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), -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.
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
5hydroxymethylcytosine 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 N6methyladenine 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
-D-glucosyl-5-hydroxymethyluracil in genomic DNA.
Chapter16. Determination
of 8-oxo-7,8-dihydroguanine in DNA at single-base resolution by
polymerase-mediated differential coding.
Dr. Yuan received his bachelors 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. Yuans 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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