Repair Fidelity Sequencing
Repair Fidelity Sequencing - Related Videos
18:10
Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
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Cited by 40 •
2011
The present article describes the steps required to isolate and characterize RNA polymerase fidelity variants of RNA viruses and how to use mutation frequency data to confirm fidelity changes in tissue culture.
02:25
Overview of DNA Repair
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2020
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...
13:10
Analysis of DNA Double-strand Break (DSB) Repair in Mammalian Cells
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Cited by 116 •
2010
This article describes GFP-based fluorescence in vivo assays that separately quantify homologous recombination and nonhomologous end joining in mammalian cells.
08:57
Amplicon Sequencing using the Long-Read Sequencing Technologies
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2025
This protocol was optimized for targeted deep sequencing of 18 drug-resistance regions in Mycobacterium tuberculosis using a long-read sequencing platform, followed by analysis with a tuberculosis-specific bioinformatics pipeline designed for long-read data.
01:54
Base Excision Repair
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2020
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...
FAQs
Accuracy is assessed by comparing recovered sequences with the intended sequence of the repair substrate. Reads that match the expected product represent precise restoration, whereas substitutions, insertions, deletions, and other sequence changes indicate altered outcomes. This classification converts sequencing data into a repair-fidelity profile, allowing researchers to characterize the genetic errors associated with a defined lesion.
Defined lesions or substrates provide a controlled starting point for evaluating repair. Because the initial DNA alteration is specified, sequence changes detected after cellular processing can be related to the repair event rather than an unknown source of damage. This design supports meaningful comparisons between repair mechanisms, cellular conditions, and experimental treatments.
The repair pathways available in a cell and the surrounding cellular conditions can influence whether damage is restored precisely or produces sequence changes. Differences in these factors may shift the balance among accurate repair, nucleotide substitutions, insertions, and deletions. Examining those shifts helps connect cellular biology with genome stability and mutagenic outcomes.
Repair-fidelity profiles show how different repair mechanisms handle the same or comparable DNA alterations. A profile enriched for precise restoration suggests greater genetic accuracy, while specific classes of substitutions or indels identify mutagenic outcomes. Comparing these patterns helps researchers investigate pathway behavior and determine how repair contributes to maintaining or disrupting genome stability.
The workflow begins by introducing a defined DNA lesion or repair substrate into a biological system. The system is then given an opportunity to process the alteration through cellular repair. DNA products are analyzed with high-throughput sequencing, and the resulting sequences are classified according to precise restoration, substitutions, insertions, deletions, or other changes.
This approach is useful when researchers need to compare DNA repair mechanisms, characterize mutagenic outcomes, or examine changes in genome maintenance. It can also support studies of disease-associated repair defects and evaluations of treatments that affect repair accuracy. The resulting profiles provide sequence-level evidence for how specific conditions influence genetic fidelity.