]. As required by the FBI s CODIS (combined DNA index system) for forensic identification, all 13 loci of STR are needed [543]. 

Short tandem repeat (STR) or microsatellite loci consist of DNA sequence motifs that have core repeats of two to seven base pairs. Examples include the dinucleotide 5 CACACACA 3 and the tetranucleotide 5 TTTATTTATTTA 3". Thousands of STRs are scattered throughout the genome. Because they are flanked by unique sequences, each can be specifically amplified with the polymerase chain reaction (PGR) for analysis. In populations of individuals, multiple alleles may be present based on differences in the number of repeated motifs at the locus. STRs have many characteristics that make them ideal for identity testing (1) They can be analyzed in fluorescent automated systems (2) alleles can be assigned in a definitive manner following analysis (3) STR loci are almost always transmitted in families in a Mendelian fashion (4) the loci may have 10 or more alleles, often with... 

Corrigan, D.K., Gale, N., Brown, T., and Bartlett, P.N. (2010) Analysis of short tandem repeats (STRs) using SERS monitoring and electrochemical melting. Angewandte Chemie International Edition, 49, 5917-5920. 

The human genome contains approximately 3 billion base pairs (bp) of DNA. The DNA is folded to fit within the nucleus. It is divided among chromosomes and compactly packed into chromatin by histones and other accessory proteins. Each normal somatic cell contains two copies of 22 different somatic chromosomes and two sex chromosomes (XX or XY). Less than 5% of DNA actually encodes protein and other functional products, such as tRNA, rRNA, miRNA, and other small nuclear RNAs. The majority (>95%) of human DNA consists of non-coding sequences, typically repetitive sequences such as minisatellites, microsatellites, SINEs, and LINEs. Microsatellites are short tandem repeats with each repeat unit of 1 to 13 bp long. Mini-satellites are tandemly repeated DNA sequences with the size of repeat unit of 14 to 500 bp. Microsatellite and minisatellite repeats are also known as short tandem repeats (STRs). Highly repetitive sequences containing thousands of repeated units are also found at the... 

This group contains a number of classes of highly repetitive short repeat sequences (1) short tandem repeats (STRs 2-5 bp), (2) microsateUites (1-13 bp), and (3) minisatellites (14-500 bp). 

A third type of polymorphism is due to tandem repeats of short sequences that can be detected by PCR-based analysis. These are known variously as microsatellites, short tandem repeats (STRs), STR polymorphisms (STRPs), or short sequence length polymorphisms (SSLPs). These repeat sequences usually consist of two, three, or four nucleotides and are plentiful in most organisms. All PCR-converted STR markers (those for which a pair of oligonucleotides flanking the polymorphic site suitable for PCR amplification of the locus has been designed) are considered to be STSs. The advent of PCR-based analysis quickly made microsatellites the markers of choice for mapping. 

The major application of CE in forensic biology is in the detection and analysis of short tandem repeats (STRs). STR markers are preferred because of the powerful statistical result that is possible with these markers and the large databases that exist for convicted offenders profiles. Other related applications include the analysis of haploid markers in the Y chromosome and in mitochondrial DNA (mtDNA). Nonhuman DNA testing can also be performed depending on the circumstances of the case. The techniques involved include genotyping, DNA sequencing, and mutation detection. 

Gilmore, S., Peakall, R., and Robertson, J., Short tandem repeat (STR) DNAmarkers are hypervariable and informative in Cannabis sativa Implications for forensic investigations. Forensic Sci Int, 131,65,... 

Karlinsey, J.M., Multicolor Short Tandem Repeat (STR) Analysis on Microchip, Advances and Applications of Microfluidic Analysis Systems, 2007, University of Virginia Charlottesville, VA. 

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