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Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates
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The Increasing Role of QM/MM in Drug Discovery
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Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis
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On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family
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Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
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Making and Breaking Nucleic Acids: Two-Mg2+-Ion Catalysis and Substrate Specificity
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Crystal Structures of RNase H2 in Complex with Nucleic Acid Reveal the Mechanism of RNA-DNA Junction Recognition and Cleavage
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Investigating biological systems using first principles Car–Parrinello molecular dynamics simulations
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Nucleases: diversity of structure, function and mechanism
inferredcites →https://doi.org/10.1021/ar010018uopenalex-snapshot
The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems
inferredcites →https://doi.org/10.1021/ar040198iopenalex-snapshot
Metadynamics as a Tool for Exploring Free Energy Landscapes of Chemical Reactions
inferredcites →https://doi.org/10.1021/bi0499056openalex-snapshot
DNA Cleavage by EcoRV Endonuclease: Two Metal Ions in Three Metal Ion Binding Sites
inferredcites →https://doi.org/10.1021/bi9828932openalex-snapshot
Metal Ion Catalysis of RNA Cleavage by the Influenza Virus Endonuclease
inferredcites →https://doi.org/10.1021/cr200325fopenalex-snapshot
Contemporary Challenges in the Design of Topoisomerase II Inhibitors for Cancer Chemotherapy
inferredcites →https://doi.org/10.1021/cr4004665openalex-snapshot
Competition among Metal Ions for Protein Binding Sites: Determinants of Metal Ion Selectivity in Proteins
inferredcites →https://doi.org/10.1021/ct050066qopenalex-snapshot
Double-Metal-Ion/Single-Metal-Ion Mechanisms of the Cleavage Reaction of Ribozymes: First-Principles Molecular Dynamics Simulations of a Fully Hydrated Model System
inferredcites →https://doi.org/10.1021/ct300691uopenalex-snapshot
Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase
inferredcites →https://doi.org/10.1021/ja053049jopenalex-snapshot
Computational Study of Phosphatase Activity in Soluble Epoxide Hydrolase: High Efficiency through a Water Bridge Mediated Proton Shuttle
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Role of Zinc Content on the Catalytic Efficiency of B1 Metallo β-Lactamases
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Proton Shuttles and Phosphatase Activity in Soluble Epoxide Hydrolase
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Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?
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Catalytic Mechanism of RNA Backbone Cleavage by Ribonuclease H from Quantum Mechanics/Molecular Mechanics Simulations
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Differential Role of the Protein Matrix on the Binding of a Catalytic Aspartate to Mg2+ vs Ca2+: Application to Ribonuclease H
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Calcium Inhibition of Ribonuclease H1 Two-Metal Ion Catalysis
inferredcites →https://doi.org/10.1021/ja8005786openalex-snapshot
Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism
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Two-Metal-Ion Mechanism for Hammerhead-Ribozyme Catalysis
inferredcites →https://doi.org/10.1021/jp408383gopenalex-snapshot
Magnesium-Dependent RNA Binding to the PA Endonuclease Domain of the Avian Influenza Polymerase
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Three-dimensional structure of ribonuclease H from E. coli
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Specific recognition of RNA/DNA hybrid and enhancement of human RNase H1 activity by HBD
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Crystal structure of an avian influenza polymerase PAN reveals an endonuclease active site
inferredcites →https://doi.org/10.1038/nature08300openalex-snapshot
Metalloproteins and metal sensing
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Design of functional metalloproteins
inferredcites →https://doi.org/10.1038/nature08974openalex-snapshot
A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases
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Structure and mechanism of human DNA polymerase η
inferredcites →https://doi.org/10.1038/nature11181openalex-snapshot
Watching DNA polymerase η make a phosphodiester bond
inferredcites →https://doi.org/10.1038/nsmb.1502openalex-snapshot
An equivalent metal ion in one- and two-metal-ion catalysis
inferredcites →https://doi.org/10.1038/nsmb.1779openalex-snapshot
Structures of influenza A proteins and insights into antiviral drug targets
inferredcites →https://doi.org/10.1038/nsmb.2932openalex-snapshot
Visualizing phosphodiester-bond hydrolysis by an endonuclease
inferredcites →https://doi.org/10.1038/sj.emboj.7601076openalex-snapshot
Stepwise analyses of metal ions in RNase H catalysis from substrate destabilization to product release
inferredcites →https://doi.org/10.1039/c001097aopenalex-snapshot
Atomistic details of the associative phosphodiester cleavage in human ribonuclease H
inferredcites →https://doi.org/10.1073/pnas.0603468104openalex-snapshot
Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV
inferredcites →https://doi.org/10.1073/pnas.1303126110openalex-snapshot
Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η
inferredcites →https://doi.org/10.1073/pnas.90.14.6498openalex-snapshot
A general two-metal-ion mechanism for catalytic RNA.
