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Cited by 692Enzyme Structure and FunctionDNA and Nucleic Acid ChemistryChemical Reaction Mechanisms

Nucleases: diversity of structure, function and mechanism

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Yang, Wei·2011·Quarterly Reviews of Biophysics
DOI 10.1017/s0033583510000181PMC PMC6320257
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Abstract

Nucleases cleave the phosphodiester bonds of nucleic acids and may be endo or exo, DNase or RNase, topoisomerases, recombinases, ribozymes, or RNA splicing enzymes. In this review, I survey nuclease activities with known structures and catalytic machinery and classify them by reaction mechanism and metal-ion dependence and by their biological function ranging from DNA replication, recombination, repair, RNA maturation, processing, interference, to defense, nutrient regeneration or cell death. Several general principles emerge from this analysis. There is little correlation between catalytic mechanism and biological function. A single catalytic mechanism can be adapted in a variety of reactions and biological pathways. Conversely, a single biological process can often be accomplished by multiple tertiary and quaternary folds and by more than one catalytic mechanism. Two-metal-ion-dependent nucleases comprise the largest number of different tertiary folds and mediate the most diverse set of biological functions. Metal-ion-dependent cleavage is exclusively associated with exonucleases producing mononucleotides and endonucleases that cleave double- or single-stranded substrates in helical and base-stacked conformations. All metal-ion-independent RNases generate 2',3'-cyclic phosphate products, and all metal-ion-independent DNases form phospho-protein intermediates. I also find several previously unnoted relationships between different nucleases and shared catalytic configurations.

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  • Nucleases cleave the phosphodiester bonds between nucleotides of nucleic acids, facilitating the removal of nucleic materials following cell rupture.

    “Nucleases cleave the phosphodiester bonds between nucleotides of nucleic acids (DNA and RNA), facilitating the removal of nucleic materials following cell rupture [151].”

    From Liver tissue engineering using decellularized scaffolds: Current progress, challenges, and opportunities (2024) · cites this paper as [151]

    The Basic chemistry section states that nucleases cleave phosphodiester bonds in nucleic acids, and the Introduction identifies DNA and RNA as substrates. The Introduction also links nuclease activity to removal of endogenously produced nucleic acids, but it does not specify removal following cell rupture. Page numbers are unavailable in our copy. (LLM, conf=0.86)

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Authors
Yang, W.
Affiliations
National Institutes of Health (US)
Corresponding author
Yang, Wei
ORCID
Yang, Wei
Venue
Quarterly Reviews of Biophysics
Publisher
Cambridge University Press (CUP)
Published
2010-09-21
Volume
44
Issue
1
Pages
1-93
ISSN
  • 0033-5835 (ISSN-L)
  • 1469-8994
DOI
10.1017/s0033583510000181
PMC
PMC6320257
OpenAlex
W2118022632
Cited by
692
References
10
Citations by year
2026: 60 · 2025: 63 · 2024: 84 · 2023: 55 · 2022: 76 · 2021: 57 · 2020: 55 · 2019: 37 · 2018: 21 · 2017: 35 · 2016: 23 · 2015: 25 · 2014: 33 · 2013: 31 · 2012: 25
FWCI
1.04
Type
journal article
Language
en
Open access
Licence
www.cambridge.org/core/terms (unspecified)
Locations
  • Quarterly Reviews of Biophysics (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Institute of Diabetes and Digestive and Kidney Diseases (Z01DK036145, Z01DK036119, Z01DK036144, ZIADK036144)
Topics
  • Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
  • Physical Sciences › Chemistry › Organic Chemistry › Chemical Reaction Mechanisms
Keywords
nucleases, endonuclease, exonuclease, DNase, ribonuclease, topoisomerases, recombinases, ribozymes, phosphodiester bond cleavage, DNA replication, DNA repair, RNA processing
MeSH terms
Animals, DNA, Esterases, Humans, Metals, RNA

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