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A Strategically Located Arg/Lys Residue Promotes Correct Base Paring During Nucleic Acid Biosynthesis in Polymerases
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
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A historical account of hoogsteen base‐pairs in duplex DNA
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Development and testing of a general amber force field
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Improved side‐chain torsion potentials for the Amber ff99SB protein force field
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GROMACS: A message-passing parallel molecular dynamics implementation
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Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
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Constrained molecular dynamics and the mean potential for an ion pair in a polar solvent
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DNA- and RNA-dependent DNA polymerases
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Inhibition of Bacterial RNA Polymerase by Streptolydigin: Stabilization of a Straight-Bridge-Helix Active-Center Conformation
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Structural Insight into Translesion Synthesis by DNA Pol II
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Observing a DNA Polymerase Choose Right from Wrong
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PLUMED 2: New feathers for an old bird
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Mechanisms for recurrent and complex human genomic rearrangements
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Modeling the charge distribution at metal sites in proteins for molecular dynamics simulations
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Investigating biological systems using first principles Car–Parrinello molecular dynamics simulations
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Human DNA Polymerase ι Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair
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Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes
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Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4. VOLUME 281 (2006) PAGES 2358-2372
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Crystal Structure of Thermus aquaticus Core RNA Polymerase at 3.3 Å Resolution
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Structure of the Replicating Complex of a Pol α Family DNA Polymerase
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The Structural Mechanism of Translocation and Helicase Activity in T7 RNA Polymerase
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Enhanced ribonucleotide incorporation by an O-helix mutant of Thermus aquaticus DNA polymerase I
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Calculations of electrostatic interactions in biological systems and in solutions
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The Role and Perspective of Ab Initio Molecular Dynamics in the Study of Biological Systems
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Catalytic Metal Ions and Enzymatic Processing of DNA and RNA
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Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems
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DNA Polymerase β: Contributions of Template-Positioning and dNTP Triphosphate-Binding Residues to Catalysis and Fidelity
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An Overview of Y-Family DNA Polymerases and a Case Study of Human DNA Polymerase η
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How a Low-Fidelity DNA Polymerase Chooses Non-Watson–Crick from Watson–Crick Incorporation
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The Molecular Mechanism of the Catalase-like Activity in Horseradish Peroxidase
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Relative Binding Free Energies of Adenine and Guanine to Damaged and Undamaged DNA in Human DNA Polymerase η: Clues for Fidelity and Overall Efficiency
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A Self-Activated Mechanism for Nucleic Acid Polymerization Catalyzed by DNA/RNA Polymerases
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The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase η
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Replication of a cis–syn thymine dimer at atomic resolution
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Preferential cis–syn thymine dimer bypass by DNA polymerase η occurs with biased fidelity
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Replication by human DNA polymerase-ι occurs by Hoogsteen base-pairing
inferredcites →https://doi.org/10.1038/nature04199openalex-snapshot
Hoogsteen base-pairing in DNA replication?
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Hoogsteen base-pairing in DNA replication? (reply)
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Structure and mechanism of human DNA polymerase η
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Transient Hoogsteen base pairs in canonical duplex DNA
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Watching DNA polymerase η make a phosphodiester bond
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Protection against filovirus diseases by a novel broad-spectrum nucleoside analogue BCX4430
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Visualizing transient Watson–Crick-like mispairs in DNA and RNA duplexes
inferredcites →https://doi.org/10.1038/ncomms5786openalex-snapshot
Widespread transient Hoogsteen base pairs in canonical duplex DNA with variable energetics
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Hypermutation in human cancer genomes: footprints and mechanisms
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Nucleosome positioning and gene regulation: advances through genomics
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Nucleic acid polymerases use a general acid for nucleotidyl transfer
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How a homolog of high-fidelity replicases conducts mutagenic DNA synthesis
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Time-lapse crystallography snapshots of a double-strand break repair polymerase in action
inferredcites →https://doi.org/10.1038/s41570-017-0068openalex-snapshot
How DNA polymerases catalyse replication and repair with contrasting fidelity
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Structural basis for proteolysis‐dependent activation of the poliovirus RNA‐dependent RNA polymerase
inferredcites →https://doi.org/10.1038/sj.emboj.7601780openalex-snapshot
Structures of phi29 DNA polymerase complexed with substrate: the mechanism of translocation in B‐family polymerases
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Chapter 9. First Principles Methods in Biology: From Continuum Models to Hybrid Ab initio Quantum Mechanics/Molecular Mechanics
