1
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Mu H, Li H, Sun C, Gao J, Yang M, Xin C, Jin G. Different competition mechanism between ESPT and TICT process regulated by protic and aprotic solvent in DHP. J Mol Liq 2023. [DOI: 10.1016/j.molliq.2023.121278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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2
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Computational investigation on potential energy surface evolution: The tautomerization from enediyne to enyne-allene. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2021.139298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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3
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Li C, Hu B, Cao Y, Li Y. Elaborating the excited-state double proton transfer mechanism and multiple fluorescent characteristics of 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119854. [PMID: 33933943 DOI: 10.1016/j.saa.2021.119854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/28/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Recently, Krishnamoorthy and coworkers reported a new type of proton transfer, which was labeled as 'proton transfer triggered proton transfer', in 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole (bis-HPTA). In this work, the excited-state double proton transfer (ESDPT) mechanism and multiple fluorescent characteristics of bis-HPTA were investigated. Upon photo-excitation, the intramolecular hydrogen bonding strength changed and the electron density of bis-HPTA redistributed. These changes will affect the proton transfer process. In S0 state, the proton transfer processes of bis-HPTA were prohibited on the stepwise and concerted pathways. After vertical excitation to the S1 state, the ESIPT-II process was more likely to occur than the ESIPT-I process, which was contrary to the conclusion that the ESIPT-II process is blocked and the ESIPT-II process takes place after the ESIPT-I process proposed by Krishnamoorthy and coworkers. When the K2 tautomer was formed through the ESIPT-II process, the second proton transfer process on the stepwise pathway was prohibited. On another stepwise pathway, after the ESIPT-I process (form the K1 tautomer), the second proton transfer process should overcome a higher potential barrier than the ESIPT-I process to form ESDPT tautomer. On the concerted pathway, the bis-HPTA can synchronous transfer double protons to form the ESDPT tautomer. The ESDPT tautomer was unstable and immediately converted to the K2 tautomer via a barrierless reverse proton transfer process. Thus, the fluorescent maximum at 465 nm from the ESDPT tautomer reported by Krishnamoorthy and coworkers was ascribed to the K2 tautomer. Most of the fluorophores show dual fluorescent properties, while the bis-HPTA undergoing ESDPT process exhibited three well-separated fluorescent peaks, corresponding to its normal form (438 nm), K1 tautomer (462 nm) and K2 tautomer (450 nm), respectively.
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Affiliation(s)
- Chaozheng Li
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Bo Hu
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yonghua Cao
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yongfeng Li
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
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4
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Yu XF, Fu TH, Xiao B, Yu HY, Li Q. A theoretical study on the excited-state deactivation paths for the A-5FU dimer. Phys Chem Chem Phys 2021; 23:16089-16106. [PMID: 34291779 DOI: 10.1039/d1cp00030f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.
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Affiliation(s)
- Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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5
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Gheorghiu A, Coveney PV, Arabi AA. The influence of base pair tautomerism on single point mutations in aqueous DNA. Interface Focus 2020; 10:20190120. [PMID: 33178413 PMCID: PMC7653342 DOI: 10.1098/rsfs.2019.0120] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2020] [Indexed: 12/11/2022] Open
Abstract
The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.
