Mitochondrial DNA : Methods and Protocols / edited by Thomas J. Nicholls, Jay P. Uhler, Maria Falkenberg.

Format:

Book

Contributor:

Nicholls, Thomas J., Editor.

Uhler, Jay P., Editor.

Falkenberg, Maria., Editor.

Series:

Methods in Molecular Biology, 1940-6029 ; 2615

Language:

English

Subjects (All):

Genomics.

Local Subjects:

Genomics.

Physical Description:

1 online resource (XV, 469 p. 85 illus., 68 illus. in color.)

Edition:

1st ed. 2023.

Place of Publication:

New York, NY : Springer US : Imprint: Humana, 2023.

Summary:

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.

Contents:

Isolation of functional mitochondria and pure mtDNA from murine tissues

Isolating mitochondria, mitoplasts, and mtDNA from cultured mammalian cells

Coupling differential centrifugation with exonuclease treatment and size exclusion chromatography (DIFSEC) for purification of mtDNA from mammalian cells

Isolation and Quality Control of Yeast Mitochondria

Mitochondrial DNA isolation from plants

Visualize the Distribution and Dynamics of Mitochondrial DNA (mtDNA) nucleoids with Multiple Labelling Strategies

Visualization of mtDNA using FISH

In situ analysis of mitochondrial DNA synthesis using metabolic labeling coupled to fluorescence microscopy

Measurement of nucleoid size using STED microscopy

How to quantify DNA compaction by TFAM with Acoustic Force Spectroscopy and Total Internal Reflection Fluorescence microscopy

Assessing TFAM binding to human mitochondrial DNA

Identification of proximity interactors of mammalian nucleoid proteins by BioID

Localization of mitochondrial nucleoids by transmission electron microscopy using the transgenic expression of the mitochondrial helicase TWINKLE and APEX2

In vitro assays of TWINKLE function

Rolling Circle Replication and Bypass of Damaged Nucleotides

Studying mitochondrial nucleic acid synthesis utilizing intact isolated mitochondria

Functional assessment of mitochondrial DNA maintenance by depletion and repopulation using 2’,3’-dideoxycytidine in cultured cells

Analysis of mitochondrial DNA replication by two-dimensional agarose gel electrophoresis

Quantitative analysis of nucleoside triphosphate pools in mouse muscle using hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry detection

Detection of UV-Induced Deletions in Mitochondrial DNA

Determination of the ribonucleotide content of mtDNA using alkaline gels

5´-end mapping in human mitochondrial DNA

Manipulation of murine mitochondrial DNA heteroplasmy with mtZFNs

Biolistic transformation of Chlamydomonas reinhardtii and Saccharomyces cerevisiae mitochondria

A method for precisely identifying modifications to plant mitochondrial genomes by mitoTALENs

Mitochondrial DNA sequencing and heteroplasmy quantification by Next Generation Sequencing

Genomic strategies in mitochondrial diagnostics

Mitochondrial DNA enrichment for sensitive next-generation sequencing

Single cell analysis of mitochondrial DNA deletions.

ISBN:

9781071629222

1071629220