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A Hamiltonian electrostatic coupling scheme for hybrid Car–Parrinello molecular dynamics simulations
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Comparison of simple potential functions for simulating liquid water
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A unified formulation of the constant temperature molecular dynamics methods
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Sequential structures provide insights into the fidelity of RNA replication
inferredcites →https://doi.org/10.1073/pnas.0809989106openalex-snapshot
Structure of PolC reveals unique DNA binding and fidelity determinants
inferredcites →https://doi.org/10.1073/pnas.0910121106openalex-snapshot
Highly error-free role of DNA polymerase η in the replicative bypass of UV-induced pyrimidine dimers in mouse and human cells
inferredcites →https://doi.org/10.1073/pnas.1013909108openalex-snapshot
Unique active site promotes error-free replication opposite an 8-oxo-guanine lesion by human DNA polymerase iota
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.1502368112openalex-snapshot
CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition
inferredcites →https://doi.org/10.1073/pnas.1511207112openalex-snapshot
Requirement for transient metal ions revealed through computational analysis for DNA polymerase going in reverse
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.m114.551820openalex-snapshot
Kinetics, Structure, and Mechanism of 8-Oxo-7,8-dihydro-2′-deoxyguanosine Bypass by Human DNA Polymerase η
inferredcites →https://doi.org/10.1074/jbc.m115.653691openalex-snapshot
Roles of Residues Arg-61 and Gln-38 of Human DNA Polymerase η in Bypass of Deoxyguanosine and 7,8-Dihydro-8-oxo-2′-deoxyguanosine
inferredcites →https://doi.org/10.1074/jbc.m116.748285openalex-snapshot
Kinetic and Structural Impact of Metal Ions and Genetic Variations on Human DNA Polymerase ι
inferredcites →https://doi.org/10.1074/jbc.m117.809723openalex-snapshot
Human DNA polymerase η accommodates RNA for strand extension
inferredcites →https://doi.org/10.1074/jbc.m510889200openalex-snapshot
Efficient and High Fidelity Incorporation of dCTP Opposite 7,8-Dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA Polymerase Dpo4
inferredcites →https://doi.org/10.1074/jbc.m702159200openalex-snapshot
Increased Catalytic Activity and Altered Fidelity of Human DNA Polymerase ι in the Presence of Manganese
inferredcites →https://doi.org/10.1074/jbc.m807296200openalex-snapshot
Lesion Bypass of N2-Ethylguanine by Human DNA Polymerase ι
inferredcites →https://doi.org/10.1074/jbc.r116.742494openalex-snapshot
Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases
inferredcites →https://doi.org/10.1093/emboj/20.24.7303openalex-snapshot
Mutations in human DNA polymerase η motif II alter bypass of DNA lesions
inferredcites →https://doi.org/10.1093/nar/30.10.2154openalex-snapshot
Unique condensation patterns of triplex DNA: physical aspects and physiological implications
inferredcites →https://doi.org/10.1093/nar/30.6.1354openalex-snapshot
Heat-induced formation of reactive oxygen species and 8-oxoguanine, a biomarker of damage to DNA
inferredcites →https://doi.org/10.1093/nar/gkp1095openalex-snapshot
Critical amino acids in human DNA polymerases η and κ involved in erroneous incorporation of oxidized nucleotides
inferredcites →https://doi.org/10.1093/nar/gks383openalex-snapshot
Active site opening and closure control translocation of multisubunit RNA polymerase
inferredcites →https://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
inferredcites →https://doi.org/10.1093/nar/gkw204openalex-snapshot
Structure and mechanism of error-free replication past the major benzo[a]pyrene adduct by human DNA polymerase κ
inferredcites →https://doi.org/10.1103/physreva.31.1695openalex-snapshot
Canonical dynamics: Equilibrium phase-space distributions
inferredcites →https://doi.org/10.1103/physreva.33.3628openalex-snapshot
Molecular dynamics simulation for polymers in the presence of a heat bath
inferredcites →https://doi.org/10.1103/physrevb.43.8861openalex-snapshot
Efficient pseudopotentials for plane-wave calculations. II. Operators for fast iterative diagonalization
inferredcites →https://doi.org/10.1103/physrevlett.100.020603openalex-snapshot
Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
inferredcites →https://doi.org/10.1103/physrevlett.55.2471openalex-snapshot
Unified Approach for Molecular Dynamics and Density-Functional Theory
inferredcites →https://doi.org/10.1107/s0365110x63002437openalex-snapshot
The crystal and molecular structure of a hydrogen-bonded complex between 1-methylthymine and 9-methyladenine
inferredcites →https://doi.org/10.1126/science.1116336openalex-snapshot
Rev1 Employs a Novel Mechanism of DNA Synthesis Using a Protein Template
inferredcites →https://doi.org/10.1126/science.282.5394.1669openalex-snapshot
Structure of a Covalently Trapped Catalytic Complex of HIV-1 Reverse Transcriptase: Implications for Drug Resistance
inferredcites →https://doi.org/10.1126/science.aad9633openalex-snapshot
Capture of a third Mg 2+ is essential for catalyzing DNA synthesis
inferredcites →https://doi.org/10.1146/annurev-biochem-060408-091030openalex-snapshot
Origins of Specificity in Protein-DNA Recognition
inferredcites →https://doi.org/10.1146/annurev.bi.63.070194.004021openalex-snapshot
FUNCTION AND STRUCTURE RELATIONSHIPS IN DNA POLYMERASES
inferredcites →https://doi.org/10.1146/annurev.biophys.37.032807.130008openalex-snapshot
Structure of Eukaryotic RNA Polymerases
inferredcites →https://doi.org/10.1371/journal.pbio.1002599openalex-snapshot
Unique 5′-P recognition and basis for dG:dGTP misincorporation of ASFV DNA polymerase X
inferredcites →https://doi.org/10.15252/embj.201489643openalex-snapshot
Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair
inferredcites →https://doi.org/10.1529/biophysj.106.097782openalex-snapshot
Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
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Atomistic Simulations Decode the Mechanisms of DNA and RNA Processing Enzymes: Function through Motion
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inferred← citeshttps://doi.org/10.1021/acs.jctc.2c00848openalex-snapshot
Alchemical Free-Energy Calculations of Watson–Crick and Hoogsteen Base Pairing Interconversion in DNA
inferred← citeshttps://doi.org/10.1021/acs.jctc.6c00345openalex-snapshot
Decoding Cancer-Associated Mutations in DNA Polymerase η through Atomistic Simulations
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Free Energy Landscape between Watson–Crick to Hoogsteen Base Pairing Transitions
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Local Structural Dynamics at the Metal-Centered Catalytic Site of Polymerases is Critical for Fidelity
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The Catalytic Mechanism of DNA and RNA Polymerases
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