Citations (67)
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Mauricio Alcolea Palafox, Maria Lourdes de Pedraza Velasco, Josefa Isasi Marín & Paloma Posada-Moreno. (2022) How proton transfer affects the helical parameters in DNA:DNA microhelices. Journal of Biomolecular Structure and Dynamics 40:24, pages 13759-13777.
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Ol’ha O. Brovarets’, Alona Muradova & Dmytro M. Hovorun. (2022) Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation. Molecular Physics 120:7.
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Zahra Anvari, Hamid Reza Masoodi & Sotoodeh Bagheri. (2020) DFT simulation of Watson–Crick-like guanine–thymine mismatch in quaternary systems involving DNA bases. Molecular Simulation 46:3, pages 186-192.
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. (2019) Key microstructural mechanisms of the 2-aminopurine mutagenicity: Results of extensive quantum-chemical research. Journal of Biomolecular Structure and Dynamics 37:10, pages 2716-2732.
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Hamid Reza Masoodi, Sotoodeh Bagheri & Zahra Ghaderi. (2019) The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study. Journal of Biomolecular Structure and Dynamics 37:8, pages 1923-1934.
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. (2019) Atomistic mechanisms of the double proton transfer in the H-bonded nucleobase pairs: QM/QTAIM computational lessons. Journal of Biomolecular Structure and Dynamics 37:7, pages 1880-1907.
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Ol’ha O. Brovarets’, Ivan S. Voiteshenko, Horacio Pérez-Sánchez & Dmytro M. Hovorun. (2018) A QM/QTAIM detailed look at the Watson–Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs. Journal of Biomolecular Structure and Dynamics 36:7, pages 1649-1665.
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R. Radhika, R. Shankar, S. Vijayakumar & P. Kolandaivel. (2018) Role of 6-Mercaptopurine in the potential therapeutic targets DNA base pairs and G-quadruplex DNA: insights from quantum chemical and molecular dynamics simulations. Journal of Biomolecular Structure and Dynamics 36:6, pages 1369-1401.
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Ebrahim Azarhazin, Mohammad Izadyar & Mohammad Reza Housaindokht. (2018) Molecular dynamic simulation and DFT study on the Drug-DNA interaction; Crocetin as an anti-cancer and DNA nanostructure model. Journal of Biomolecular Structure and Dynamics 36:4, pages 1063-1074.
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Ruby Srivastava. (2018) Complexes of DNA bases and Watson–Crick base pairs interaction with neutral silver Ag (n = 8, 10, 12) clusters: a DFT and TDDFT study. Journal of Biomolecular Structure and Dynamics 36:4, pages 1050-1062.
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Ol’ha O. Brovarets’ & Horacio Pérez-Sánchez. (2017) Whether 2-aminopurine induces incorporation errors at the DNA replication? A quantum-mechanical answer on the actual biological issue. Journal of Biomolecular Structure and Dynamics 35:15, pages 3398-3411.
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Nadezhda Markova, Ljupco Pejov, Nina Stoyanova & Venelin Enchev. (2017) Hybrid MC/QC simulations of water-assisted proton transfer in nucleosides. Guanosine and its analog acyclovir. Journal of Biomolecular Structure and Dynamics 35:6, pages 1168-1188.
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Drielli G. Vital, Flávia S. Damasceno, Ludmila N. Rapado, Ariel M. Silber, Filipe S. Vilella, Rafaela S. Ferreira, Vinícius G. Maltarollo & Gustavo H. G. Trossini. (2017) Application of bioisosterism in design of the semicarbazone derivatives as cruzain inhibitors: a theoretical and experimental study. Journal of Biomolecular Structure and Dynamics 35:6, pages 1244-1259.
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Umadevi Palanivel & Senthilkumar Lakshmipathi. (2016) Hydrogen bonds in Zif268 proteins – a theoretical perspective. Journal of Biomolecular Structure and Dynamics 34:8, pages 1607-1624.
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Hamid Reza Masoodi, Sotoodeh Bagheri & Mahsa Abareghi. (2016) The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study. Journal of Biomolecular Structure and Dynamics 34:6, pages 1143-1155.
