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  Single-nucleotide polymorphisms: analysis by mass spectrometry

Sauer, S., Reinhardt, R., Lehrach, H., & Gut, I. G. (2006). Single-nucleotide polymorphisms: analysis by mass spectrometry. Nature Protocols, 1(4), 1761-1771. doi:10.1038/nprot.2006.257.

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Sauer, Sascha1, Author           
Reinhardt, Richard2, Author           
Lehrach, Hans3, Author           
Gut, Ivo G., Author
Affiliations:
1Nutrigenomics and Gene Regulation (Sascha Sauer), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479662              
2High Throughput Technologies, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433552              
3Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              

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 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.

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Language(s): eng - English
 Dates: 2006
 Publication Status: Issued
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 Identifiers: eDoc: 312540
DOI: 10.1038/nprot.2006.257
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Title: Nature Protocols
Source Genre: Journal
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Pages: - Volume / Issue: 1 (4) Sequence Number: - Start / End Page: 1761 - 1771 Identifier: ISSN: 1754-2189