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In Vitro Reconstitutive Base Excision Repair (BER) Assay

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Base Excision Repair Pathway

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2701))

Abstract

The mammalian cell genome is continuously exposed to endogenous and exogenous insults that modify its DNA. These modifications can be single-base lesions, bulky DNA adducts, base dimers, base alkylation, cytosine deamination, nitrosation, or other types of base alteration which interfere with DNA replication. Mammalian cells have evolved with a robust defense mechanism to repair these base modifications (damages) to preserve genomic stability. Base excision repair (BER) is the major defense mechanism for cells to remove these oxidative or alkylated single-base modifications. The base excision repair process involves replacement of a single-nucleotide residue by two sub-pathways, the single-nucleotide (SN) and the multi-nucleotide or long-patch (LP) base excision repair pathways. These reactions have been reproduced in vitro using cell free extracts or purified recombinant proteins involved in the base excision repair pathway. In the present chapter, we describe the detailed methodology to reconstitute base excision repair assay systems. These reconstitutive BER assay systems use artificially synthesized and modified DNA. These reconstitutive assay system will be a true representation of biologically occurring damages and their repair.

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Acknowledgments

Robert Hromas is supported by the National Institutes of Health (NIH) R01 CA139429 grants.

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Authors and Affiliations

  1. Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA

    Aruna S. Jaiswal, Elizabeth A. Williamson, Arunima S. Jaiswal, Kimi Kong & Robert A. Hromas

  2. Division of Hematology and Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX, USA

    Aruna S. Jaiswal

Authors
  1. Aruna S. Jaiswal
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  2. Elizabeth A. Williamson
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  3. Arunima S. Jaiswal
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  4. Kimi Kong
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  5. Robert A. Hromas
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Corresponding author

Correspondence to Aruna S. Jaiswal .

Editor information

Editors and Affiliations

  1. Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA

    Kishor K. Bhakat

  2. Department of Internal Medicine, The University of Texas Medical Branch, Galveston, TX, USA

    Tapas K. Hazra

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© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature

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Jaiswal, A.S., Williamson, E.A., Jaiswal, A.S., Kong, K., Hromas, R.A. (2023). In Vitro Reconstitutive Base Excision Repair (BER) Assay. In: Bhakat, K.K., Hazra, T.K. (eds) Base Excision Repair Pathway. Methods in Molecular Biology, vol 2701. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3373-1_6

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  • DOI: https://doi.org/10.1007/978-1-0716-3373-1_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-3372-4

  • Online ISBN: 978-1-0716-3373-1

  • eBook Packages: Springer Protocols

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