Clinical Chemistry 45: 1578, 1999;
(Clinical Chemistry. 1999;45:1578.)
© 1999 American Association for Clinical Chemistry, Inc.
Mass Spectrometry of Nucleic Acids
Norman H.L. Chiu1,2,a and
Charles R. Cantor1,2
1
Sequenom Inc., 11555 Sorrento Valley Rd., San Diego, CA 92121
2
Boston University, Center for Advanced Biotechnology, 36 Cummington St., Boston, MA 02215
a Author for correspondence. Fax 619-350-9237; e-mail nchiu{at}sequenom.com
To the Editor:
We read with interest the review by Kricka (1) on
nucleic acid detection technologies, in which he mentioned that nucleic
acids do not have any intrinsic properties for direct detection. In
response to this, we would like to point out the determination of
intrinsic molecular weights of nucleic acids using mass spectrometry
(MS) has been widely accepted as one of the most accurate methods to
detect nucleic acids (2). Using matrix-assisted laser
desorption/ionization time-of-flight (MALDI-TOF) MS, a mass resolution
of 1 per 1000 and the detection of low femtomole quantities of
DNA can be achieved routinely (3). Nucleic acids ranging
from 2 to 2000 nucleotides can be detected by using MALDI-TOF MS
(4). Because of the mass differences of the nucleobases, MS
can also be used to analyze mixtures of different nucleic acid
fragments without the use of any label (5). Furthermore, in
most cases, the separation of the fragments before MS measurements is
not required. The minimum sample volume required for MALDI-TOF MS is
only a few nanoliters (3). MS can, therefore, be easily
linked to any miniaturization of sample processing. Typically, each
mass spectroscopic measurement including acquisition and interpretation
of mass spectrum takes <10 s. With the availability of automatic
high-throughput MS systems that include sample preparation
(6), the cost-effectiveness of using MS to analyze nucleic
acids has become comparable to other analytical techniques. Currently,
the size of a MALDI-TOF mass spectrometer is similar to an immunoassay
analyzer. However, as stated in a recent report (7), the
size of mass spectrometers can be substantially reduced. Together with
the continued development of software for automated interpretation of
mass spectra, MS has a great potential to become one of the most
important analytical tools for clinical laboratories. Some of the
current clinical applications of MS are (a) DNA sequencing
(8); (b) detection of genetic variations such as
single-nucleotide polymorphisms (9), microsatellites
(10), short tandem repeats (11), and small
insertions/deletions; and (c) gene expression.
References
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Kricka LJ. Nucleic acid detection technologies—labels, strategies, and formats [Review]. Clin Chem 1999;45:453-458.
[Abstract/Free Full Text]
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Crain PF, McCloskey JA. Applications of mass spectrometry to the characterization of oligonucleotides and nucleic acids [Review]. Curr Opin Biotechnol 1998;9:25-34.
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Little DJ, Cornish TJ, O'Donnell MJ, Braun A, Cotter RJ, Koster H. MALDI on a chip: analysis of arrays of low-femtomole to subfemtomole quantities of synthetic oligonucleotides and DNA diagnostic products dispensed by a piezoelectric pipet. Anal Chem 1997;69:4540-4546.
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Berkenkamp S, Kirpekar F, Hillenkamp F. Infrared MALDI mass spectrometry of large nucleic acids. Science 1998;281:260-262.
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Ross P, Hall L, Smirnov I, Haff L. High level multiplex genotyping by MALDI-TOF mass spectrometry. Nat Biotechnol 1998;16:1347-1351.
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O'Donnell MJ, Little DP, Braun A. MassArray as an enabling technology for the industrial-scale analysis of DNA. Genet Eng News 1997;17:39.
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Henry CM. The incredible shrinking mass spectrometers. Anal Chem 1999;71:264A-268A.
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Fu DJ, Tang K, Braun A, Reuter D, Darnhofer-Demar B, Little DP, et al. Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry. Nat Biotechnol 1998;16:381-384.
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Braun A, Little DP, Koster H. Detecting CFTR gene mutations by using primer oligo base extension and mass spectrometry. Clin Chem 1997;43:1151-1158.
[Abstract/Free Full Text]
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Braun A, Little DP, Reuter D, Muller-Mysok B, Koster H. Improved analysis of microsatellites using mass spectrometry. Genomics 1997;46:18-23.
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Ross P, Belgrader P. Analysis of short tandem repeat polymorphisms in human DNA by matrix-assisted laser desorption/ionization mass spectrometry. Anal Chem 1997;69:3966-3972.
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