Nuclease Catalysis in DNA and RNA Processing

Nucleases are essential enzymes that catalyse the cleavage and remodelling of DNA and RNA, driving processes such as replication, repair, recombination and immune surveillance. These enzymes function as exonucleases or endonucleases, often employing a two-metal-ion mechanism in which divalent cations, typically Mg2+ or Mn2+, activate a water nucleophile and stabilise transition states. Recent structural and kinetic studies have revealed that conserved second-shell residues and transient third-metal ions can fine-tune catalytic efficiency, directionality and substrate specificity. Single-molecule approaches have elucidated dynamic facets of nuclease processivity and pausing, while fluorescence-based assays now permit real-time measurement of cleavage kinetics across diverse substrates. Collectively, these advances underpin applications ranging from precision genome editing and biomarker discovery to the design of novel antimicrobial and anticancer agents, emphasising the global significance of nuclease research.

Research from Nature Portfolio

Investigations into a model exonuclease have demonstrated that the coordination and release of active-site metal ions dictate processivity and transient pausing during DNA degradation. At physiological metal concentrations, one metal remains tightly bound throughout successive cleavages, whereas the second metal cycles on and off, promoting efficient product release and enzyme translocation. In parallel, a universal fluorescence-based toolkit has been developed for real-time quantification of nuclease activity. By employing a substrate library bearing fluorescent reporters, researchers have mapped catalytic rates, determined cleavage directionality and defined substrate preferences across both DNA and RNA nucleases, enabling direct mechanistic comparisons under near-physiological conditions.

Nuclease Catalysis in DNA and RNA Processing publication trend

The graph below shows the total number of articles in nuclease catalysis in dna and rna processing across all publications each year (not limited to Nature Index journals).

Technical terms

Nuclease: an enzyme that cleaves the phosphodiester bonds of nucleic acids.

Exonuclease: a nuclease that removes nucleotides sequentially from the ends of DNA or RNA strands.

Endonuclease: a nuclease that cleaves phosphodiester bonds within the internal region of a nucleic acid chain.

Two-metal-ion mechanism: a catalytic strategy in which two divalent metal ions coordinate the substrate and water molecules to facilitate phosphodiester bond hydrolysis.

Processivity: the capacity of an enzyme to catalyse successive reactions without dissociating from its substrate.

Distributive cleavage: a cleavage mode in which an enzyme dissociates from the substrate after each catalytic event.

References

1. Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes. Structure (2017).
2. Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5′ Structure-Specific Nucleases. Journal of the American Chemical Society (2020).
3. Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis. Nature Communications (2018).
4. A universal fluorescence-based toolkit for real-time quantification of DNA and RNA nuclease activity. Scientific Reports (2019).
5. Nuclease-induced stepwise photodropping (NISP) to precisely investigate single-stranded DNA degradation behaviors of exonucleases and endonucleases. Nucleic Acids Research (2024).
6. RNase H is an exo- and endoribonuclease with asymmetric directionality, depending on the binding mode to the structural variants of RNA:DNA hybrids. Nucleic Acids Research (2021).