On the public citation graph

The Effect of a G:T Mispair on the Dynamics of DNA

https://doi.org/10.1371/journal.pone.0053305

0 signed · 96 inferred · view as graph

Inferred edges come from two machine sources: sweeps of open repository metadata (mostly SSRN and Zenodo), and a bulk OpenAlex citation snapshot. Every row below is labelled with the one it came from. Neither is a complete citation index — absence here is not evidence of absence.

Is this your work? Sign in with ORCID and put your name on the claims that are yours.

Claim with ORCID

Reference health. See whether every reference in this work resolves to a known work and none has been retracted — and get a dated CiteStamped badge you can embed.

See reference health

What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/1096-987x(200009)21:12<1049::aid-jcc3>3.0.co;2-fopenalex-snapshot

How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?

inferredcites →https://doi.org/10.1002/1097-0282(2000)56:4<257::aid-bip10029>3.0.co;2-wopenalex-snapshot

Development and current status of the CHARMM force field for nucleic acids

inferredcites →https://doi.org/10.1002/chem.200701501openalex-snapshot

Extrahelical Damaged Base Recognition by DNA Glycosylase Enzymes

inferredcites →https://doi.org/10.1002/jcc.20289openalex-snapshot

Scalable molecular dynamics with NAMD

inferredcites →https://doi.org/10.1002/jcc.20291openalex-snapshot

GROMACS: Fast, flexible, and free

inferredcites →https://doi.org/10.1002/jcc.540040211openalex-snapshot

CHARMM : A program for macromolecular energy, minimization, and dynamics calculations

inferredcites →https://doi.org/10.1002/jcc.540160303openalex-snapshot

The double cubic lattice method: Efficient approaches to numerical integration of surface area and volume and to dot surface contouring of molecular assemblies

inferredcites →https://doi.org/10.1007/978-1-4020-4851-3_3openalex-snapshot

Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm

inferredcites →https://doi.org/10.1016/0021-9991(77)90098-5openalex-snapshot

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

inferredcites →https://doi.org/10.1016/0022-2836(88)90236-7openalex-snapshot

Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

inferredcites →https://doi.org/10.1016/0263-7855(96)00018-5openalex-snapshot

VMD: Visual molecular dynamics

inferredcites →https://doi.org/10.1016/j.dnarep.2011.03.004openalex-snapshot

Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs

inferredcites →https://doi.org/10.1016/j.jmb.2010.06.026openalex-snapshot

Mechanism of DNA Recognition by the Restriction Enzyme EcoRV

inferredcites →https://doi.org/10.1016/j.sbi.2004.05.001openalex-snapshot

Simulation and modeling of nucleic acid structure, dynamics and interactions

inferredcites →https://doi.org/10.1016/j.sbi.2008.01.005openalex-snapshot

Recent advances in the study of nucleic acid flexibility by molecular dynamics

inferredcites →https://doi.org/10.1016/s0022-2836(02)00194-8openalex-snapshot

Free Energy and Structural Pathways of Base Flipping in a DNA GCGC Containing Sequence

inferredcites →https://doi.org/10.1016/s0022-2836(02)00617-4openalex-snapshot

Local Deformations Revealed by Dynamics Simulations of DNA Polymerase β with DNA Mismatches at the Primer Terminus

inferredcites →https://doi.org/10.1016/s0076-6879(95)61018-9openalex-snapshot

[16] Studies of base pair kinetics by NMR measurement of proton exchange

inferredcites →https://doi.org/10.1021/bi00151a005openalex-snapshot

Kinetics and energetics of base-pair opening in 5'-d(CGCGAATTCGCG)-3' and a substituted dodecamer containing G.cntdot.T mismatches