inferredcites →https://doi.org/10.1074/jbc.c200664200openalex-snapshot
Why Do Divalent Metal Ions Either Promote or Inhibit Enzymatic Reactions?
inferredcites →https://doi.org/10.1074/jbc.m009626200openalex-snapshot
Co-crystal of Escherichia coli RNase HI with Mn2+ Ions Reveals Two Divalent Metals Bound in the Active Site
inferredcites →https://doi.org/10.1093/emboj/cdg193openalex-snapshot
Unified two‐metal mechanism of RNA synthesis and degradation by RNA polymerase
inferredcites →https://doi.org/10.1111/j.1742-4658.2009.06909.xopenalex-snapshot
Ribonuclease H: properties, substrate specificity and roles in retroviral reverse transcription
inferredcites →https://doi.org/10.1126/science.1114994openalex-snapshot
Structural Evidence for a Two-Metal-Ion Mechanism of Group I Intron Splicing
inferredcites →https://doi.org/10.1126/science.1204117openalex-snapshot
Structural Basis of Type II Topoisomerase Inhibition by the Anticancer Drug Etoposide
inferredcites →https://doi.org/10.1371/journal.pone.0011338openalex-snapshot
Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases
inferredcites →https://doi.org/10.1371/journal.ppat.1002830openalex-snapshot
Structural and Biochemical Basis for Development of Influenza Virus Inhibitors Targeting the PA Endonuclease
inferredcites →https://doi.org/10.1371/journal.ppat.1002831openalex-snapshot
Structural Analysis of Specific Metal Chelating Inhibitor Binding to the Endonuclease Domain of Influenza pH1N1 (2009) Polymerase
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Bridging quantum mechanics and structure-based drug design
inferredcites →https://doi.org/10.3109/10409238.2010.513375openalex-snapshot
Topoisomerases and site-specific recombinases: similarities in structure and mechanism
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inferred← citeshttps://doi.org/10.1021/jacs.2c11713openalex-snapshot
Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity
inferred← citeshttps://doi.org/10.1021/jacs.3c13981openalex-snapshot
Flexibility of Binding Site is Essential to the Ca2+ Selectivity in EF-Hand Calcium-Binding Proteins
inferred← citeshttps://doi.org/10.1021/jacs.5c05888openalex-snapshot
Coordinated Residue Motions at the Enzyme–Substrate Interface Promote DNA Translocation in Polymerases
inferred← citeshttps://doi.org/10.1021/jacs.6b01363openalex-snapshot
Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
inferred← citeshttps://doi.org/10.1021/jacs.6b05475openalex-snapshot
A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases
inferred← citeshttps://doi.org/10.1021/jacs.6c06167openalex-snapshot
Mg2+ Catalyzes Nonenzymatic RNA Primer Extension through a Concerted Outer-Sphere Mechanism
inferred← citeshttps://doi.org/10.1021/jacs.6c08579openalex-snapshot
Origins of Reactivity in SAM-Utilizing Ribozyme SAMURI-Catalyzed RNA Alkylation
inferred← citeshttps://doi.org/10.1021/jacs.7b05313openalex-snapshot
Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9
inferred← citeshttps://doi.org/10.1021/jacs.7b12446openalex-snapshot
A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases
inferred← citeshttps://doi.org/10.1021/jacs.9b03193openalex-snapshot
GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases
inferred← citeshttps://doi.org/10.1021/jacs.9b03663openalex-snapshot
A Transient and Flexible Cation?? Interaction Promotes Hydrolysis of Nucleic Acids in DNA and RNA Nucleases
