Single nucleotide repeat polymorphisms SNPs

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. 

In a recent study, Mandola et al. showed that the 28 bp TSER tandem repeats contain elements that bind upstream stimulating factor (USF), and also that ligand binding by USF-1 and USF-2 enhances the transcriptional activity of the TS gene (Fig. 2) (42). Electrophoretic mobility shift analysis has shown that the presence of a G-to-C single nucleotide polymorphism (SNP) within the second repeat of the 3R allele leads to decreased ability of upstream stimulatory factor (USF) to bind within the repeat and therefore sequentially result in decreased transcriptional activity of the 3R TS gene variant (42). 

Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation. URL http //www.ncbi.nlm. nih.gov/SNP/index.html. Uses SNP in the much looser sense of minor genetic variations and includes microsatellite repeats and small insertion/deletion polymorphisms. 

This amounts to 4 x 10 differences in the whole genome. In addition to these single nucleotide polymorphisms (SNPs) there are many differences in the >100,000 nearly randomly dispersed short tandem repeats of microsatellite The latter form... 

Key Words Genotyping polymorphism single nucleotide polymorphism (SNP) simple sequence repeat (SSR) tandem repeat insertion deletion. 

Figure 1 Schematic presentation of the DNA from two individuals and zoom on a region of their DNA to show that DNA is a linear molecule made of nucleotides, and to illustrate the two main types of polymorphisms used in forensics the short tandem repeats (STRs) and the single nucleotide polymorphisms (SNPs).

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