inferredcites →https://doi.org/10.1021/bi100593aopenalex-snapshot

Detection of Damaged DNA Bases by DNA Glycosylase Enzymes

inferredcites →https://doi.org/10.1021/cr010219bopenalex-snapshot

A Mechanistic Perspective on the Chemistry of DNA Repair Glycosylases

inferredcites →https://doi.org/10.1021/cr040475zopenalex-snapshot

Computational Approaches for Investigating Base Flipping in Oligonucleotides

inferredcites →https://doi.org/10.1021/ct0501957openalex-snapshot

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS

inferredcites →https://doi.org/10.1021/ja025980xopenalex-snapshot

Base Flipping in DNA: Pathways and Energetics Studied with Molecular Dynamic Simulations

inferredcites →https://doi.org/10.1021/ja037333ropenalex-snapshot

Insight into G−T Mismatch Recognition Using Molecular Dynamics with Time-Averaged Restraints Derived from NMR Spectroscopy

inferredcites →https://doi.org/10.1021/ja0470721openalex-snapshot

Opening Mechanism of G·T/U Pairs in DNA and RNA Duplexes: A Combined Study of Imino Proton Exchange and Molecular Dynamics Simulation

inferredcites →https://doi.org/10.1021/ja0753546openalex-snapshot

Dynamics of B-DNA on the Microsecond Time Scale

inferredcites →https://doi.org/10.1038/328089a0openalex-snapshot

A single mode of DNA base-pair opening drives imino proton exchange

inferredcites →https://doi.org/10.1038/nsmb791openalex-snapshot

DNA binding and nucleotide flipping by the human DNA repair protein AGT

inferredcites →https://doi.org/10.1039/b713318aopenalex-snapshot

Sequence dependence in base flipping: experimental and computational studies

inferredcites →https://doi.org/10.1063/1.1410978openalex-snapshot

Calculating free energies using average force

inferredcites →https://doi.org/10.1063/1.2138694openalex-snapshot

Exploring the free-energy landscape of a short peptide using an average force

inferredcites →https://doi.org/10.1063/1.2829861openalex-snapshot

Adaptive biasing force method for scalar and vector free energy calculations

inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot

Comparison of simple potential functions for simulating liquid water

inferredcites →https://doi.org/10.1063/1.449071openalex-snapshot

The Nose–Hoover thermostat

inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems

inferredcites →https://doi.org/10.1073/pnas.0135427100openalex-snapshot

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase

inferredcites →https://doi.org/10.1073/pnas.0708058105openalex-snapshot

A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

inferredcites →https://doi.org/10.1073/pnas.0711061105openalex-snapshot

Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence-specific mismatch recognition

inferredcites →https://doi.org/10.1073/pnas.1201010109openalex-snapshot

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

inferredcites →https://doi.org/10.1073/pnas.2036378100openalex-snapshot

Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA

inferredcites →https://doi.org/10.1074/jbc.m109.062356openalex-snapshot

Role of Two Strictly Conserved Residues in Nucleotide Flipping and N-Glycosylic Bond Cleavage by Human Thymine DNA Glycosylase

inferredcites →https://doi.org/10.1080/07391102.1988.10506483openalex-snapshot

The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids

inferredcites →https://doi.org/10.1080/07391102.1989.10507729openalex-snapshot

Conformational and Helicoidal Analysis of 30 PS of Molecular Dynamics on the d(CGCGAATTCGCG) Double Helix: “Curves”, Dials and Windows

inferredcites →https://doi.org/10.1093/nar/26.21.4925openalex-snapshot

NMR solution structure of a DNA dodecamer containing single G*T mismatches

inferredcites →https://doi.org/10.1093/nar/gkg239openalex-snapshot

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

inferredcites →https://doi.org/10.1093/nar/gkm1135openalex-snapshot

Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites

inferredcites →https://doi.org/10.1093/nar/gkm622openalex-snapshot

DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics

inferredcites →https://doi.org/10.1093/nar/gkm627openalex-snapshot

Sequence-dependent DNA deformability studied using molecular dynamics simulations

inferredcites →https://doi.org/10.1093/nar/gkn622openalex-snapshot

Central base pair flipping and discrimination by PspGI

inferredcites →https://doi.org/10.1093/nar/gkp834openalex-snapshot

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA

inferredcites →https://doi.org/10.1093/nar/gkq812openalex-snapshot

On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics

inferredcites →https://doi.org/10.1098/rsta.2004.1383openalex-snapshot

Atomistic view of base flipping in DNA

inferredcites →https://doi.org/10.1111/j.1574-6976.2009.00188.xopenalex-snapshot

DNA base repair – recognition and initiation of catalysis

inferredcites →https://doi.org/10.1146/annurev.bi.51.070182.000425openalex-snapshot