inferred← citeshttps://doi.org/10.1021/jacs.9b03986openalex-snapshot
Unveiling a Single-Metal-Mediated Phosphodiester Bond Cleavage Mechanism for Nucleic Acids: A Multiscale Computational Investigation of a Human DNA Repair Enzyme
inferred← citeshttps://doi.org/10.1021/jacs.9b09269openalex-snapshot
DOTA-Branched Organic Frameworks as Giant and Potent Metal Chelators
inferred← citeshttps://doi.org/10.1021/jacs.9b10656openalex-snapshot
Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5′ Structure-Specific Nucleases
inferred← citeshttps://doi.org/10.1038/s41467-017-01496-2openalex-snapshot
Structural insights into DNA cleavage activation of CRISPR-Cas9 system
inferred← citeshttps://doi.org/10.1038/s41467-018-06750-9openalex-snapshot
Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis
inferred← citeshttps://doi.org/10.1038/s41467-023-39105-0openalex-snapshot
An unnatural enzyme with endonuclease activity towards small non-coding RNAs
inferred← citeshttps://doi.org/10.1038/s41467-024-47506-yopenalex-snapshot
RNA targeting and cleavage by the type III-Dv CRISPR effector complex
inferred← citeshttps://doi.org/10.1038/s41565-025-02114-9openalex-snapshot
Rational design of rigid mRNA folding architecture to enhance intracellular processing and protein production
inferred← citeshttps://doi.org/10.1038/s41598-025-04773-zopenalex-snapshot
Tetrahydropyrido[4,3-d]pyrimidines as a new active scaffold for human topoisomerase II inhibitors
inferred← citeshttps://doi.org/10.1038/s41929-022-00848-6openalex-snapshot
Principles of target DNA cleavage and the role of Mg2+ in the catalysis of CRISPR–Cas9
inferred← citeshttps://doi.org/10.1038/srep25448openalex-snapshot
Mechanism of Ribonuclease III Catalytic Regulation by Serine Phosphorylation
inferred← citeshttps://doi.org/10.1039/9781788010139-00165openalex-snapshot
Molecular Modelling of Nucleic Acids
inferred← citeshttps://doi.org/10.1039/9781788010139-00317openalex-snapshot
Molecular Modelling and Simulations Applied to Challenging Drug Discovery Targets
inferred← citeshttps://doi.org/10.1039/9781837671328-00096openalex-snapshot
Nucleosides and Nucleotides
inferred← citeshttps://doi.org/10.1039/c5cc05065kopenalex-snapshot
An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512
inferred← citeshttps://doi.org/10.1039/c5cc10212jopenalex-snapshot
Isotope effect analyses provide evidence for an altered transition state for RNA 2′-O-transphosphorylation catalyzed by Zn 2+
inferred← citeshttps://doi.org/10.1039/d2cp04338fopenalex-snapshot
The metal dependence of single-metal mediated phosphodiester bond cleavage: a QM/MM study of a multifaceted human enzyme
inferred← citeshttps://doi.org/10.1039/d2nj06127aopenalex-snapshot
Tailor-made isostructural copper( ii ) and nickel( ii ) complexes with a newly designed ( N , N )-donor scaffold as functional mimics of alkaline phosphatase
inferred← citeshttps://doi.org/10.1039/d3cp06201eopenalex-snapshot
Elucidation of the catalytic mechanism of a single-metal dependent homing endonuclease using QM and QM/MM approaches: the case study of I- Ppo I
inferred← citeshttps://doi.org/10.1073/pnas.1707645114openalex-snapshot
CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
inferred← citeshttps://doi.org/10.1073/pnas.1817041116openalex-snapshot
Two symmetric arginine residues play distinct roles in Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage
inferred← citeshttps://doi.org/10.1080/07391102.2022.2103032openalex-snapshot
