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DNA Modifications

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Alexey Ruzov

    1. Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK

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    You can also search for this editor in PubMed   Google Scholar

  2. Martin Gering

    1. School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK

    View editor publications

    You can also search for this editor in PubMed   Google Scholar

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 2198)

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Table of contents (34 protocols)

  1. Front Matter

    Pages i-xvi
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  2. Introduction

    1. Front Matter

      Pages 1-1
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    2. Modified Forms of Cytosine in Eukaryotes: DNA (De)methylation and Beyond

      • Maria Eleftheriou, Alexey Ruzov
      Pages 3-13

    3. Evidence for Noncytosine Epigenetic DNA Modifications in Multicellular Eukaryotes: An Overview

      • Paige Lowe, Ryszard Olinski, Alexey Ruzov
      Pages 15-25

    4. Mass Spectrometry-Based Analysis of DNA Modifications: Potential Applications in Basic Research and Clinic

      • Ryszard Olinski, Rafal Rozalski, Daniel Gackowski
      Pages 27-35

    5. Mapping DNA Methylation in Mammals: The State of the Art

      • Antonio Lentini, Colm E. Nestor
      Pages 37-50

  3. Detection and Quantification of DNA Modifications Using Mass Spectrometry and Capillary Gel Electrophoresis

    1. Front Matter

      Pages 51-51
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    2. Detection of Modified Bases in Bacteriophage Genomic DNA

      • Yan-Jiun Lee, Peter R. Weigele
      Pages 53-66

    3. Liquid Chromatography–Mass Spectrometry Analysis of Cytosine Modifications

      • Nan Dai, Ivan R. Corrêa Jr
      Pages 67-78

    4. Detection of DNA Methylation in Genomic DNA by UHPLC-MS/MS

      • Konstantinos Boulias, Eric Lieberman Greer
      Pages 79-90

    5. Quantification of DNA Modifications Using Two-Dimensional Ultraperformance Liquid Chromatography Tandem Mass Spectrometry (2D-UPLC-MS/MS)

      • Marta Starczak, Maciej Gawronski, Ryszard Olinski, Daniel Gackowski
      Pages 91-108

    6. MS Analysis of DNA Modifications in Urinary/Body Fluids

      • Aleksandra Skalska, Agnieszka Siomek-Gorecka, Ryszard Olinski, Rafal Rozalski
      Pages 109-122

    7. Preparation of Internal Standards for 2D-UPLC-MS/MS Quantification of Noncanonical DNA Bases

      • Marta Starczak, Aleksandra Skalska, Rafal Rozalski, Ryszard Olinski, Daniel Gackowski
      Pages 123-136

    8. Detection of TET-Oxidized 5-Methylcytosine Bases by Capillary Gel Electrophoresis

      • Romualdas Vaisvila, Lise Hunault, Lana Saleh
      Pages 137-144

  4. Assessing the Levels and Spatial Distribution of DNA Modifications Using Antibody-Based Approaches

    1. Front Matter

      Pages 145-145
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    2. Immunochemical Detection of Modified Cytosine Species in Mammalian Preimplantation Embryos

      • Tie-Bo Zeng, Piroska E. Szabó
      Pages 147-157

    3. Immunochemical Detection of Modified Cytosine Species in Lampbrush Chromatin

      • Garry T. Morgan
      Pages 159-168

    4. Detection of Low-Abundance DNA Modifications Using Signal Amplification-Based Immunocytochemistry

      • Abdulkadir Abakir, Alexey Ruzov
      Pages 169-181

    5. Immunohistochemical Detection of Modified Cytosine Bases in Rodent Brain

      • Marcus D. Wallis, Rebecca C. Trueman
      Pages 183-191

    6. Immunohistochemical Detection of 5-Hydroxymethylcytosine and 5-Carboxylcytosine in Sections of Zebrafish Embryos

      • Peter Jessop, Martin Gering
      Pages 193-208
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Keywords

About this book

This book provides an overview of methods and experimental protocols that are currently used to analyze the presence and abundance of non-canonical DNA nucleotides in different biological systems. Focusing particularly on the newly discovered and less studied DNA modifications that are enzymatically produced and are likely to play specific roles in various biological processes, the volume explores chromatography- and mass spectrometry-based techniques for the detection and quantification of DNA modifications, antibody-based approaches to study their spatial distribution in different cells and tissues, and methods to analyze their genomic distribution with the help of bioinformatics tools that interrogate the corresponding datasets. Written for the highly successful Methods in Molecular Biology series, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. 

Authoritative and comprehensive, DNA Modifications: Methods and Protocols serves as an ideal guide to research scientists and PhD students in this rapidly developing discipline, and, thus, will ultimately contribute to deciphering the roles of non-canonical DNA nucleotides in different biological systems.

Editors and Affiliations

  • Centre for Biomolecular Sciences, University Park, University of Nottingham, Nottingham, UK

    Alexey Ruzov

  • School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham, UK

    Martin Gering

Bibliographic Information

  • Book Title: DNA Modifications

  • Book Subtitle: Methods and Protocols

  • Editors: Alexey Ruzov, Martin Gering

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-0876-0

  • 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 2021

  • Hardcover ISBN: 978-1-0716-0875-3Published: 22 August 2020

  • Softcover ISBN: 978-1-0716-0878-4Published: 22 August 2021

  • eBook ISBN: 978-1-0716-0876-0Published: 21 August 2020

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XVI, 495

  • Number of Illustrations: 27 b/w illustrations, 70 illustrations in colour

  • Topics: Biological Techniques, Genetics and Genomics

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