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Affiliation(s)
- A Gheorghiu
- Centre for Computational Science, University College London, London, UK
| | - P V Coveney
- Centre for Computational Science, University College London, London, UK.,Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - A A Arabi
- Centre for Computational Science, University College London, London, UK.,College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, PO Box 17666, Al Ain, United Arab Emirates
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6
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Li C, Tang Z, Zhou P, Guo W. A distinct excited-state proton transfer mechanism for 4-(N-Substituted-amino)-1H-pyrrolo[2,3-b]pyridines in aprotic and protic solvents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:117800. [PMID: 31836400 DOI: 10.1016/j.saa.2019.117800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Time-dependent density functional theory (TDDFT) method was used to study the different excited states proton transfer mechanism of DPP in cyclohexane (CHE) and Methanol (MeOH). The results indicate that the concerted mechanism and the stepwise mechanism coexist in the double proton transfer process of DPP dimer in the aprotic solvent CHE, the stepwise mechanism predominates. The stepwise mechanism can only carry out single proton transfer (DPP-SPT), the second proton cannot be transferred because it is hindered by high energy barriers. The concerted mechanism produces a double proton transfer (DPP-DPT). The potential energy surface of the DPP dimer was calculated and the double fluorescence phenomenon of DPP dimer observed by Chou et al. (P.T. Chou, Y.I. Liu, H.W. Liu, W.S. Yu, Dual Excitation behavior of double proton transfer versus Charge Transfer in 4-(N-Substituted Amino)-1H-pyrrolo[2,3-b]pyridines tuned by dielectric and hydrogen-bonding perturbation, J. Am. Chem. Soc., 123 (2001) 12119-12120) was explained. In view of the protonic solvent effect of methanol, the potential energy curve of the DPP/MeOH cluster was constructed. The fluorescence quenching process of DPP/MeOH clusters was elucidated. The proton transfer pathways of DPP/MeOH clusters are revealed in two different concerted ways (Type A: protons transfer from DPP molecules to MeOH solvent molecules; Type B: protons transfer from MeOH solvent to DPP molecules). The ESPT process of DPP molecules in the protic solvent MeOH was found to be more prone to Type B. The results can help to better understand the intermolecular hydrogen bonding mechanism of DPP molecules.
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Affiliation(s)
- Changming Li
- School of Electrical Engineering, University of South China, Hengyang 421001, PR China; Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China
| | - Zhe Tang
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China; State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Wei Guo
- School of Electrical Engineering, University of South China, Hengyang 421001, PR China.
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7
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Sun Y, Moe MM, Liu J. Is non-statistical dissociation a general feature of guanine–cytosine base-pair ions? Collision-induced dissociation of a protonated 9-methylguanine–1-methylcytosine Watson–Crick base pair, and comparison with its deprotonated and radical cation analogues. Phys Chem Chem Phys 2020; 22:24986-25000. [DOI: 10.1039/d0cp04243a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Non-statistical dissociation of a protonated guanine–cytosine Watson–Crick base pair.
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Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
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8
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Soler-Polo D, Mendieta-Moreno JI, Trabada DG, Mendieta J, Ortega J. Proton Transfer in Guanine-Cytosine Base Pairs in B-DNA. J Chem Theory Comput 2019; 15:6984-6991. [DOI: 10.1021/acs.jctc.9b00757] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Diego Soler-Polo
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jesús I. Mendieta-Moreno
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Daniel G. Trabada
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
| | - Jesús Mendieta
- Departamento de Biotecnología, Universidad Francisco de Vitoria, E-28223 Pozuelo de Alarcón, Madrid, Spain
| | - José Ortega
- Departamento de Física Teórica de la Materia Condensada and Condensed Matter Physics Center (IFIMAC), Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain
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9
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Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
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10
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i-Motif DNA structures upon electric field exposure: completing the map of induced genetic errors. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2423-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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11
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Weingart O, Reschke B, Marian C. Solvent mediated catalysis and proton-shuttling in the formation of 3-methylphthalide from a ketene intermediate. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Das S, Nam K, Major DT. Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA. J Chem Theory Comput 2018; 14:1695-1705. [DOI: 10.1021/acs.jctc.7b00964] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Susanta Das
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Kwangho Nam
- Department of Chemistry, Umeå University, 901 87 Umeå, Sweden
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019-0065, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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13
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Mechanisms for guanine–cytosine tautomeric equilibrium in solution via steered molecular dynamic simulations. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.12.091] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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14
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Consequences of EPR–Proton Qubits Populating DNA. ADVANCES IN QUANTUM CHEMISTRY 2018. [DOI: 10.1016/bs.aiq.2017.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Pohl R, Socha O, Slavíček P, Šála M, Hodgkinson P, Dračínský M. Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations. Faraday Discuss 2018; 212:331-344. [PMID: 30234207 DOI: 10.1039/c8fd00070k] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.
