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Genotyping Single Nucleotide Polymorphisms with Molecular Beacons


Stratagenes custom molecular beacon synthesis assists in detecting SNPs quickly and easily

Fei Bao
University of Colorado Health Sciences Center, Denver, Colorado

We used Stratagenes custom molecular beaconsff, to detect a single nucleotide polymorphism (SNP) in a region of chromosome 10q25.1 and showed clear discrimination among the different genotypes carried in family members. This molecular beacons application provides a fast and simple method that can be performed in 2 hours in a 96-well format and is especially suitable for high-throughout, high-quality genotyping of SNPs.

SNPs are the most frequently found DNA sequence variations in the human genome (about 1 per 350 bp frequency).1 The ability to efficiently genotype SNPs is increasingly seen as fundamental to identifying genetic factors associated with complex diseases. There are a number of available methods for SNP genotyping, ranging from traditional gel-based formats to detection with the TaqMan system2 and DNA microarrays3 that have offered the promise of high-throughput screening.

Molecular Beacon Technology

Molecular beacons are hairpin-shaped fluorescent hybridization probes that can be used to monitor the accumulation of specific product in a closed-tube in real time PCR. The homogeneous format eliminates the need for gel electrophoresis, reduces the time, effort, and risk of contamination involved with performing PCR analysis. Molecular beacons contain a fluorophore and a quencher moiety at opposite ends of an oligonucleotide. The ends of the oligonucleotide are designed to be complementary to each other and can form a stem structure, while the intervening loop is complementary to a sequence within the amplified product. When the unhybridized probe is in solu
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