DNA Repair Enzymes

inferredcites →https://doi.org/10.1146/annurev.bi.57.070188.000333openalex-snapshot

DNA REPAIR ENZYMES

inferredcites →https://doi.org/10.1529/biophysj.104.040915openalex-snapshot

In Silico Evidence for DNA Polymerase-β’s Substrate-Induced Conformational Change

inferredcites →https://doi.org/10.1529/biophysj.104.045252openalex-snapshot

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. I. Research Design and Results on d(CpG) Steps

inferredcites →https://doi.org/10.1529/biophysj.105.067397openalex-snapshot

Molecular Dynamics Simulations of the 136 Unique Tetranucleotide Sequences of DNA Oligonucleotides. II: Sequence Context Effects on the Dynamical Structures of the 10 Unique Dinucleotide Steps

inferredcites →https://doi.org/10.1529/biophysj.106.083816openalex-snapshot

Minor Groove Deformability of DNA: A Molecular Dynamics Free Energy Simulation Study

inferredcites →https://doi.org/10.1529/biophysj.106.091751openalex-snapshot

A Molecular Dynamics Study of Slow Base Flipping in DNA using Conformational Flooding

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.

inferred← citeshttps://doi.org/10.2139/ssrn.4192652openalex-extracted

Complementary Base Pairing Interactions between Different Rare Tautomers of the Second-Generation Artificial Genetic Alphabets

inferred← citeshttps://doi.org/10.2139/ssrn.4192659openalex-extracted

Complementary Base Pairing Interactions between Different Rare Tautomers of the Second-Generation Artificial Genetic Alphabets

inferred← citeshttps://doi.org/10.1002/adts.201800191openalex-snapshot

Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations

inferred← citeshttps://doi.org/10.1002/asia.202401335openalex-snapshot

Ribose Sugar Alters Conformational Sampling of G⋅T Mismatched Duplex DNA

inferred← citeshttps://doi.org/10.1002/cbic.202200360openalex-snapshot

Self‐Assembled Micro‐Sized Hexagons Built from Short DNA in a Crowded Environment

inferred← citeshttps://doi.org/10.1007/s00894-023-05537-0openalex-snapshot

Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets

inferred← citeshttps://doi.org/10.1007/s11224-024-02299-0openalex-snapshot

The base flipping of A-DNA—a molecular dynamic simulation study

inferred← citeshttps://doi.org/10.1016/j.bpc.2022.106779openalex-snapshot

Effect of a U:G mispair on the water around DNA

inferred← citeshttps://doi.org/10.1016/j.bpj.2018.10.029openalex-snapshot

MutSγ-Induced DNA Conformational Changes Provide Insights into Its Role in Meiotic Recombination

inferred← citeshttps://doi.org/10.1016/j.cplett.2017.07.003openalex-snapshot

Protonation-dependent base flipping in the catalytic triad of a small RNA

inferred← citeshttps://doi.org/10.1016/j.dnarep.2013.10.002openalex-snapshot

DNA modifications repaired by base excision repair are epigenetic

inferred← citeshttps://doi.org/10.1016/j.jarmap.2022.100374openalex-snapshot

Rapid identification of Atractylodes macrocephala Koidz., Atractylodes lancea (Thunb.) DC. and hybrids with MLPA-qPCR based on nuclear genome

inferred← citeshttps://doi.org/10.1016/j.pbiomolbio.2021.05.008openalex-snapshot

The Physics–Biology continuum challenges darwinism: Evolution is directed by the homeostasis-dependent bidirectional relation between genome and phenotype