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Affiliation(s)
- Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Ondřej Socha
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Petr Slavíček
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague, Czech Republic
| | - Michal Šála
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
| | - Paul Hodgkinson
- Department of Chemistry, Durham University, South Road, DH1 3LE, Durham, UK
| | - Martin Dračínský
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610, Prague, Czech Republic.
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16
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Giribet CG, Ruiz de Azúa MC. IPPP-CLOPPA Analysis of the Influence of the Methylation on the Potential Energy and the Molecular Polarizability of the Hydrogen Bonds in the Cytosine-Guanine Base Pair. J Phys Chem A 2017; 121:2960-2970. [PMID: 28350166 DOI: 10.1021/acs.jpca.6b10059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The IPPP-CLOPPA method is applied to investigate the influence of a methyl group on the energy of the hydrogen bonds and the potential energy curve of the bridge protons in model compounds, which mimic the methylated and unmethylated cytosine-guanine base pairs. On the same grounds, this influence on the polarizability of the intermolecular hydrogen bonds of these compounds is also addressed, in order to determine whether this linear response property provides a significant proof of the electronic mechanisms that affect the stabilization of the hydrogen bonds. Results obtained show that the methyl electronic system delocalizes on the hydrogen bond region, and changes of these intermolecular hydrogen bonds are due to this effect of delocalization.
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Affiliation(s)
- Claudia G Giribet
- Facultad de Ciencias Exactas y Naturales, Departamento de Física, Universidad de Buenos Aires , 1428 Buenos Aires, Argentina.,Instituto de Física de Buenos Aires (IFIBA), CONICET, Universidad de Buenos Aires , 1428 Buenos Aires, Argentina
| | - Martín C Ruiz de Azúa
- Facultad de Ciencias Exactas y Naturales, Departamento de Física, Universidad de Buenos Aires , 1428 Buenos Aires, Argentina.,Instituto de Física de Buenos Aires (IFIBA), CONICET, Universidad de Buenos Aires , 1428 Buenos Aires, Argentina
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17
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Roßbach S, Ochsenfeld C. Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA. J Chem Theory Comput 2017; 13:1102-1107. [PMID: 28195707 DOI: 10.1021/acs.jctc.6b00727] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of embedding and coupling schemes on the convergence of the QM size in the QM/MM approach is investigated for the transfer of a proton in a DNA base pair. We find that the embedding scheme (mechanical or electrostatic) has a much greater impact on the convergence behavior than the coupling scheme (additive QM/MM or subtractive ONIOM). To achieve size convergence, QM regions with up to 6000 atoms are necessary for pure QM or mechanical embedding. In contrast, electrostatic embedding converges faster: for the example of the transfer of a proton between DNA base pairs, we recommend including at least five base pairs and 5 Å of solvent (including counterions) into the QM region, i.e., a total of 1150 atoms.
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Affiliation(s)
- Sven Roßbach
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr. 7, D-81377 Munich, Germany.,Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr, 5-13, D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr. 7, D-81377 Munich, Germany.,Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry, University of Munich (LMU Munich) , Butenandtstr, 5-13, D-81377 Munich, Germany
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18
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Li C, Yang Y, Li D, Liu Y. A theoretical study of the potential energy surfaces for the double proton transfer reaction of model DNA base pairs. Phys Chem Chem Phys 2017; 19:4802-4808. [DOI: 10.1039/c6cp07716a] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited-state double proton transfer (ESDPT) mechanism in a model DNA base pair, 7-azaindole (7AI) dimer, has been debated over the years.
