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TdT-dUTP DSB End Labeling (TUDEL), for Specific, Direct In Situ Labeling of DNA Double Strand Breaks

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Biomedical Engineering Technologies

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2394))

Abstract

The genome of a living cell is continuously damaged by various exogenous and endogenous factors yielding multiple types of DNA damage including base damage and damage to the sugar-phosphate backbone of DNA. Double Strand Breaks (DSBs) are the most severe form of DNA damage and if left unchecked, may precipitate genomic rearrangements, cell death or contribute to malignancy. In clinical contexts, radiation is often used to induce DSBs as a form of genotoxic therapy. Despite the importance of DSBs and their repair, as yet there is no facile assay to detect DSBs in situ or to quantify their location or proximity to other cellular constituents. Such an assay would help to disentangle DDR signaling pathways and identify new molecular players involved in DSB repair. These efforts, in turn, may facilitate drug screening and accelerate the discovery of novel, more effective genotoxic agents. We have developed such an assay, presented here, and term it TdT-dUTP DSB End Labeling (TUDEL).

TUDEL makes use of Terminal Deoxynucleotidyl Transferase (TdT), a template-independent DNA polymerase. TdT is commonly used in TUNEL assays to yield a binary output of DNA damage. We have adapted this approach, using TdT and EdUTP to label individual DNA double strand breaks in irradiated cells and detecting the incorporated EdU with fluorescent probes via Click chemistry. This tool complements and is compatible with existing, indirect methods to track DSBs such as immunofluorescent detection of γH2AX. TUDEL is also sufficiently specific, sensitive, quantitative, and robust to replace the neutral Comet assay for routine measurement of DSB formation and repair. Here we present a protocol for TUDEL.

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Acknowledgements

We thank Vytas Bindokas and staff of the Integrated Light Microscopy Core for guidance with conventional and superresolution microscopy and image analysis. This work was funded by NCI IMAT grant R21 CA213247 to S.J.K. and NCI CCSG P30 CA014599 that supports the Integrated Light Microscopy Core. TdT-UTP DSB End Labeling (TUDEL), for Specific, Direct In Situ Labeling of DNA Double Strand Breaks.

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Authors and Affiliations

  1. The Committee on Cancer Biology, The University of Chicago, Chicago, IL, USA

    Julian Lutze

  2. Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL, USA

    Sara E. Warrington

  3. The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA

    Stephen J. Kron

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  1. Julian Lutze
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  2. Sara E. Warrington
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  3. Stephen J. Kron
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Correspondence to Stephen J. Kron .

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Editors and Affiliations

  1. Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA

    Avraham Rasooly

  2. Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA

    Houston Baker

  3. Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, USA

    Miguel R. Ossandon

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Lutze, J., Warrington, S.E., Kron, S.J. (2022). TdT-dUTP DSB End Labeling (TUDEL), for Specific, Direct In Situ Labeling of DNA Double Strand Breaks. In: Rasooly, A., Baker, H., Ossandon, M.R. (eds) Biomedical Engineering Technologies. Methods in Molecular Biology, vol 2394. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1811-0_18

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  • DOI: https://doi.org/10.1007/978-1-0716-1811-0_18

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1810-3

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