DNA Modification Detection Methods

ISBN-13: 9781071612316 / Angielski / Miękka / 2022

Yuan, Bi-Feng

Opis

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.

Spis treści

Part 1. Detection of 5mC, 5hmC, 5fC, and 5caC.- Chapter 1. Quantitative assessment of the oxidation products of 5-methylcytosine in DNA by liquid chromatography-tandem mass spectrometry.- Chapter 2. Determination of cytosine modifications in DNA by chemical labeling-mass spectrometry analysis.- Chapter 3. Analysis of 5-methylcytosine and 5-hydroxymethylcytosine in genomic DNA by capillary electrophoresis-mass spectrometry.- Chapter 4. Simple quantification of epigenetic DNA modifications and DNA damage on multi-well slides.- Chapter 5. Label-free and immobilization-free electrochemical magnetobiosensor for sensitive detection of 5-hydroxymethylcytosine in genomic DNA.- Chapter 6. Electrochemical assay for continuous monitoring of dynamic DNA methylation process.- Chapter 7. Electrogenerated chemiluminescence method for determination of 5‑hydroxymethylcytosine in DNA.- Chapter 8. Quantification of site-specific 5-formylcytosine by integrating peptide nucleic acid-clamped ligation with loop-mediated isothermal amplification.- Chapter 9. Global DNA methylation analysis using methylcytosine dioxygenase.- Part 2. Detection of 6mA.- Chapter 10. Metabolically generated stable isotope for identification of DNA N6-methyladenine origin in cultured mammalian cells.- Chapter 11. Determination of N6‑methyladenine in DNA of mammals and plants by Dpn I digestion combined with size-exclusion ultrafiltration and mass spectrometry analysis.- Part 3. Detection of 5hmU and 5fU.- Chapter 12. Isotope-dilution liquid chromatography-tandem mass spectrometry for detection of 5-hydroxymethyluracil and 5-formyluracil in DNA.- Chapter 13. Detection of 5 Formylcytosine and 5 Formyluracil based on Photo-assisted Domino Reaction.- Chapter 14. Detection of 5-formyluracil and 5-formylcytosine in DNA by fluorescence labelling.- Part 4. Detection of Base J and 8-oxo-7, 8-dihydroguanine.- Chapter 15. Mass spectrometry-based quantification of β-D-glucosyl-5-hydroxymethyluracil in genomic DNA.- Chapter 16. Determination of 8-oxo-7,8-dihydroguanine in DNA at single-base resolution by polymerase-mediated differential coding.

O autorze

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.