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i-Motif DNA: structural features and significance to cell biology

Nucleic acids research, 2018-09, Vol.46 (16), p.8038

2018

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Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA

Journal of chemical theory and computation, 2015-12, Vol.11 (12), p.5723-5736

2015

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Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor

Immunity (Cambridge, Mass.), 2012-04, Vol.36 (4), p.561-571

2012

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Assessing the Current State of Amber Force Field Modifications for DNA

Journal of chemical theory and computation, 2016-08, Vol.12 (8), p.4114-4127

2016

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μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Nucleic acids research, 2014-10, Vol.42 (19), p.12272

2014

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Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

Genome research, 2018-09, Vol.28 (9), p.1264

2018

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Biomolecular Simulations under Realistic Macroscopic Salt Conditions

The journal of physical chemistry. B, 2018-05, Vol.122 (21), p.5466-5486

2018

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Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations

Journal of the American Chemical Society, 2020-06, Vol.142 (25), p.11183-11191

2020

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The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

Nucleic acids research, 2019-12, Vol.47 (21), p.11090

2019

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Probing Allostery Through DNA

Science (American Association for the Advancement of Science), 2013-02, Vol.339 (6121), p.816-819

2013

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Long-timescale dynamics of the Drew-Dickerson dodecamer

Nucleic acids research, 2016-05, Vol.44 (9), p.4052

2016

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Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics

Journal of chemical theory and computation, 2017-05, Vol.13 (5), p.2053-2071

2017

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Structural basis of human PCNA sliding on DNA

Nature communications, 2017-01, Vol.8 (1), p.13935-13935, Article 13935

2017

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Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B‑DNA Oligonucleotide

Journal of the American Chemical Society, 2019-03, Vol.141 (11), p.4644-4652

2019

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Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

Journal of chemical theory and computation, 2017-05, Vol.13 (5), p.2072-2085

2017

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Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

Proceedings of the National Academy of Sciences - PNAS, 2019-08, Vol.116 (35), p.17169-17174

2019

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Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels

The journal of physical chemistry. B, 2020-01, Vol.124 (1), p.38-49

2020

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Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability

DNA repair, 2014-07, Vol.19, p.143-151

2014

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Z‑DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

Journal of chemical theory and computation, 2021-10, Vol.17 (10), p.6292-6301

2021

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Zeta potential of Z-DNA: A new signature to study B-Z transition in linear and branched DNA

International journal of biological macromolecules, 2024-05, Vol.266 (Pt 1), p.131238-131238, Article 131238

2024

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Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs

Angewandte Chemie International Edition, 2014-02, Vol.53 (9), p.2385-2388

2014

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Transitions of Double-Stranded DNA Between the A- and B‑Forms

The journal of physical chemistry. B, 2016-08, Vol.120 (33), p.8449-8456

2016

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Free energy analysis and mechanism of base pair stacking in nicked DNA

Nucleic acids research, 2016-09, Vol.44 (15), p.7100

2016

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The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex

Nucleic acids research, 2020-04, Vol.48 (6), p.3366

2020

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How accurate are accurate force-fields for B-DNA?

Nucleic acids research, 2017-04, Vol.45 (7), p.4217

2017

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i-Motif DNA: structural features and significance to cell biology

Refinement of the Sugar–Phosphate Backbone Torsion Beta for AMBER Force Fields Improves the Description of Z- and B‑DNA

Structures of the HIN Domain:DNA Complexes Reveal Ligand Binding and Activation Mechanisms of the AIM2 Inflammasome and IFI16 Receptor

Assessing the Current State of Amber Force Field Modifications for DNA

μABC: a systematic microsecond molecular dynamics study of tetranucleotide sequence effects in B-DNA

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis

Biomolecular Simulations under Realistic Macroscopic Salt Conditions

Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations

The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules

Probing Allostery Through DNA

Long-timescale dynamics of the Drew-Dickerson dodecamer

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics

Structural basis of human PCNA sliding on DNA

Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B‑DNA Oligonucleotide

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA

Hydrophobic catalysis and a potential biological role of DNA unstacking induced by environment effects

Modeling DNA Flexibility: Comparison of Force Fields from Atomistic to Multiscale Levels

Impact of alternative DNA structures on DNA damage, DNA repair, and genetic instability

Z‑DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA Torsions for AMBER

Zeta potential of Z-DNA: A new signature to study B-Z transition in linear and branched DNA

Crystal structure of metallo DNA duplex containing consecutive Watson-Crick-like T-Hg(II)-T base pairs

Transitions of Double-Stranded DNA Between the A- and B‑Forms

Free energy analysis and mechanism of base pair stacking in nicked DNA

The complex formed between a synthetic RNA aptamer and the transcription repressor TetR is a structural and functional twin of the operator DNA-TetR regulator complex

How accurate are accurate force-fields for B-DNA?

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