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Long-patch Base Excision Repair01:02

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Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
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In order to be passed through generations, genomic DNA must be undamaged and error-free. However, every day, DNA in a cell undergoes several thousand to a million damaging events by natural causes and external factors. Ionizing radiation such as UV rays, free radicals produced during cellular respiration, and hydrolytic damage from metabolic reactions can alter the structure of DNA. Damages caused include single-base alteration, base dimerization, chain breaks, and cross-linkage.
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In response to DNA damage, cells can pause the cell cycle to assess and repair the breaks. However, the cell must check the DNA at certain critical stages during the cell cycle. If the cell cycle pauses before DNA replication, the cells will contain twice the amount of DNA. On the other hand, if cells arrest after DNA replication but before mitosis, they will contain four times the normal amount of DNA. With a host of specialized proteins at their disposal,cells must use the right protein at...
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Translesion (TLS) polymerases rescue stalled DNA polymerases at sites of damaged bases by replacing the replicative polymerase and installing a nucleotide across the damaged site. Doing so, TLS allows additional time for the cell to repair the damage before resuming regular DNA replication.
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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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Updated: Nov 8, 2025

Optimized Bone Sampling Protocols for the Retrieval of Ancient DNA from Archaeological Remains
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DamageProfiler: fast damage pattern calculation for ancient DNA.

Judith Neukamm1,2,3, Alexander Peltzer2,4, Kay Nieselt2

  • 1Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland.

Bioinformatics (Oxford, England)
|April 23, 2021
PubMed
Summary
This summary is machine-generated.

DamageProfiler software simplifies ancient DNA authentication by analyzing DNA damage patterns. This user-friendly tool, with both graphical and command-line interfaces, aids researchers in verifying ancient sample integrity.

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Area of Science:

  • Ancient DNA Research
  • Bioinformatics Tools
  • Genomic Data Analysis

Background:

  • Authenticating ancient DNA samples is critical for reliable data analysis.
  • Existing methods may require advanced programming skills, limiting accessibility.
  • A user-friendly tool is needed for basic damage authentication in ancient DNA studies.

Purpose of the Study:

  • To introduce DamageProfiler, a software tool for ancient DNA damage pattern analysis.
  • To provide an accessible solution for researchers without extensive programming expertise.
  • To facilitate easy integration of damage authentication into existing analysis pipelines.

Main Methods:

  • Developed DamageProfiler as a Java-based, stand-alone software.
  • Implemented both a graphical user interface (GUI) and a command-line interface (CLI).
  • Made the source code freely available on GitHub for transparency and collaboration.

Main Results:

  • DamageProfiler accurately determines DNA damage patterns in ancient samples.
  • Outputs are provided in versatile file formats and visual plots for downstream analysis.
  • The software's dual interface design ensures ease of use and pipeline integration.

Conclusions:

  • DamageProfiler offers a robust and accessible solution for ancient DNA authentication.
  • The tool empowers researchers to perform essential damage analysis efficiently.
  • Its design supports seamless incorporation into diverse ancient DNA research workflows.