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Related Concept Videos

Base Excision Repair01:54

Base Excision Repair

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One of the common DNA damages is the chemical alteration of single bases by alkylation, oxidation, or deamination. The altered bases cause mispairing and strand breakage during replication. This type of damage causes minimal change to the DNA double helix structure and can be repaired by the base excision repair (BER) pathways. BER corrects damaged DNA sequences by removing the damaged base and restoring the original base sequence using the complementary strand as a template.
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DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
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Assessment of Global DNA Double-Strand End Resection using BrdU-DNA Labeling coupled with Cell Cycle Discrimination Imaging
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Base Excision Repair Variants in Cancer.

Carolyn G Marsden1, Julie A Dragon1, Susan S Wallace1

  • 1The Markey Center for Molecular Genetics, University of Vermont, Burlington, VT, United States.

Methods in Enzymology
|June 25, 2017
PubMed
Summary

This study introduces computational and cellular methods to identify and analyze functional phenotypes of base excision repair (BER) gene variants. Understanding these variants is crucial for investigating their role in genome stability and cancer development.

Keywords:
Base excision repairCancerCellular transformationDNA glycosylaseDNA polymeraseGenomic instabilityMutagenesisReplication stress

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Area of Science:

  • Genetics
  • Molecular Biology
  • Cancer Research

Background:

  • Base excision repair (BER) is essential for removing endogenous DNA damage, preventing mutagenesis and chromosomal instability.
  • Accumulated DNA damage and BER dysfunction are linked to carcinogenesis.
  • Genomic sequencing has revealed numerous rare mutations in BER genes.

Purpose of the Study:

  • To present in silico methods for identifying and prioritizing BER variants for functional analysis.
  • To provide detailed protocols for initial cellular assays to dissect BER variant phenotypes.
  • To evaluate the strengths and weaknesses of these analytical approaches.

Main Methods:

  • In silico identification and prioritization of base excision repair (BER) variants.
  • Initial cellular assays for dissecting functional phenotypes of human BER variants.
  • Comparative analysis of assay strengths and weaknesses.

Main Results:

  • Established computational pipeline for BER variant prioritization.
  • Detailed protocols for initial functional characterization of BER variants.
  • Identified key considerations for selecting and interpreting BER variant assays.

Conclusions:

  • Functional characterization of BER variants is critical for understanding their role in genome maintenance.
  • The presented in silico and cellular methods provide a framework for dissecting BER variant phenotypes.
  • Further detailed studies of functionally relevant BER variants can yield mechanistic insights into carcinogenesis.