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Minisequencing the Mitochondrial DNA Control Region Using Time-of-Flight Mass Spectrometry



John Butler


The control region of mitochondrial DNA (mtDNA), commonly referred to as the D-loop, is highly polymorphic and contains a number of possible single nucleotide polymorphism (SNP) sites for analysis. MITOMAP, an internet database containing fairly comprehensive information on mtDNA that has been reported in the literature (6), lists 408 polymorphisms at 362 different sites across 1121 nucleotides of the control region (positions 16020-576). With such a variety of possible polymorphisms, DNA sequence analysis is the most comprehensive method of detecting differences between samples. However, many of these polymorphisms are rare and population specific. Variation in hot spots can often be almost as informative as complete sequence analysis in some situations. A number of screening techniques have been described in the literature and are reviewed by Butler and Levin (2). These methods are less costly and time consuming than complete sequence analysis and can lead to an early exclusion when two samples do not match. Screening tests for determining the nucleotides at specific sites in the mtDNA control region include dot blot assays (10), minisequencing (11), and PCR-RFLP (1). This chapter will describe the use of time-of-flight mass spectrometry and multiplex SNP analysis (5) as a new technique to detect mitochondrial DNA polymorphisms at specific hot spots along the control region.


DNA, DNA typing, mass spectrometry, mitochondrial DNA, single nucleotide polymorphism


Butler, J. (2008), Minisequencing the Mitochondrial DNA Control Region Using Time-of-Flight Mass Spectrometry, Biotechniques (Accessed May 22, 2024)


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Created October 16, 2008