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Nucleic Acids Research, 2001, Vol. 29, No. 13 e61
© 2001 Oxford University Press

Rapid characterization of DNA oligomers and genotyping of single nucleotide polymorphism using nucleotide-specific mass tags

Fadi Abdi, E. Morton Bradbury1,3, Norman Doggett2 and Xian Chen* C-ACS, 1BN-2, MS M888, Chemistry Division, Bioscience Division, 2Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87544, USA and 3Department of Biological Chemistry, School of Medicine, University of California at Davis, Davis, CA 95616, USA

Using currently available MS-based methods, accurate mass measurements are essential for the characterization of DNA oligomers. However, there is a lack of specificity in mass peaks when the characterization of individual DNA species in a mass spectrum is dependent solely upon the mass-to-charge ratio (m/z). Here, we utilize nucleotide-specific tagging with stable isotopes to provide internal signatures that quantitatively display the nucleotide content of oligomer peaks in MS spectra. The characteristic mass-split patterns induced by the partially 13C/15N-enriched dNTPs in DNA oligomers indicate the number of labeled precursors and in turn the base substitution in each mass peak, and provide for efficient SNP detection. Signals in mass spectra not only reflect the masses of particular DNA oligomers, but also their specific composition of particular nucleotides. The measurements of mass tags are relative in the mass-split pattern and, hence, the accuracy of the determination of nucleotide substitution is indirectly increased. For high sample throughput, 13C/15N-labeled sequences of interest have been generated, excised in solution and purified for MS analysis in a single-tube format. This method can substantially improve the specificity, accuracy and efficiency of mass spectrometry in the characterization of DNA oligomers and genetic variations.

* To whom correspondence should be addressed at: C-ACS, MS M888, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87544, USA. Tel: +1 505 665 0781; Fax: +1 505 665 3024; Email: xchen{at}telomere.lanl.gov


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