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Nucleic Acids Research Advance Access published online on April 10, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm056
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

DNA sequencing by MALDI-TOF MS using alkali cleavage of RNA/DNA chimeras

Florence Mauger1, Keith Bauer2, Cassandra D. Calloway2, Jérémy Semhoun1, Tetsuya Nishimoto2, Thomas W. Myers2, David H. Gelfand2 and Ivo G. Gut1,*

1Centre National de Génotypage, Bâtiment G2, 2 rue Gaston Crémieux, 91057 Evry Cedex, France and 2Roche Molecular Systems Inc., 1145 Atlantic Avenue, Alameda, California 94501, USA

*To whom correspondence should be addressed. Tel: +33 160 87 84 00; Fax: +33 160 87 83 83; E-mail: ivo.gut{at}cng.fr

Received November 9, 2006. Revised January 17, 2007. Accepted January 19, 2007.

Approaches developed for sequencing DNA with detection by mass spectrometry use strategies that deviate from the Sanger-type methods. Procedures demonstrated so far used the sequence specificity of RNA endonucleases, as unfortunately equivalent enzymes for DNA do not exist and therefore require transcription of DNA into RNA prior to fragmentation.

We have developed a novel, rapid and accurate concept for DNA sequencing using mass spectrometry and RNA/DNA chimeras and applied it to sequence mitochondrial DNA. Our method is based on the preparation of a chimeric RNA/DNA with a DNA polymerase that also incorporates ribonucleotides. Sequencing is carried out with one ribonucleotide (ATP, CTP or GTP) and the other three nucleotides in their deoxyribo-form. The product is treated with alkali, which cleaves 3' of all ribonucleotides to form a terminal 3' phosphate. Conditions have been streamlined so that molecular, biological and alkali cleavage conditions are compatible with matrix-assisted laser desorption/ionization time-of-flight (MALDI) mass spectrometric analysis. Fragment analysis by MALDI MS provides a sequence-specific fingerprint, which allows the identification of differences between a reference and another sequence. Due to the mass profile, the position and kind of the mutation can be assigned. These differences between signatures are indicative of known, unidentified, rare and private mutations.

This novel DNA sequencing protocol was applied to sequence the hypervariable region 1 (HV1) of mitochondrial DNA in 22 individuals.


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