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Single-nucleotide polymorphisms: analysis by mass spectrometry

Item Type:Article
Title:Single-nucleotide polymorphisms: analysis by mass spectrometry
Creators Name:Sauer, S. and Reinhardt, R. and Lehrach, H. and Gut, I.G.
Abstract:Matrix-assisted laser desorption-ionization (MALDI) mass spectrometry has evolved as a powerful method for analyzing nucleic acids. Here we provide protocols for genotyping single-nucleotide polymorphisms (SNPs) by MALDI based on PCR and primer extension to generate allele-specific products. Furthermore, we present three different approaches for sample preparation of primer-extension products before MALDI analysis and discuss their potential areas of application. The first approach, the 'GOOD' assay, is a purification-free procedure that uses DNA-modification chemistry, including alkylation of phosphorothioate linkages in the extension primers. The other two approaches use either solid-phase extraction or microarray purification for the purification of primer-extension products. Depending on the reaction steps of the various approaches, the protocols take about 6-8 hours.
Keywords:Alkylation, DNA Primers, Exonucleases, Genotype, Mass Spectrometry, Matrix-Assisted Laser Desorption-Ionization Mass Spectrometry, Microarray Analysis, Oligonucleotides, Polymerase Chain Reaction, Single Nucleotide Polymorphism, Solid Phase Extraction, Transferases
Source:Nature Protocols
Publisher:Nature Publishing Group
Page Range:1761-1771
Date:22 November 2006
Official Publication:https://doi.org/10.1038/nprot.2006.257
PubMed:View item in PubMed

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