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Affiliation(s)
- Chaozheng Li
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Yonggang Yang
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Donglin Li
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Yufang Liu
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
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19
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Cerón-Carrasco JP, Jacquemin D. Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors. Phys Chem Chem Phys 2017; 19:9358-9365. [DOI: 10.1039/c7cp01034f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.
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Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics and High Performance Computing Research Group (BIO-HPC)
- Universidad Católica San Antonio de Murcia (UCAM)
- Murcia
- Spain
| | - Denis Jacquemin
- CEISAM
- UMR CNRS 6230
- BP 92208
- Université de Nantes
- 44322 Nantes Cedex 3
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20
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Cerón-Carrasco JP, Jacquemin D. DNA spontaneous mutation and its role in the evolution of GC-content: assessing the impact of the genetic sequence. Phys Chem Chem Phys 2015; 17:7754-60. [DOI: 10.1039/c4cp05806b] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We use theoretical tools to investigate the possible role played by a DNA sequence in the base pair tautomerization phenomena.
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21
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Godbeer AD, Al-Khalili JS, Stevenson PD. Modelling proton tunnelling in the adenine–thymine base pair. Phys Chem Chem Phys 2015; 17:13034-44. [DOI: 10.1039/c5cp00472a] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Environment-assisted quantum tunnelling is unlikely to play a significant role in adenine–thymine tautomerisation.
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22
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Jacquemin D, Zúñiga J, Requena A, Céron-Carrasco JP. Assessing the importance of proton transfer reactions in DNA. Acc Chem Res 2014; 47:2467-74. [PMID: 24849375 DOI: 10.1021/ar500148c] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.
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Affiliation(s)
- Denis Jacquemin
- CEISAM, UMR CNRS 6230, Université de Nantes, 2, Rue de la Houssinière, Nantes 44322 Cedex 3, France
- Institut Universitaire de France, 103 bd St Michel, Paris 75005 Cedex 5, France
| | - José Zúñiga
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - Alberto Requena
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
| | - José Pedro Céron-Carrasco
- Departamento
de Química Física, Facultad de Química, Campus
de Excelencia Internacional Regional “Campus Mare Nostrum”, Universidad de Murcia, 30100 Murcia, Spain
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23
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Zheng S, Pfaendtner J. Enhanced sampling of chemical and biochemical reactions with metadynamics. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.923574] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Kim KT, Kim HW, Moon D, Rhee YM, Kim BH. (DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences. Org Biomol Chem 2014; 11:5605-14. [PMID: 23846401 DOI: 10.1039/c3ob41222a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
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25
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Lee W, Engels B. The Protonation State of Catalytic Residues in the Resting State of KasA Revisited: Detailed Mechanism for the Activation of KasA by Its Own Substrate. Biochemistry 2014; 53:919-31. [DOI: 10.1021/bi401308j] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Wook Lee
- Institut für Physikalische
und Theoretische Chemie, Universität Würzburg, Emil-Fischer
Strasse 42, 97074 Würzburg, Germany
| | - Bernd Engels
- Institut für Physikalische
und Theoretische Chemie, Universität Würzburg, Emil-Fischer
Strasse 42, 97074 Würzburg, Germany
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26
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Klippenstein SJ, Pande VS, Truhlar DG. Chemical Kinetics and Mechanisms of Complex Systems: A Perspective on Recent Theoretical Advances. J Am Chem Soc 2014; 136:528-46. [DOI: 10.1021/ja408723a] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Stephen J. Klippenstein
- Chemical
Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Vijay S. Pande
- Department
of Chemistry and Structural Biology, Stanford University, Stanford, California 94305, United States
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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27
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Abstract
Photoinduced processes in nucleic acids are phenomena of fundamental interest in diverse fields, from prebiotic studies, through medical research on carcinogenesis, to the development of bioorganic photodevices. In this contribution we survey many aspects of the research across the boundaries. Starting from a historical background, where the main milestones are identified, we review the main findings of the physical-chemical research of photoinduced processes on several types of nucleic-acid fragments, from monomers to duplexes. We also discuss a number of different issues which are still under debate.