Implementing accelerated dynamics to unravel the effects of high-fidelity Cas9 mutants on target DNA and guide RNA hybrid stability
inferred← citeshttps://doi.org/10.1088/2516-1075/acb410openalex-snapshot
The electronic structure of genome editors from the first principles
inferred← citeshttps://doi.org/10.1093/mtomcs/mfag027openalex-snapshot
Specificity and regulatory mechanism of metal ions in Cas12a enzymatic cleavage activity
inferred← citeshttps://doi.org/10.1093/nar/gkac1199openalex-snapshot
Trypanosoma brucei RRP44: a versatile enzyme for processing structured and non-structured RNA substrates
inferred← citeshttps://doi.org/10.1093/nar/gkad309openalex-snapshot
Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides
inferred← citeshttps://doi.org/10.1093/nar/gkae1148openalex-snapshot
Principles of ion binding to RNA inferred from the analysis of a 1.55 Å resolution bacterial ribosome structure – Part I: Mg2+
inferred← citeshttps://doi.org/10.1093/nar/gkaf1515openalex-snapshot
Structure and function of the nairovirus cap-snatching endonuclease
inferred← citeshttps://doi.org/10.1093/nar/gkw128openalex-snapshot
Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η
inferred← citeshttps://doi.org/10.1093/nar/gky492openalex-snapshot
Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site
inferred← citeshttps://doi.org/10.1093/nar/gky838openalex-snapshot
Structural insights into the mechanism of double strand break formation by Hermes, a hAT family eukaryotic DNA transposase
inferred← citeshttps://doi.org/10.1093/nar/gkz703openalex-snapshot
Structural characterization of Class 2 OLD family nucleases supports a two-metal catalysis mechanism for cleavage
inferred← citeshttps://doi.org/10.1107/s2052252518001021openalex-snapshot
Crystal structures ofLymphocytic choriomeningitis virusendonuclease domain complexed with diketo-acid ligands
inferred← citeshttps://doi.org/10.1107/s205979831700866xopenalex-snapshot
Activity inhibition and crystal polymorphism induced by active-site metal swapping
inferred← citeshttps://doi.org/10.1111/mmi.15074openalex-snapshot
Everything OLD is new again: How structural, functional, and bioinformatic advances have redefined a neglected nuclease family
inferred← citeshttps://doi.org/10.1140/epjp/s13360-025-06000-0openalex-snapshot
A brief study of the effects of magnesium divalent ions on the Dickerson DNA sequence at varying molar concentrations
inferred← citeshttps://doi.org/10.1146/annurev-physchem-082423-030241openalex-snapshot
Emerging Mechanisms of Metal-Catalyzed RNA and DNA Modifications
inferred← citeshttps://doi.org/10.1186/s12951-025-03800-5openalex-snapshot
mRNA vaccines: immunogenicity and quality characteristics
inferred← citeshttps://doi.org/10.1186/s13065-016-0188-6openalex-snapshot
Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand
inferred← citeshttps://doi.org/10.1261/rna.060442.116openalex-snapshot
Understanding in-line probing experiments by modeling cleavage of nonreactive RNA nucleotides
inferred← citeshttps://doi.org/10.1360/ssc-2025-0123openalex-snapshot
Study on aggregation-driven biomimetic hydrolases with high activity and spectral sensing
inferred← citeshttps://doi.org/10.1371/journal.pcbi.1004231openalex-snapshot
Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets
inferred← citeshttps://doi.org/10.1371/journal.pone.0156972openalex-snapshot
