Short tandem repeat DNA

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). 

Ruitberg, C. M., Reeder, D. J., and Butler, J. M., STRBase A short tandem repeat DNA database for the human identity testing community. Nucleic Acids Res, 29, 320, 2001. 

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. 

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]. 

Second, it is important to consider whether a clone library will be representative of a particular repeated sequence. Besides the genetic factors, above, unusual patterns of restriction sites in some repeated sequences may influence their relative abundance in a library. This would be more likely for a tandemly repeated sequence or a very long repeated sequence than for short, interspersed repeated DNA sequences. Traditional A or plasmid libraries would be sufficient for most studies, but in certain situations it might be necessary to resort to DNA libraries of randomly frag-... 

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... 

There are several major types of DNA sequence variation in the human genome. One type comprises repeated sequences with variations in the number of repeat units, such as short tandem repeat polymorphisms (STRPs, also known as microsatellites) in the form of mono-, di-, tri-, and tetra-nu-cleotide repeats, or more complex sequence repeats such as variable number tandem repeats (VNTRs) [2-4]. Repeat polymorphisms are relatively... 

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... 

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