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Mitochondrial DNA

Methods and Protocols

  • Book
  • © 2023

Overview

Editors:
  1. Thomas J. Nicholls

    1. Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK

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  2. Jay P. Uhler

    1. Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden

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    You can also search for this editor in PubMed   Google Scholar

  3. Maria Falkenberg

    1. Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden

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    You can also search for this editor in PubMed   Google Scholar

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2615)

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Table of contents (29 protocols)

  1. Front Matter

    Pages i-xv
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  2. Purification Methods for Mitochondrial DNA

    1. Front Matter

      Pages 1-1
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    2. Isolation of Functional Mitochondria and Pure mtDNA from Murine Tissues

      • Dieu Hien Rozsivalova, Milica Popovic, Harshita Kaul, Aleksandra Trifunovic
      Pages 3-16

    3. Isolating Mitochondria, Mitoplasts, and mtDNA from Cultured Mammalian Cells

      • Katja E. Menger, Thomas J. Nicholls
      Pages 17-30

    4. Coupling Differential Centrifugation with Exonuclease Treatment and Size Exclusion Chromatography (DIFSEC) for Purification of mtDNA from Mammalian Cells

      • Andrew M. Shaw, Payam A. Gammage
      Pages 31-40

    5. Isolation and Quality Control of Yeast Mitochondria

      • Asli Aras Taskin, Daiana Nerina Moretti, F. Nora Vögtle, Chris Meisinger
      Pages 41-55

    6. Mitochondrial DNA Isolation from Plants

      • Frédérique Weber-Lotfi, Arnaud Fertet, Rokas Kubilinskas, Clémentine Wallet, José M. Gualberto
      Pages 57-75

  3. Visualising mtDNA

    1. Front Matter

      Pages 77-77
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    2. Visualize the Distribution and Dynamics of Mitochondrial DNA (mtDNA) Nucleoids with Multiple Labeling Strategies

      • Xiangjun Di, Jinshan Qin, Yujie Sun, Qian Peter Su
      Pages 79-88

    3. Visualization of mtDNA Using FISH

      • Xie Xie, Xuefeng Zhu
      Pages 89-98

    4. In Situ Analysis of Mitochondrial DNA Synthesis Using Metabolic Labeling Coupled to Fluorescence Microscopy

      • John A. Smolka, Samantha C. Lewis
      Pages 99-106

    5. Measurement of Nucleoid Size Using STED Microscopy

      • Elisa Motori
      Pages 107-117

  4. Mitochondrial DNA Interacting Proteins

    1. Front Matter

      Pages 119-119
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    2. How to Quantify DNA Compaction by TFAM with Acoustic Force Spectroscopy and Total Internal Reflection Fluorescence Microscopy

      • Martial Martucci, Louis Debar, Siet van den Wildenberg, Geraldine Farge
      Pages 121-137

    3. Assessing TFAM Binding to Human Mitochondrial DNA

      • Takehiro Yasukawa, Dongchon Kang
      Pages 139-151

    4. Identification of Proximity Interactors of Mammalian Nucleoid Proteins by BioID

      • Mari J. Aaltonen, Hana Antonicka
      Pages 153-172

    5. Localization of Mitochondrial Nucleoids by Transmission Electron Microscopy Using the Transgenic Expression of the Mitochondrial Helicase Twinkle and APEX2

      • David Pla-Martín, Felix Babatz, Astrid C. Schauss
      Pages 173-188

  5. Mitochondrial DNA Replication and Repair

    1. Front Matter

      Pages 189-189
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    2. In Vitro Assays of TWINKLE Function

      • Jay P. Uhler, Ulrika Alexandersson, Maria Falkenberg
      Pages 191-201

    3. Rolling Circle Replication and Bypass of Damaged Nucleotides

      • Josefin M. E. Forslund, Gorazd Stojkovič, Sjoerd Wanrooij
      Pages 203-217
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Keywords

About this book

This volume compiles a comprehensive range of methods to study key aspects of mitochondrial DNA including nucleoid structure and packaging, replication, genome integrity, and disease. Chapters are organized into eight methodological sections that cover in vitro and in vivo methods, including for mtDNA isolation, visualization, deep sequencing,  gene editing, and diagnostic aspects of mtDNA disease. Written in the format of the highly successful Methods in Molecular Biology series, each chapter includes an introduction to the topic, lists necessary materials and methods, includes tips on troubleshooting and known pitfalls, and step-by-step, readily reproducible protocols.

Authoritative and cutting-edge, Mitochondrial DNA: Methods and Protocols aims to be useful and informative for researchers and clinicians with an interest in mitochondrial DNA.

Editors and Affiliations

  • Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK

    Thomas J. Nicholls

  • Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden

    Jay P. Uhler, Maria Falkenberg

Bibliographic Information

  • Book Title: Mitochondrial DNA

  • Book Subtitle: Methods and Protocols

  • Editors: Thomas J. Nicholls, Jay P. Uhler, Maria Falkenberg

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-2922-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature 2023

  • Hardcover ISBN: 978-1-0716-2921-5Published: 21 February 2023

  • Softcover ISBN: 978-1-0716-2924-6Published: 21 February 2024

  • eBook ISBN: 978-1-0716-2922-2Published: 20 February 2023

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XV, 469

  • Number of Illustrations: 17 b/w illustrations, 68 illustrations in colour

  • Topics: Genetics and Genomics

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