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Muhammad Arba, Rahmana E. Kartasasmita & Daryono H. Tjahjono. (2016) Molecular docking and dynamics simulations on the interaction of cationic porphyrin–anthraquinone hybrids with DNA G-quadruplexes. Journal of Biomolecular Structure and Dynamics 34:2, pages 427-438.
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. (2015) Proton tunneling in the A∙T Watson-Crick DNA base pair: myth or reality?. Journal of Biomolecular Structure and Dynamics 33:12, pages 2716-2720.
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. (2015) How many tautomerization pathways connect Watson–Crick-like G*·T DNA base mispair and wobble mismatches?. Journal of Biomolecular Structure and Dynamics 33:11, pages 2297-2315.
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Shaoming Chi, Wei Xie, Jiwei Zhang & Sichuan Xu. (2015) Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin. Journal of Biomolecular Structure and Dynamics 33:10, pages 2234-2254.
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Ol’ha O. Brovarets’, Yevgen P. Yurenko & Dmytro M. Hovorun. (2015) The significant role of the intermolecular CH⋯O/N hydrogen bonds in governing the biologically important pairs of the DNA and RNA modified bases: a comprehensive theoretical investigation. Journal of Biomolecular Structure and Dynamics 33:8, pages 1624-1652.
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Articles from other publishers (47)
Louie Slocombe, Max WinokanJim Al-KhaliliMarco Sacchi. (2022) Quantum Tunnelling Effects in the Guanine-Thymine Wobble Misincorporation via Tautomerism. The Journal of Physical Chemistry Letters 14:1, pages 9-15.
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Kei Odai & Keisho Umesaki. (2021) Kinetic Study of Transition Mutations from G–C to A–T Base Pairs in Watson–Crick DNA Base Pairs: Double Proton Transfers. The Journal of Physical Chemistry A 125:37, pages 8196-8204.
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Ol'ha O. Brovarets', Alona Muradova & Dmytro M. Hovorun. (2021)
Novel mechanisms of the conformational transformations of the biologically important G·C nucleobase pairs in Watson–Crick, Hoogsteen and wobble configurations
via
the mutual rotations of the bases around the intermolecular H-bonds: a QM/QTAIM study
. RSC Advances 11:41, pages 25700-25730.
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Shreya Chandorkar, Shampa Raghunathan, Tanashree Jaganade & U. Deva Priyakumar. (2021) Multiscale Modeling of Wobble to Watson–Crick-Like Guanine–Uracil Tautomerization Pathways in RNA. International Journal of Molecular Sciences 22:11, pages 5411.
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Ol’ha O. Brovarets & Dmytro M. Hovorun. (2020) Quantum dancing of the wobble G•T(U/5BrU) nucleobase pairs and its biological roles. Chemical Physics Impact 1, pages 100006.
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Ol'ha O. Brovarets'Alona Muradova & Dmytro M. Hovorun. (2020) A Quantum-Mechanical Looking Behind the Scene of the Classic G·C Nucleobase Pairs Tautomerization. Frontiers in Chemistry 8.
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Pengfei Li, Atul Rangadurai, Hashim M. Al-Hashimi & Sharon Hammes-Schiffer. (2020) Environmental Effects on Guanine-Thymine Mispair Tautomerization Explored with Quantum Mechanical/Molecular Mechanical Free Energy Simulations. Journal of the American Chemical Society 142:25, pages 11183-11191.
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Elena O. Levina, Maria G. Khrenova, Andrey A. Astakhov & Vladimir G. Tsirelson. (2020) Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-β-lactamase. RSC Advances 10:15, pages 8664-8676.
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Safinaz H. El-Demerdash & Shaimaa F. Gad. (2019) A computational study of gas-phase acidity and basicity of azulene-based uracil analogue. Structural Chemistry 31:1, pages 319-328.
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Ol'ha O. Brovarets'Timothy A. Oliynyk & Dmytro M. Hovorun. (2019) Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey. Frontiers in Chemistry 7.
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Christopher Maffeo, Han‐Yi Chou & Aleksei Aksimentiev. (2019) Molecular Mechanisms of DNA Replication and Repair Machinery: Insights from Microscopic Simulations. Advanced Theory and Simulations 2:5, pages 1800191.
