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DNA Modification Detection Methods

  • Book
  • © 2022

Overview

Editors:
  1. Bi-Feng Yuan

    1. Department of Chemistry, Wuhan University, Wuhan, China

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  • Provides a comprehensive overview of available techniques and methods for studying various types of DNA modifications
  • Organized as detailed step-by-step protocols for experimental procedures required to successfully perform analysis
  • Offers new opportunities for researchers to manipulate the modification status to affect gene expression, and develop small molecules to tune the DNA functions

Part of the book series: Springer Protocols Handbooks (SPH)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-vi
    Download chapter PDF

  2. Detection of 5mC, 5hmC, 5fC, and 5caC

    1. Front Matter

      Pages 1-1
      Download chapter PDF

    2. Quantitative Assessment of the Oxidation Products of 5-Methylcytosine in DNA by Liquid Chromatography-Tandem Mass Spectrometry

      • Jiekai Yin, Shuo Liu, Yinsheng Wang
      Pages 3-11

    3. Determination of Cytosine Modifications in DNA by Chemical Labeling-Mass Spectrometry Analysis

      • Qing-Yun Cheng, Bi-Feng Yuan
      Pages 13-21

    4. Analysis of 5-Methylcytosine and 5-Hydroxymethylcytosine in Genomic DNA by Capillary Electrophoresis-Mass Spectrometry

      • Fang Yuan, Yu-Fang Ma, Ying-Lin Zhou, Xin-Xiang Zhang
      Pages 23-30

    5. Simple Quantification of Epigenetic DNA Modifications and DNA Damage on Multi-Well Slides

      • Yael Michaeli, Sapir Margalit, Sigal Avraham, Hila Erez, Noa Gilat, Zuzana Tulpová et al.
      Pages 31-44

    6. A Label-Free Electrochemical Biosensor for Sensitive Detection of 5-Hydroxymethylcytosine

      • Lin Cui, Juan Hu, Meng Wang, Chen-Chen Li, Chun-Yang Zhang
      Pages 45-52

    7. Electrochemical Assay for Continuous Monitoring of Dynamic DNA Methylation Process

      • Zong Dai, Li Zhang, Si-Yang Liu, Yuzhi Xu, Danping Chen, Jun Chen et al.
      Pages 53-63

    8. Electrogenerated Chemiluminescence Method for Determination of 5-Hydroxymethylcytosine in DNA

      • Shangxian Ma, Yan Li, Honglan Qi
      Pages 65-75

    9. Quantification of Site-Specific 5-Formylcytosine by Integrating Peptide Nucleic Acid-Clamped Ligation with Loop-Mediated Isothermal Amplification

      • Zhenhao Zhang, Weimin Tian, Wei Ren, Zhengping Li, Chenghui Liu
      Pages 77-91

    10. Global DNA Methylation Analysis Using Methylcytosine Dioxygenase

      • Natsumi Taka, Wataru Yoshida
      Pages 93-102

  5. Detection of Base J and 8-oxo-7,8-dihydroguanine

    1. Front Matter

      Pages 163-163
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    2. Mass Spectrometry-Based Quantification of β-d-Glucosyl-5-Hydroxymethyluracil in Genomic DNA

      • Shuo Liu, Yinsheng Wang
      Pages 165-180
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Keywords

About this book

Understanding the functional roles of DNA modifications relies on the accurate detection, quantification, and mapping of DNA modifications. Methods for deciphering DNA modifications have substantially improved over the last several years, which greatly revolutionize the field of DNA modifications. In addition to DNA cytosine methylation (5-methylcytosine, 5mC), the best-characterized epigenetic modification, many new modifications have been discovered to present in DNA in recent years.  

This book provides a comprehensive overview of available techniques and methods together with detailed step-by-step protocols for experimental procedures required to successfully perform analysis on various types of DNA modifications, including 5mC, 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), 5-carboxycytosine (5caC), 5-hydroxymethyluracil (5hmU), 5-formyluracil (5fU), N6-methyladenine (6mA), β-D-glucosyl-5-hydroxymethyluracil (base J) and 8-oxo-7,8-dihydroguanine (OG). This laboratory manual is a valuable source for biochemists and molecular biologists from different fields who wish to investigate DNA modifications.



Editors and Affiliations

  • Department of Chemistry, Wuhan University, Wuhan, China

    Bi-Feng Yuan

About the editor

Dr. Yuan received his bachelor’s degree and PhD degree from Wuhan University in 2001 and 2006, respectively. After completing the postdoctoral research in National University of Singapore (2006-2007, Singapore) and University of California, Riverside (2007-2010, USA), Dr. Yuan started to work as a professor in the College of Chemistry and Molecular Sciences of Wuhan University from 2011. Dr. Yuan’s research focuses on the development and application of new analytical techniques in the investigation of the occurrence, location, and biological functions of nucleic acid modifications. By establishing highly sensitive analytical methods, Dr. Yuan discovered many new types of modifications in nucleic acids. He also revealed the mechanisms of the formation and metabolism of some nucleic acid modifications, which promotes the understanding of the biological functions of nucleic acid modifications.

Bibliographic Information

  • Book Title: DNA Modification Detection Methods

  • Editors: Bi-Feng Yuan

  • Series Title: Springer Protocols Handbooks

  • DOI: https://doi.org/10.1007/978-1-0716-1229-3

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2022

  • Hardcover ISBN: 978-1-0716-1228-6Published: 07 July 2021

  • Softcover ISBN: 978-1-0716-1231-6Published: 07 July 2022

  • eBook ISBN: 978-1-0716-1229-3Published: 06 July 2021

  • Series ISSN: 1949-2448

  • Series E-ISSN: 1949-2456

  • Edition Number: 1

  • Number of Pages: VI, 194

  • Number of Illustrations: 18 b/w illustrations, 30 illustrations in colour

  • Topics: Biomedical Engineering/Biotechnology, Gene Expression, Biological Techniques

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