inferred← citeshttps://doi.org/10.1021/acs.biochem.8b00409openalex-snapshot

Interactions of the DNA Repair Enzyme Human Thymine DNA Glycosylase with Cognate and Noncognate DNA

inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00636openalex-snapshot

Molecular Mechanism, Dynamics, and Energetics of Protein-Mediated Dinucleotide Flipping in a Mismatched DNA: A Computational Study of the RAD4-DNA Complex

inferred← citeshttps://doi.org/10.1021/acs.jpcb.1c09896openalex-snapshot

Oxidation Enhances Binding of Extrahelical 5-Methyl-Cytosines by Thymine DNA Glycosylase

inferred← citeshttps://doi.org/10.1021/acs.jpcb.2c00340openalex-snapshot

Energy Landscapes for Base-Flipping in a Model DNA Duplex

inferred← citeshttps://doi.org/10.1021/acs.jpcb.8b06007openalex-snapshot

DNA Base Pair Mismatches Induce Structural Changes and Alter the Free-Energy Landscape of Base Flip

inferred← citeshttps://doi.org/10.1021/acs.jpclett.6c00991openalex-snapshot

Influence of DNA Mispairing and Abasic Sites on Duplex Dynamics: A Temperature-Jump Infrared Spectroscopy Study

inferred← citeshttps://doi.org/10.1021/acsnano.1c06963openalex-snapshot

3D Hexagonal Arrangement of DNA Tensegrity Triangles

inferred← citeshttps://doi.org/10.1021/jacs.3c10406openalex-snapshot

Z-Form Adoption of Nucleic Acid is a Multi-Step Process Which Proceeds through a Melted Intermediate

inferred← citeshttps://doi.org/10.1038/s41598-020-72102-7openalex-snapshot

Automated AFM analysis of DNA bending reveals initial lesion sensing strategies of DNA glycosylases

inferred← citeshttps://doi.org/10.1039/c5ra27591aopenalex-snapshot

Comparative simulative analysis of single and double stranded truncated octahedral DNA nanocages

inferred← citeshttps://doi.org/10.1073/pnas.1400667111openalex-snapshot

Dynamics of spontaneous flipping of a mismatched base in DNA duplex

inferred← citeshttps://doi.org/10.1093/nar/gkaa896openalex-snapshot

Importance of base-pair opening for mismatch recognition

inferred← citeshttps://doi.org/10.1093/nar/gkac241openalex-snapshot

Mismatch discrimination and sequence bias during end-joining by DNA ligases

inferred← citeshttps://doi.org/10.1093/nar/gkac691openalex-snapshot

Markov state models elucidate the stability of DNA influenced by the chiral 5S-Tg base

inferred← citeshttps://doi.org/10.1093/nar/gkv139openalex-snapshot

Lesion search and recognition by thymine DNA glycosylase revealed by single molecule imaging

inferred← citeshttps://doi.org/10.1093/nar/gky386openalex-snapshot

Base-flipping dynamics from an intrahelical to an extrahelical state exerted by thymine DNA glycosylase during DNA repair process

inferred← citeshttps://doi.org/10.3389/fimmu.2021.807015openalex-snapshot

Tandem Substitutions in Somatic Hypermutation

inferred← citeshttps://doi.org/10.3390/ijms150711799openalex-snapshot

Base Flip in DNA Studied by Molecular Dynamics Simulationsof Differently-Oxidized Forms of Methyl-Cytosine

inferred← citeshttps://doi.org/10.3390/ijms20174271openalex-snapshot

Mismatch Recognition by Saccharomyces cerevisiae Msh2-Msh6: Role of Structure and Dynamics

inferred← citeshttps://doi.org/10.3390/molecules26195728openalex-snapshot

Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms

inferred← citeshttps://doi.org/10.7124/bc.0008f0openalex-snapshot

Development of MLPA approach for SNP detection in MTHFR, F and F2 genes

Editorial review for independent work. ICSAC — the Institute for Complexity Science and Advanced Computing — runs a structured editorial panel for researchers publishing outside journals, and publishes on CiteStamp rails. Submission is free and goes through ORCID: icsacinstitute.org/submit.