New Insight into Metal Ion-Driven Catalysis of Nucleic Acids by Influenza PA-Nter
inferred← citeshttps://doi.org/10.1515/pac-2025-0507openalex-snapshot
Unlocking the chemistry facilitated by enzymes that process nucleic acids using quantum mechanical and combined quantum mechanics–molecular mechanics techniques
inferred← citeshttps://doi.org/10.2174/0929867327666200114115632openalex-snapshot
Insights into RNA-dependent RNA Polymerase Inhibitors as Antiinfluenza Virus Agents
inferred← citeshttps://doi.org/10.3389/fmolb.2019.00062openalex-snapshot
Unraveling the Molecular Mechanism of Pre-mRNA Splicing From Multi-Scale Simulations
inferred← citeshttps://doi.org/10.3389/fmolb.2021.653262openalex-snapshot
Active-Site Models of Streptococcus pyogenes Cas9 in DNA Cleavage State
inferred← citeshttps://doi.org/10.3389/fmolb.2022.824794openalex-snapshot
Two-Metal-Ion Catalysis: Inhibition of DNA Polymerase Activity by a Third Divalent Metal Ion
inferred← citeshttps://doi.org/10.3390/ijms23126373openalex-snapshot
Structural and Molecular Kinetic Features of Activities of DNA Polymerases
inferred← citeshttps://doi.org/10.3390/molecules24152814openalex-snapshot
Factors Influencing the Activity of Nanozymes in the Cleavage of an RNA Model Substrate
inferred← citeshttps://doi.org/10.3390/molecules27092625openalex-snapshot
Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations
inferred← citeshttps://doi.org/10.3390/molecules28010191openalex-snapshot
Inspection on the Mechanism of SARS-CoV-2 Inhibition by Penciclovir: A Molecular Dynamic Study
inferred← citeshttps://doi.org/10.3390/molecules28031428openalex-snapshot
A Practical Approach to Bicyclic Carbamoyl Pyridones with Application to the Synthesis of HIV-1 Integrase Strand Transfer Inhibitors
inferred← citeshttps://doi.org/10.3390/nano16020106openalex-snapshot
Assessing Hydrolytic Activity of Surfactant-Based Nanozymes: Methodological and Kinetic Considerations
inferred← citeshttps://doi.org/10.3762/bjoc.14.68openalex-snapshot
Phosphodiester models for cleavage of nucleic acids
inferred← citeshttps://doi.org/10.4155/fmc-2018-0495openalex-snapshot
Can Multiscale Simulations Unravel the Function of metallo-enzymes to Improve knowledge-based Drug discovery?
inferred← citeshttps://doi.org/10.64898/2026.04.24.720726openalex-snapshot
Origins of reactivity in SAM-utilizing ribozyme SAMURI-catalyzed RNA alkylation
inferred← citeshttps://doi.org/10.70675/69f00960z9dd9z44d1za615za040059cba77openalex-snapshot
Développement de molécules antivirales contre les Arenavirus
inferred← citeshttps://doi.org/10.70675/fd141c5fz0b58z443ez9904zfe9e99196053openalex-snapshot
Characterization of Arenaviridae nucleases and design of inhibitors
inferred← citeshttps://doi.org/10.7554/elife.93099openalex-snapshot
Wide transition-state ensemble as key component for enzyme catalysis
inferred← citeshttps://doi.org/10.7554/elife.93099.1openalex-snapshot
Wide Transition-State Ensemble as Key Component for Enzyme Catalysis
inferred← citeshttps://doi.org/10.7554/elife.93099.2openalex-snapshot
Wide Transition-State Ensemble as Key Component for Enzyme Catalysis
inferred← citeshttps://doi.org/10.7554/elife.93099.3openalex-snapshot
Wide Transition-State Ensemble as Key Component for Enzyme Catalysis
inferred← citeshttps://doi.org/10.7554/elife.93099.4openalex-snapshot
Wide transition-state ensemble as key component for enzyme catalysis
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