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Iuzzolino G, Perrella F, Valadan M, Petrone A, Altucci C, Rega N. Photophysics of a nucleic acid-protein crosslinking model strongly depends on solvation dynamics: an experimental and theoretical study. Phys Chem Chem Phys 2024; 26:11755-11769. [PMID: 38563904 DOI: 10.1039/d3cp06254f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
We present a combined experimental and theoretical study of the photophysics of 5-benzyluracil (5BU) in methanol, which is a model system for interactions between nucleic acids and proteins. A molecular dynamics study of 5BU in solution through efficient DFT-based hybrid ab initio potentials revealed a remarkable conformational flexibility - allowing the population of two main conformers - as well as specific solute-solvent interactions, which both appear as relevant factors for the observed 5BU optical absorption properties. The simulated absorption spectrum, calculated on such an ensemble, enabled a molecular interpretation of the experimental UV-Vis lowest energy band, which is also involved in the induced photo-reactivity upon irradiation. In particular, the first two excited states (mainly involving the uracil moiety) both contribute to the 5BU lowest energy absorption. Moreover, as a key finding, the nature and brightness of such electronic transitions are strongly influenced by 5BU conformation and the microsolvation of its heteroatoms.
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Affiliation(s)
- Gabriele Iuzzolino
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
| | - Fulvio Perrella
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
| | - Mohammadhassan Valadan
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, via Pansini 5, Napoli I-80131, Italy
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
| | - Alessio Petrone
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Biomediche Avanzate, Università degli Studi di Napoli Federico II, via Pansini 5, Napoli I-80131, Italy
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
- Istituto di Scienze Applicate e Sistemi Intelligenti "Eduardo Caianiello", URT UNINA, via Cintia 21, Napoli I-80126, Italy
| | - Nadia Rega
- Scuola Superiore Meridionale, Largo San Marcellino 10, Napoli I-80138, Italy
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, via Cintia 21, Napoli I-80126, Italy.
- Istituto Nazionale di Fisica Nucleare, Unità di Napoli, via Cintia 21, Napoli I-80126, Italy
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2
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Wang Y, Wei S. Influence of hydrogen bonds on the reaction of guanine and hydroxyl radical: DFT calculations in C(H +)GC motif. Phys Chem Chem Phys 2024; 26:5683-5692. [PMID: 38288746 DOI: 10.1039/d3cp05885a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
A comprehensive theoretical investigation was performed to illuminate the influence of hydrogen bonds (H-bonds) on the obscure reaction of a hydroxyl radical (HO˙) and guanine (G) by selecting the building block of parallel triplex DNA, C(H+)GC, as the model. By mapping the energy profiles for addition and hydrogen abstraction reactions, the favorable pathway is predicted. The results reveal that in the C(H+)GC context, barrierless hydrogen abstraction from N2 of G leading to a neutral radical G(N2-H)˙ appears to become significant, but electrophilic attack by HO˙ on C8 of G resulting in 8-oxoG is the most thermodynamically favorable course. This shows a strong structural dependence due to the context constrained by the H-bond, which is dramatically different from the situation in unencumbered G. More interestingly, it proves that the stability order of resulting adduct radicals is not altered by H-bonding, but the activity for possible sites of the hydroxylation reaction changes. The significant influence of the H-bond on elementary reactions involved in the reaction is emphasized in the C(H+)GC context but is not restricted to the H-abstraction reaction. It is greatly anticipated that the present study could provide thoughtful insights into the vague hydroxyl radical-induced oxidation chemistry.
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Affiliation(s)
- Yinghui Wang
- College of Science, Chang'an University, Xi'an 710064, China.
| | - Simin Wei
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Co-Construction Collaborative Innovation Center for Chinese Medicine Resources Industrialization by Shaanxi & Education Ministry, Shaanxi University of Chinese Medicine, Xianyang 712083, China.