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Shaimaa F. Gad, Safinaz H. El-Demerdash, Ibrahim M. El-Mehasseb & Ahmed M. El-Nahas. (2019) Structure, stability and conversions of tautomers and rotamers of azulene-based uracil analogue. Journal of Molecular Structure 1182, pages 271-282.
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Leo F. Holroyd, Michael Bühl, Marie-Pierre Gaigeot & Tanja van Mourik. 2019. Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results. Quantum Systems in Physics, Chemistry and Biology - Theory, Interpretation, and Results
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. 2018. Mitochondrial DNA - New Insights. Mitochondrial DNA - New Insights.
S. Tolosa, J. A. Sansón & A. Hidalgo. (2018)
Theoretical study of mechanisms for the hydrolytic deamination of cytosine
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steered molecular dynamic simulations
. RSC Advances 8:61, pages 34867-34876.
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Ol'ha O. Brovarets', Kostiantyn S. Tsiupa & Dmytro M. Hovorun. (2018) Unexpected A·T(WC)↔A·T(rWC)/A·T(rH) and A·T(H)↔A·T(rH)/A·T(rWC) conformational transitions between the classical A·T DNA base pairs: A QM/QTAIM comprehensive study. International Journal of Quantum Chemistry 118:18, pages e25674.
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S. Tolosa, J.A. Sansón & A. Hidalgo. (2018) Theoretical study of mechanisms for double proton transfer in adenine–uracil base pair via steered molecular dynamic simulations. Journal of Molecular Liquids 265, pages 487-495.
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Ol’ha O. Brovarets’, Kostiantyn S. Tsiupa & Dmytro M. Hovorun. (2018) Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Scientific Reports 8:1.
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Carlo Gatti, Giovanni Macetti, Russell J. Boyd & Chérif F. Matta. (2018)
An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States
†
. Journal of Computational Chemistry 39:18, pages 1112-1128.
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Ol’ha O. Brovarets’, Kostiantyn S. Tsiupa & Dmytro M. Hovorun. (2018) Novel pathway for mutagenic tautomerization of classical А∙Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation. PLOS ONE 13:6, pages e0199044.
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Guixiu Wang, Fenghai Li, Juan Zhao, Yifang Wu & Jianping Wang. (2018) Methylation Mediated Anharmonic Vibrational Signature of Nucleobases: A Case Study of Uracil and Thymine. ChemistrySelect 3:16, pages 4374-4381.
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Saeed K. Amini. (2018) Relative Populations of Some Tautomeric Forms of 2′-Deoxyguanosine-5-Fluorouridine Mismatch. The Journal of Physical Chemistry B 122:16, pages 4433-4444.
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Saeid Ebrahimi, Hossein A. Dabbagh & Kiamars Eskandari. (2017) Arrangement and nature of intermolecular hydrogen bonding in complex biomolecular systems: modeling the vitamin C---L-alanine interaction. Structural Chemistry 29:2, pages 491-502.
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Ol'ha O. Brovarets'Kostiantyn S. Tsiupa & Dmytro M. Hovorun. (2018) Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs. Frontiers in Chemistry 6.
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Isaac J. Kimsey, Eric S. Szymanski, Walter J. Zahurancik, Anisha Shakya, Yi Xue, Chia-Chieh Chu, Bharathwaj Sathyamoorthy, Zucai Suo & Hashim M. Al-Hashimi. (2018) Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 554:7691, pages 195-201.
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S. Tolosa, J.A. Sansón & A. Hidalgo. (2018) Mechanisms for guanine–cytosine tautomeric equilibrium in solution via steered molecular dynamic simulations. Journal of Molecular Liquids 251, pages 308-316.
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Ol'ha O. Brovarets', Kostiantyn S. Tsiupa & Dmytro M. Hovorun. (2018)
The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rw
WC
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H
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H
) mutagenic tautomerization
via
sequential proton transfer: a QM/QTAIM study
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Ol'ha O. Brovarets', Ivan S. Voiteshenko & Dmytro M. Hovorun. (2018) Physico-chemical profiles of the wobble ↔ Watson–Crick G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) tautomerisations: a QM/QTAIM comprehensive survey. Physical Chemistry Chemical Physics 20:1, pages 623-636.
