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

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Abstract

Chemical modifications of DNA bases have a major effect on the execution of the DNA code. The global amount of DNA modifications provides valuable information regarding various biological processes as well as for disease development. Therefore, development of simple and reliable methods to quantify these markers is of great importance. Here we describe in detail protocols for global quantification of DNA modifications. Specifically, we describe quantification of two types of epigenetic modifications, unmethylated CpGs and 5-hydroxymethylcytosine (5-hmC), and two types of DNA damage lesions, oxidation and UV-induced damage. All methods are based on utilizing enzymatic recognition for covalent binding of a fluorescent dye to the DNA modification. Up to 90 labeled DNA samples are then loaded on a custom multi-well slide, which is imaged by a conventional slide scanner. The global amount of the measured modification can be calculated by the obtained fluorescence intensity.

Keywords

  • 5-Methylcytosine
  • 5-Hydroxymethylcytosine
  • Single-strand DNA damage
  • Oxidation DNA damage
  • UV DNA damage
  • Single-strand breaks
  • DNA modifications
  • Multi-well slide
  • Fluorescent labeling

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  • DOI: 10.1007/978-1-0716-1229-3_4
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Acknowledgments

The authors acknowledge financial support from the BeyondSeq Consortium (EC program 634890), the European Research Council Proof of Concept grant by the EU-Horizon2020 program (grant no. 767931), the European Research Council Consolidator grant (grant No. 817811), the NIH R21 grant (R21ES028015-011), and the Joint Israeli German R&D Nanotechnology (grant no. 61976).

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Correspondence to Yael Michaeli or Yuval Ebenstein .

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Michaeli, Y. et al. (2022). Simple Quantification of Epigenetic DNA Modifications and DNA Damage on Multi-Well Slides. In: Yuan, BF. (eds) DNA Modification Detection Methods . Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1229-3_4

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  • DOI: https://doi.org/10.1007/978-1-0716-1229-3_4

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1228-6

  • Online ISBN: 978-1-0716-1229-3

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