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Related Concept Videos

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...
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...
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:
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...
Nucleotide Excision Repair01:08

Nucleotide Excision Repair

Overview
Nucleotide Excision Repair01:08

Nucleotide Excision Repair

Overview

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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

Base sequence context effects on nucleotide excision repair.

Yuqin Cai1, Dinshaw J Patel, Suse Broyde

  • 1Department of Biology, New York University, New York, NY 10003, USA.

Journal of Nucleic Acids
|September 28, 2010
PubMed
Summary

Disturbed DNA base pairing, not DNA bending, signals bulky lesions like benzo[a]pyrene for crucial genome repair. Sequence context impacts lesion recognition for nucleotide excision repair (NER) to prevent mutations and cancer.

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Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair
10:59

Atomic Force Microscopy Investigations of DNA Lesion Recognition in Nucleotide Excision Repair

Published on: May 24, 2017

Area of Science:

  • Molecular Biology
  • Genetics
  • Biochemistry

Background:

  • Nucleotide excision repair (NER) is vital for genomic integrity, removing bulky DNA lesions to prevent mutations and diseases like cancer.
  • Understanding how DNA lesion structure influences NER is crucial for disease prevention.

Purpose of the Study:

  • To investigate the structural determinants of DNA lesion recognition by NER.
  • To examine the role of sequence context on the repair of benzo[a]pyrene-induced DNA damage.

Main Methods:

  • Utilized Nuclear Magnetic Resonance (NMR) and Molecular Dynamics (MD) simulations for structural analysis.
  • Assessed DNA bending using gel electrophoresis.
  • Quantified NER efficiency using human HeLa cell extracts.

Main Results:

  • Disturbed Watson-Crick base pairing emerged as a stronger recognition signal for NER than DNA flexibility.
  • Steric hindrance between the benzo[a]pyrene lesion and guanine amino groups dictates lesion distortion.
  • Both immediate and distant DNA sequence contexts influence lesion recognition and repair.

Conclusions:

  • NER likely recognizes DNA damage through local thermodynamic destabilization signals arising from structural distortions.
  • Disturbed base pairing, influenced by sequence context, is a key factor in NER's recognition of bulky DNA lesions.
  • This research provides insights into DNA repair mechanisms relevant to environmental mutagenesis and cancer.