Real‐Time Quantitative PCR Analysis of Mitochondrial DNA Content

Victor Venegas1, Jing Wang1, David Dimmock2, Lee‐Jun Wong1

1 Baylor College of Medicine, Houston, Texas, 2 Medical College of Wisconsin, Milwaukee, Wisconsin
Publication Name:  Current Protocols in Human Genetics
Unit Number:  Unit 19.7
DOI:  10.1002/0471142905.hg1907s68
Online Posting Date:  January, 2011
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Mitochondrial disorders are a group of complex and heterogeneous diseases that may be caused by molecular defects in the nuclear or mitochondrial genome. The biosynthesis and integrity of the small 16.6‐kb mitochondrial genome require a group of nuclear encoded genes. The mitochondrial DNA (mtDNA) depletion syndromes (MDDSs) are autosomal recessive disorders caused by molecular defects in nuclear genes, and characterized by a reduction in mtDNA content. To date, mutations in at least nine genes (POLG, DGUOK, TK2, TYMP, MPV17, SUCLA2, SUCLG1, RRM2B, and C10orf2) have been reported to cause various forms of MDDSs. In the clinical setting, a simple method to determine mtDNA depletion would be useful prior to undertaking gene sequence analysis. This unit outlines the real‐time quantitative polymerase chain reaction (qPCR) analysis of mtDNA content in tissues. MtDNA content varies among different tissues and at different ages in the same individual. Detailed protocols for the selection of nuclear genes for normalization, PCR set up, validation procedures, tissue and age matched controls, and sensitivity and specificity in various tissues, as well as interpretation of results are discussed. Curr. Protoc. Hum. Genet. 68:19.7.1‐19.7.12 © 2011 by John Wiley & Sons, Inc.

Keywords: mtDNA copy number; mtDNA content; mtDNA qPCR; quantification of mtDNA content; mtDNA depletion

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Table of Contents

  • Introduction
  • Strategic Planning
  • Basic Protocol 1: Real‐Time Quantitative PCR for the Quantification of mtDNA Content
  • Support Protocol 1: Generation of mtDNA Age‐Matched Controls
  • Support Protocol 2: Preparation and Quantification of DNA Samples
  • Commentary
  • Literature Cited
  • Figures
  • Tables
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Basic Protocol 1: Real‐Time Quantitative PCR for the Quantification of mtDNA Content

  • Genomic DNA samples (see protocol 4)
  • qPCR primers for mitochondrial tRNALeu(UUR) gene, alternate primers for mtDNA 16S rRNA gene and nuclear β‐2‐microglobulin (β2M) gene (Table 19.7.2), 5 µM working concentration diluted in water
  • iTaq SYBR Green SuperMix with ROX (Bio‐Rad, cat. no. 170‐8852)
  • Tissue‐ and age‐matched pooled controls (see protocol 3)
  • PCR hood
  • 96‐well thin‐walled PCR plates
  • Adhesive plate sealer
  • ABI Prism 7900HT sequence detector system (Applied Biosystems)
  • Data analysis software: SDS software (version 2.2)
    Table 9.7.2   MaterialsqPCR Primer Sequences and Conditions

    Gene Primer name Primer sequence (5′ to 3′) Amplicon size (bp) Annealing temperature (°C)
    nDNA β2‐microglobulin β2M F594 TGCTGTCTCCATGTTTGATGTATCT 86 62
    Alternate primers:mtDNA 16S rRNA mtF3163 GCCTTCCCCCGTAAATGATA 97 62

Support Protocol 1: Generation of mtDNA Age‐Matched Controls

  • Tissues
  • Puregene kit (Gentra Systems, cat. no. D50K1) including:
    • Red cell lysis solution
    • Cell lysis solution
    • DNA hydration solution
    • Protein precipitation solution
  • 100% isopropanol
  • 70% ethanol
  • Rapid hair digestion buffer: 10 mM Tris⋅Cl (pH 8.0), 1.0% Brij 58, 35 mM DTT, 1 mM CaCl 2
  • Calf thymus DNA standards (type XV; Sigma, cat. no. D4522)
  • NanoDrop ND‐1000 UV‐Vis spectrophotometer
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Literature Cited

Literature Cited
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