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Base Excision Repair

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...

Fixing Double-strand Breaks

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

Restarting Stalled Replication Forks

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...

Base Excision Repair

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...

Homologous Recombination

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...

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Related Experiment Video

Updated: Jul 12, 2026

Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy

Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy

Published on: June 8, 2018

The RCAF complex mediates chromatin assembly during DNA replication and repair.

J K Tyler¹, C R Adams, S R Chen

¹Department of Biology and Center for Molecular Genetics, University of California at San Diego, La Jolla 92093-0347, USA.

|December 11, 1999

Summary

Researchers identified a new protein complex, replication-coupling assembly factor (RCAF), crucial for building nucleosomes on replicated DNA. RCAF, containing ASF1 and histones H3/H4, is vital for cell cycle progression and DNA repair.

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Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

Related Experiment Videos

Last Updated: Jul 12, 2026

Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy

Characterizing DNA Repair Processes at Transient and Long-lasting Double-strand DNA Breaks by Immunofluorescence Microscopy

Published on: June 8, 2018

Visualization of DNA Repair Proteins Interaction by Immunofluorescence

Visualization of DNA Repair Proteins Interaction by Immunofluorescence

Published on: June 26, 2020

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Using Next Generation Sequencing to Identify Mutations Associated with Repair of a CAS9-induced Double Strand Break Near the CD4 Promoter

Published on: March 31, 2022

Area of Science:

Molecular Biology
Genetics
Cell Biology

Background:

Chromatin assembly is essential for eukaryotic genome replication and maintenance.
Nucleosomes, the basic units of chromatin, are formed by specific histone proteins (H3, H4, H2A, H2B).
Efficient chromatin assembly is critical during cell division.

Purpose of the Study:

To identify and characterize novel factors involved in chromatin assembly.
To investigate the role of the replication-coupling assembly factor (RCAF) in nucleosome formation.
To understand RCAF's function in DNA replication and repair.

Main Methods:

Purification and cloning of the RCAF complex.
Biochemical characterization of RCAF composition and histone acetylation patterns.
Genetic analysis in Saccharomyces cerevisiae to assess ASF1 function.

Main Results:

Identification and purification of RCAF, a novel protein complex.
RCAF consists of the anti-silencing function 1 (ASF1) protein and histones H3/H4.
ASF1 is essential for cell cycle progression, and RCAF facilitates chromatin assembly post-replication and DNA repair.

Conclusions:

RCAF is a key factor mediating chromatin assembly coupled to DNA replication.
ASF1, a component of RCAF, plays a critical role in cell cycle progression.
RCAF is implicated in both DNA replication-coupled chromatin assembly and DNA double-strand break repair.