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Affiliation(s)
- Mario Barbatti
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany,
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28
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Brovarets' OO, Zhurakivsky RO, Hovorun DM. Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question. J Comput Chem 2013; 35:451-66. [PMID: 24382756 DOI: 10.1002/jcc.23515] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Revised: 11/12/2013] [Accepted: 11/30/2013] [Indexed: 02/04/2023]
Abstract
Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form.
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Affiliation(s)
- Ol'ha O Brovarets'
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Akademika Zabolotnoho Str., 03680, Kyiv, Ukraine ; Research and Educational Center "State Key Laboratory of Molecular and Cell Biology", 150 Akademika Zabolotnoho Str., 03680, Kyiv, Ukraine; Department of Molecular Biology, Biotechnology and Biophysics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, 2-h Akademika Hlushkova Ave., 03022, Kyiv, Ukraine
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29
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Wu Y, Wang H, Lin Y, Gao S, Zhang F. Hydrogen-bonded proton transfer in the hydrated adenine–thymine anion. CAN J CHEM 2013. [DOI: 10.1139/cjc-2013-0162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The proton transfer processes of microhydrated adenine–thymine anions are studied using density functional theory with the B3LYP method and DZP++ basis set. The microhydration effects on the geometrical structures, adsorption site, and the proton transfer reaction of the adenine–thymine anion are investigated. The site N10 atom of the adenine moiety has a larger proton affinity than the site O24 atom of thymine, which facilitates the proton H26 transfers from the N25 site of thymine to the N10 site of adenine. Therefore, the first single-proton transfer pathway (SPT1) is found for the all of the monohydrated adenine–thymine anions (AN4T)−·H2O, (AN13T)−·H2O, (ATO24)−·H2O, and (ATO28)−·H2O and tetrahydrated adenine–thymine anions (AT)−·4H2O. The proton H9 at the N7 site of adenine is also found to transfer to the O24 site of thymine for (AN4T)−·H2O and (AN13T)−·H2O in the gas phase. The double-proton transferred pathway is found when one water molecule interacts with the O28 atom of thymine. The reactant structures before the proton transfer are more stable than the product structures, and the structural changes mainly occur in thymine. The reaction energies of the microhydrated adenine–thymine anion in the gas phase and in the aqueous environment predict that the proton transfer process of the microhydrated adenine–thymine anion are more favorable in the gas phase than in aqueous solution.
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Affiliation(s)
- Yingxi Wu
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Hongyan Wang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yuexia Lin
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Simin Gao
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Feng Zhang
- School of Physical Science and Technology, Southwest Jiaotong University, Chengdu 610031, P.R. China
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30
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Brovarets’ OO, Hovorun DM. Why the tautomerization of the G·C Watson–Crick base pairviathe DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis. J Biomol Struct Dyn 2013; 32:1474-99. [DOI: 10.1080/07391102.2013.822829] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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31
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Lee W, Engels B. Clarification on the Decarboxylation Mechanism in KasA Based on the Protonation State of Key Residues in the Acyl-Enzyme State. J Phys Chem B 2013; 117:8095-104. [DOI: 10.1021/jp403067m] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wook Lee
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Emil-Fischer Strasse 42, 97074, Würzburg, Germany
| | - Bernd Engels
- Institut
für Physikalische und Theoretische
Chemie, Universität Würzburg, Emil-Fischer Strasse 42, 97074, Würzburg, Germany
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32
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Cerón-Carrasco JP, Jacquemin D. Electric-field induced mutation of DNA: a theoretical investigation of the GC base pair. Phys Chem Chem Phys 2013; 15:4548-53. [DOI: 10.1039/c2cp44066k] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Cerón-Carrasco JP, Jacquemin D. Electric field induced DNA damage: an open door for selective mutations. Chem Commun (Camb) 2013; 49:7578-80. [DOI: 10.1039/c3cc42593b] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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