Short tandem repeat

Schmalzing, D., Koutny, L., Chisholm, D., Adourian, A., Matsudaira, P, and Ehrlich, D., Two-color multiplexed analysis of eight short tandem repeat loci with an electrophoretic microdevice, Anal. Biochem., 270, 148, 1999. 

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. 

Earlier attempts to use the AFM for mechanically stretching chromatin fibers have run into a rather unexpected artifact. Long native chromatin fibers isolated from chicken erythrocytes, or fibers assembled in vitro from purified histones and relatively short, tandemly repeated DNA sequences were deposited on mica or glass surfaces and pulled with the AFM tip [69,70]. In such stretching experiments the scanning of the sample in the x- and y-direction used for imaging was disabled, and the cantilever-mounted tip was allowed to move only in the z-direction, i.e., upwards and downwards, away and towards the surface. When the AFM tip is pushed into the sample, it may attach to the sample by non-specific adsorption upon retraction it stretches the sample and force-extension curves are recorded (see Fig. lb for an explanation of a typical force curve). 

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. 

Forensic analysis of DNA samples DNA fingerprinting by means of PCR has revolutionized the analysis of evidence from crime scenes. DNA isolated from a single human hair, a tiny spot of blood, or a sample of semen is sufficient to determine whether the sample comes from a specific individual. The DNA markers analyzed for such fingerprinting are most commonly short tandem repeat polymorphisms (STRs). These are very similar to the VNTRs described previously (see p. 455), but are smaller in size. [Note Verification of paternity uses the same techniques.]... 

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]. 

Mitnik, L., Carey, L., Burger, R., Desmarais, S., Koutny, L., Wernet, O., Matsu-daira, R, Ehrlich, D., High-speed analysis of multiplexed short tandem repeats with an electrophoretic microdevice. Electrophoresis 2002, 23, 719-726. 

Systematic tailored ORE-data retrieval and management Short tandem repeats Stress axis-related exon Small temporal RNA... 

H. Oberacher, W. Parson, R. Milhlmann, C.G. Huber, Analysis of PCR products by on-line LC-MS for genotyping of polymorphic short tandem repeat loci. Anal. Chem., 73 (2001)5109. 

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