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S. Abdalla, A. Obaid & F. M. Al-Marzouki. (2017) Effects of Environmental Factors and Metallic Electrodes on AC Electrical Conduction Through DNA Molecule. Nanoscale Research Letters 12:1.
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Sergey N. Maximoff, Shina Caroline Lynn Kamerlin & Jan Florián. (2017) DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study. The Journal of Physical Chemistry B 121:33, pages 7813-7822.
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Ol'ha O. Brovarets', Ivan S. Voiteshenko, Horacio Pérez-Sánchez & Dmytro M. Hovorun. (2017) A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine. New Journal of Chemistry 41:15, pages 7232-7243.
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Subhojyoti Chatterjee & Feng Wang. (2016) How different is pyrimidine as a core component of DNA base from its diazine isomers: A DFT study?. International Journal of Quantum Chemistry 116:24, pages 1836-1845.
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Hongxia Liu, Qixia Song & Haijun Wang. (2016) Optical absorption and emission properties of benzene-expanded Janus AT nucleobase analogues: A DFT study. Structural Chemistry 27:4, pages 1175-1187.
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Namık Özdemir. (2016) Quantum chemical study of tautomerism in 2-[(4-phenylthiazol-2-yl)hydrazonomethyl]phenol. Computational and Theoretical Chemistry 1086, pages 12-17.
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Arathi P.J.Parth Gupta, Jagadeesh Babu N.Sundaresan C.N.Ramanathan Venkatnarayan. (2016) Conformation analysis of 1″,4″-Dispirocyclohexane-6,6′-bis(benzothiazoline): Combined IR, Raman, XRD and DFT approach. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 157, pages 192-196.
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Ol'ha O. Brovarets' & Horacio Pérez-Sánchez. (2016) Whether the amino–imino tautomerism of 2-aminopurine is involved into its mutagenicity? Results of a thorough QM investigation. RSC Advances 6:110, pages 108255-108264.
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Ol'ha O. Brovarets', Horacio Pérez-Sánchez & Dmytro M. Hovorun. (2016) Structural grounds for the 2-aminopurine mutagenicity: a novel insight into the old problem of the replication errors. RSC Advances 6:101, pages 99546-99557.
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Dharitri Das, Abhijit Dutta & Paritosh Mondal. (2015) Interaction of aquated form of ruthenium(III) anticancer complexes with normal and mismatch base pairs: A density functional theoretical study. Computational and Theoretical Chemistry 1072, pages 28-36.
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Ferid Hammami, Houcine Ghalla & Salah Nasr. (2015) Intermolecular hydrogen bonds in urea–water complexes: DFT, NBO, and AIM analysis. Computational and Theoretical Chemistry 1070, pages 40-47.
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O.O. Brovarets & D.M. Hovorun. (2015) How Do Long Improper Purine-Purine Pairs of DNA Bases Adapt The Enzymatycally Competent Conformation? Structural Mechanism And Its Quantum-Mechanical Grounds. Ukrainian Journal of Physics 60:8, pages 748-756.
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. (2015) New structural hypostases of the A·T and G·C Watson–Crick DNA base pairs caused by their mutagenic tautomerisation in a wobble manner: a QM/QTAIM prediction. RSC Advances 5:121, pages 99594-99605.
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Ol’ha O. Brovarets’ & Dmytro M. Hovorun. (2015) Novel physico-chemical mechanism of the mutagenic tautomerisation of the Watson–Crick-like A·G and C·T DNA base mispairs: a quantum-chemical picture. RSC Advances 5:81, pages 66318-66333.
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Ol'ha O. Brovarets' & Dmytro M. Hovorun. (2015) Tautomeric transition between wobble A·C DNA base mispair and Watson–Crick-like A·C* mismatch: microstructural mechanism and biological significance. Physical Chemistry Chemical Physics 17:23, pages 15103-15110.
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Hydrogen Bond Disruption in DNA Base Pairs from
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C Transmutation
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