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Related Concept Videos

Nucleotide Excision Repair01:08

Nucleotide Excision Repair

Overview
Nucleotide Excision Repair01:38

Nucleotide Excision Repair

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...
Overview of DNA Repair02:25

Overview of DNA Repair

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.
Chemically...
Overview of DNA Repair02:25

Overview of DNA Repair

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.
Chemically...
Long-patch Base Excision Repair01:02

Long-patch Base Excision Repair

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:
Base Excision Repair01:54

Base Excision Repair

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.
The first step of...

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Related Experiment Video

Updated: Jun 5, 2026

Visualizing and Quantifying Endonuclease-Based Site-Specific DNA Damage
10:59

Visualizing and Quantifying Endonuclease-Based Site-Specific DNA Damage

Published on: August 21, 2021

DamageFormer: a damage-aware multimodal deep learning framework for DNA lesion identification from nanopore

Qiang Yang1, Lin Li1, Qin Ma2

  • 1Department of Health Outcomes and Biomedical Informatics, College of Medicine, University of Florida, Gainesville, FL 32610, USA.

Biorxiv : the Preprint Server for Biology
|June 4, 2026
PubMed
Summary

We developed DamageFormer, a deep learning tool for precise DNA lesion detection using nanopore sequencing. This framework accurately maps DNA damage, advancing cancer research and aging studies.

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In vitro Assembly of Semi-artificial Molecular Machine and its Use for Detection of DNA Damage
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Published on: January 11, 2012

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Last Updated: Jun 5, 2026

Visualizing and Quantifying Endonuclease-Based Site-Specific DNA Damage
10:59

Visualizing and Quantifying Endonuclease-Based Site-Specific DNA Damage

Published on: August 21, 2021

In vitro Assembly of Semi-artificial Molecular Machine and its Use for Detection of DNA Damage
08:56

In vitro Assembly of Semi-artificial Molecular Machine and its Use for Detection of DNA Damage

Published on: January 11, 2012

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • DNA lesions are key drivers of mutagenesis, aging, and cancer.
  • Accurate mapping of DNA damage at nucleotide resolution is challenging.
  • Nanopore sequencing offers direct detection of chemical modifications but current computational methods lack generalization.

Purpose of the Study:

  • To present DamageFormer, a multimodal deep learning framework for DNA lesion detection and localization using nanopore sequencing data.
  • To improve the representation of chemically modified bases and integrate sequence context with signal information.

Main Methods:

  • Developed LesionBERT, a damage-aware genomic foundation model based on DNABERT-2.
  • Integrated LesionBERT with a neural signal model via an adaptive gating mechanism for multimodal fusion.
  • Trained the model using joint prediction, localization, and contrastive alignment losses.

Main Results:

  • DamageFormer achieved an AUROC of 0.99997 for lesion detection and a mean absolute localization error of 0.00439 on an oxidative DNA damage benchmark.
  • The model demonstrated context-dependent modality weighting, adapting to signal quality and sequence ambiguity.
  • The framework generalized to unseen guanine lesions, showing robustness and transferability.

Conclusions:

  • DamageFormer enables accurate and interpretable identification of DNA lesions from nanopore sequencing data.
  • This framework offers a scalable approach for characterizing genome-wide DNA damage landscapes.
  • The study highlights the integration of chemical DNA information into genomic language models.