Overview
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.
Full Product Details
Author: Thomas J. Nicholls , Jay P. Uhler , Maria Falkenberg
Publisher: Springer-Verlag New York Inc.
Imprint: Springer-Verlag New York Inc.
Edition: 1st ed. 2023
Volume: 2615
Weight: 1.107kg
ISBN: 9781071629215
ISBN 10: 1071629212
Pages: 469
Publication Date: 21 February 2023
Audience:
Professional and scholarly
,
Professional & Vocational
Format: Hardback
Publisher's Status: Active
Availability: Manufactured on demand 
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Table of Contents
Section I. Purification methods for mitochondrial DNA 1 Isolation of functional mitochondria and pure mtDNA from murine tissues Dieu Hien Rozsivalova, Milica Popovic, Harshita Kaul and Aleksandra Trifunovic 2 Isolating mitochondria, mitoplasts, and mtDNA from cultured mammalian cells Katja E. Menger and Thomas J. Nicholls 3 Coupling differential centrifugation with exonuclease treatment and size exclusion chromatography (DIFSEC) for purification of mtDNA from mammalian cells Andrew M. Shaw and Payam A. Gammage 4 Isolation and Quality Control of Yeast Mitochondria Asli Aras Taskin, Daiana Nerina Moretti, F.-Nora Vögtle and Chris Meisinger 5 Mitochondrial DNA isolation from plants Frédérique Weber-Lotfi, Arnaud Fertet, Rokas Kubilinskas, Clémentine Wallet and José M. Gualberto Section II. Visualising mtDNA 6 Visualize the Distribution and Dynamics of Mitochondrial DNA (mtDNA) nucleoids with Multiple Labelling Strategies Xiangjun Di, Jinshan Qin, Yujie Sun, Qian Peter Su 7 Visualization of mtDNA using FISH Xie Xie and Xuefeng Zhu 8 In situ analysis of mitochondrial DNA synthesis using metabolic labeling coupled to fluorescence microscopy John A. Smolka and Samantha C. Lewis 9 Measurement of nucleoid size using STED microscopy Elisa Motori Section III. Mitochondrial DNA interacting proteins 10 How to quantify DNA compaction by TFAM with Acoustic Force Spectroscopy and Total Internal Reflection Fluorescence microscopy Martucci Martial, Debar Louis, van den Wildenberg Siet and Farge Geraldine 11 Assessing TFAM binding to human mitochondrial DNA Takehiro Yasukawa and Dongchon Kang 12 Identification of proximity interactors of mammalian nucleoid proteins by BioID Mari J. Aaltonen and Hana Antonicka 13 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 Schauss Section IV. Mitochondrial DNA replication and repair 14 In vitro assays of TWINKLE function Jay P. Uhler, Ulrika Alexandersson and Maria Falkenberg 15 Rolling Circle Replication and Bypass of Damaged Nucleotides Josefin M. E. Forslund, Gorazd Stojkovič and Sjoerd Wanrooij 16 Studying mitochondrial nucleic acid synthesis utilizing intact isolated mitochondria Jelena Misic and Dusanka Milenkovic 17 Functional assessment of mitochondrial DNA maintenance by depletion and repopulation using 2’,3’-dideoxycytidine in cultured cells Gábor Zsurka, Genevieve Trombly, Susanne Schöler, Daniel Blei, Wolfram S. Kunz 18 Analysis of mitochondrial DNA replication by two-dimensional agarose gel electrophoresis Steffi Goffart and Jaakko Pohjoismäki 19 Quantitative analysis of nucleoside triphosphate pools in mouse muscle using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry detection Sushma Sharma, Ziqing Kong, Shaodong Jia, Phong Tran, Anna Karin Nilsson, and Andrei Chabes 20 Detection of UV-Induced Deletions in Mitochondrial DNA Gabriele A. Fontana and Hailey L. Gahlon 21 Determination of the ribonucleotide content of mtDNA using alkaline gels Choco Michael Gorospe, Bruno Marçal Repolês and Paulina H. Wanrooij 22 5´-end mapping in human mitochondrial DNA Andranik Durgaryan, Anders R. Clausen Section V. Modifying mitochondrial DNA 23 Manipulation of murine mitochondrial DNA heteroplasmy with mtZFNs Pavel A. Nash and Michal Minczuk 24 Biolistic transformation of Chlamydomonas reinhardtii and Saccharomyces cerevisiae mitochondria Nathalie Bonnefoy and Claire Remacle 25 A method for precisely identifying modifications to plant mitochondrial genomes by mitoTALENs Tomohiko Kazama and Shin-ichi Arimura Section VI. Mitochondrial DNA in human disease 26 Mitochondrial DNA sequencing and heteroplasmy quantification by Next Generation Sequencing Andrea Legati, Daniele Ghezzi and Carlo Viscomi 27 Genomic strategies in mitochondrial diagnostics Dasha Deen, Charlotte L. Alston, Gavin Hudson, Robert W. Taylor, Angela Pyle 28 Mitochondrial DNA enrichment for sensitive next-generation sequencing Shilan Wu, Matthew J. Longley, Scott A. Lujan, Thomas A. Kunkel and William C. Copeland 29 Single cell analysis of mitochondrial DNA deletions Helen A.L. Tuppen, Amy K. Reeve, Amy E. Vincent
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