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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...

Mismatch Repair

Mismatch Repair

Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...

Long-patch Base Excision Repair

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:

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

Proofreading

Proofreading

Synthesis of new DNA molecules is carried out by the enzyme DNA polymerase, which adds nucleotides on the daughter strand complementary to the template DNA strand. DNA polymerase has a higher affinity to add the correct base and ensures fidelity during DNA replication. Furthermore, it exhibits proofreading activity during replication, using an exonuclease domain that cuts off incorrect nucleotides from the nascent DNA strand.
Errors During Replication are Corrected by the DNA Polymerase...

DNA Base Pairing

DNA Base Pairing

Erwin Chargaff’s rules on DNA equivalence paved the way for the discovery of base pairing in DNA. Chargaff’s rules state that in a double-stranded DNA molecule,

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Related Experiment Video

Updated: Jun 22, 2025

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

A modified glycosylase base editor without predictable DNA off-target effects.

Meng Lian^1,2, Tao Chen³, Min Chen³

¹Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.

|July 1, 2024

Summary

A new gene editing tool, TaC9-GBE^YE1, offers safe and efficient C-to-G gene correction for genetic disorders by separating Cas9 and deaminase components, minimizing off-target effects.

Keywords:

Cas9 TALE TaC9 glycosylase base editor off‐target

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Last Updated: Jun 22, 2025

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Functional Assessment of BRCA1 variants using CRISPR-Mediated Base Editors

Published on: February 28, 2021

CIRCLE-Seq for Interrogation of Off-Target Gene Editing

CIRCLE-Seq for Interrogation of Off-Target Gene Editing

Published on: November 1, 2024

Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms

Published on: May 25, 2018

Area of Science:

Molecular Biology
Gene Editing Technologies
Biotechnology

Background:

Glycosylase base editors (GBEs) show promise for treating genetic disorders by enabling C-to-G transversions.
Limitations include low transversion efficiency and Cas9-dependent off-target mutations, hindering clinical translation.

Purpose of the Study:

To develop a novel GBE system with enhanced safety and efficiency.
To eliminate Cas9-dependent off-target effects while maintaining high on-target editing rates.

Main Methods:

Developed TaC9-CBE and TaC9-ABE by separating nCas9 and deaminase components.
Engineered a new GBE, TaC9-GBE^YE1, using a deaminase and UNG-nCas9 guided by TALE and sgRNA.
Evaluated on-target editing efficiency and off-target effects at 19 target sites.

Main Results:

TaC9-GBE^YE1 demonstrated comparable on-target editing efficiency to traditional GBEs.
No Cas9- or TALE-dependent off-target mutations were detected.
The novel system effectively eliminates Cas9-dependent DNA off-target effects.

Conclusions:

TaC9-GBE^YE1 represents a safe and effective gene editing tool for potential therapeutic applications.
Separating nCas9 and deaminase components enhances the safety profile of GBEs.
This technology holds significant promise for the future of gene therapy.