DNA Modification Detection Methods

1. Front Matter

   Pages i-vi

   PDF

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

   1. Front Matter

      Pages 1-1

      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

3. Detection of 6mA

   1. Front Matter

      Pages 103-103

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   2. Metabolically Generated Stable Isotope for Identification of DNA N⁶-Methyladenine Origin in Cultured Mammalian Cells

      • Baodong Liu, Hailin Wang

      Pages 105-114

   3. Determination of N⁶-Methyladenine in DNA of Mammals and Plants by Dpn I Digestion Combined with Size-Exclusion Ultrafiltration and Mass Spectrometry Analysis

      • Qing-Yun Cheng, Bi-Feng Yuan

      Pages 115-125

4. Detection of 5hmU and 5fU

   1. Front Matter

      Pages 127-127

      PDF

   2. Isotope-Dilution Liquid Chromatography–Tandem Mass Spectrometry for Detection of 5-Hydroxymethyluracil and 5-Formyluracil in DNA

      • Yu Liu, Jin Wang

      Pages 129-139

   3. Detection of 5-Formylcytosine and 5-Formyluracil Based on Photo-Assisted Domino Reaction

      • Qian Zhou, Kun Li, Kang-Kang Yu, Xiao-Qi Yu

      Pages 141-153

   4. Detection of 5-Formyluracil and 5-Formylcytosine in DNA by Fluorescence Labeling

      • Chaoxing Liu

      Pages 155-162

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

   1. Front Matter

      Pages 163-163

      PDF

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

      • Shuo Liu, Yinsheng Wang

      Pages 165-180

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.

• DNA modification
• Detection
• Mapping
• Mass spectrometry
• DNA Sequencing
• gene expression

• Department of Chemistry, Wuhan University, Wuhan, China

  Bi-Feng Yuan

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.

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