Exonuclease
Exonuclease - Related Videos
06:10
A Fluorescence-based Exonuclease Assay to Characterize DmWRNexo, Orthologue of Human Progeroid WRN Exonuclease, and Its Application to Other Nucleases
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Cited by 4 •
2013
Exonucleases play critical roles in ensuring genome stability. Loss of WRN exonuclease function results in premature aging. Studying substrates and other requirements of the nuclease in vitro can help elucidate its role in vivo. Here we demonstrate a rapid and reproducible fluorescence-based assay to measure its nuclease activity.
08:11
Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates
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Cited by 2 •
2022
Presented here is a protocol for the preparation and buffer calibration of cell extracts from exonuclease V knockout strains of Escherichia coli BL21 Rosetta2 (ΔrecBCD and ΔrecB). This is a fast, easy, and direct approach for expression in cell-free protein synthesis systems using linear DNA templates.
08:40
High-Resolution Mapping of Protein-DNA Interactions in Mouse Stem Cell-Derived Neurons using Chromatin Immunoprecipitation-Exonuclease (ChIP-Exo)
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Cited by 2 •
2020
Precise determination of protein-binding locations across the genome is important for understanding gene regulation. Here we describe a genomic mapping method that treats chromatin-immunoprecipitated DNA with exonuclease digestion (ChIP-exo) followed by high-throughput sequencing. This method detects protein-DNA interactions with near base-pair mapping resolution and high signal-to-noise ratio in mammalian neurons.
14:26
Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
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Cited by 59 •
2016
This paper presents a sensitive method called Circle-Seq for purifying extrachromosomal circular DNA (eccDNA). The method encompasses column purification, removal of remaining linear chromosomal DNA, rolling-circle amplification and high-throughput sequencing. Circle-Seq is applicable to genome-scale screening of eukaryotic eccDNA and studying genome instability and copy-number variation.
02:51
mRNA Stability and Gene Expression
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2020
The structure and stability of mRNA molecules regulates gene expression, as mRNAs are a key step in the pathway from gene to protein. In eukaryotes, the half-life of mRNA varies from a few minutes up to several days. mRNA stability is essential in growth and development. The absence of the proteins regulating its stability, such as tristetraprolin in mice, can cause systemic issues, including bone marrow overgrowth, inflammation, and autoimmunity. Cis-acting Elements involved in mRNA stability
FAQs
Directionality determines which terminus an exonuclease can recognize and which nucleotide is removed first. Enzymes acting from the 5′ end process the strand toward its opposite end, whereas 3′-directed activity proceeds in the reverse orientation. This distinction helps control DNA or RNA shortening during proofreading, replication-fork processing, repair, recombination, and RNA turnover.
Exonuclease activity depends on more than the presence of DNA or RNA. The enzyme may require an exposed terminus or a particular end structure before sequential removal can begin, and cofactors can support the reaction. These requirements provide selectivity, allowing nucleic acid processing to occur on suitable substrates rather than indiscriminately shortening every strand.
Substrate specificity determines which nucleic acid and end configuration an exonuclease can process. Differences in DNA or RNA substrate recognition, strand termini, and required reaction conditions can restrict activity to particular targets. Consequently, exonucleases perform specialized roles in nucleic acid maintenance instead of producing one uniform processing outcome across all cellular substrates.
Controlled exonuclease activity supports several stages of nucleic acid metabolism. In DNA, it contributes to proofreading, replication-fork processing, repair, and recombination, where selective shortening helps prepare or refine nucleic acid structures. In RNA biology, related activity participates in maturation or degradation, linking terminal processing to both RNA function and removal.
In molecular biology, exonucleases provide controlled removal of unwanted nucleic acid components. Their activity supports sequence cleanup, primer removal, and preparation of DNA or RNA substrates for analysis. The appropriate enzyme is selected according to substrate specificity, end requirements, and processing direction, so the treatment changes the nucleic acid sample in a defined way.
Exonuclease treatment can produce nucleic acid substrates with altered length or terminal composition, creating material suitable for subsequent analysis. Because removal proceeds sequentially from an end, the outcome reflects the enzyme’s direction, substrate preference, and required end structure. Such controlled processing helps researchers examine or prepare DNA and RNA rather than merely degrade them nonspecifically.