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3
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Schaltz KF, Sauer SPA. A Theoretical Study of Hydrogen Abstraction Reactions in Guanosine and Uridine. Int J Mol Sci 2023; 24:ijms24098192. [PMID: 37175899 PMCID: PMC10179689 DOI: 10.3390/ijms24098192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/26/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
All practically possible hydrogen abstraction reactions for guanosine and uridine have been investigated through quantum chemical calculations of energy barriers and rate constants. This was done at the level of density functional theory (DFT) with the ωB97X-D functional and the 6-311++G(2df,2pd) Pople basis set. Transition state theory with the Eckart tunneling correction was used to calculate the rate constants. The results show that the reaction involving the hydrogen labelled C4' in the ribofuranose part has the largest rate constant for guanosine with the value 5.097×1010 L mol-1s-1 and the largest for uridine with the value 1.62×1010 L mol-1s-1. Based on the results for these two nucleosides, there is a noticeable similarity between the rate constants in the ribofuranose part of the molecule, even though they are bound to two entirely different nucleobases.
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Affiliation(s)
- Kasper F Schaltz
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
| | - Stephan P A Sauer
- Department of Chemistry, University of Copenhagen, DK-2100 Copenhagen Ø, Denmark
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KC S, Abolfath R. Towards the ionizing radiation induced bond dissociation mechanism in oxygen, water, guanine and DNA fragmentation: a density functional theory simulation. Sci Rep 2022; 12:19853. [PMID: 36400823 PMCID: PMC9674679 DOI: 10.1038/s41598-022-23727-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy and radio-biology, and critical to space projects. In this study, we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic acid (DNA) and the molecules surrounding DNA such as oxygen and water under non-equilibrium conditions using the first-principle calculations based on density functional theory (DFT). Our results reveal the structural stability of DNA bases and backbone that withstand up to a combined threshold of charge and hydrogen abstraction owing to simultaneously direct and indirect ionization processes. We show the hydrogen contents of the molecules significantly control the stability in the presence of radiation. This study provides comprehensive information on the impact of the direct and indirect induced bond dissociations and DNA damage and introduces a systematic methodology for fine-tuning the input parameters necessary for the large-scale Monte Carlo simulations of radio-biological responses and mitigation of detrimental effects of ionizing radiation.
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Affiliation(s)
- Santosh KC
- grid.186587.50000 0001 0722 3678Chemical and Materials Engineering, San José State University, San José, CA 95192 USA
| | - Ramin Abolfath
- grid.240145.60000 0001 2291 4776Department of Radiation Physics, University of Texas MD Anderson Cancer Center, Houston, TX 75031 USA
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5
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Lespade L, Bercion S. First principle molecular dynamics of hydroxyl radical induced oxidation of guanine and 2′-deoxyguanosine 5′-monophosphate in a cluster of water molecules. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2021.111386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Sørensen LN, Sauer SP. Implicit and explicit solvent models have opposite effects on radiation damage rate constant for thymine. ADVANCES IN QUANTUM CHEMISTRY 2022. [DOI: 10.1016/bs.aiq.2021.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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7
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Belkić D. Single charge exchange in collisions of energetic nuclei with biomolecules of interest to ion therapy. Z Med Phys 2020; 31:122-144. [PMID: 32928641 DOI: 10.1016/j.zemedi.2020.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/09/2020] [Accepted: 07/15/2020] [Indexed: 11/26/2022]
Abstract
This study is on the theory of single electron capture by fast nuclei from a variety of molecular targets of biological significance with high relevance to ion therapy of deep-seated tumors. The adopted theoretical framework is that of the first principles of quantum physics. As such, no free, adjustable parameters are used. This is in sharp contrast to the associated existing cross section input data to Monte Carlo simulations that all abound with empirical/phenomenological formulae. The present theory has the well-established track of its predictive power. This means that the computed cross sections can confidently be used in the cases for which no experimental data exist. These cross sections are from the full continuum distorted wave method (CDW). We first compute atomic cross sections in the independent electron model and then generate the corresponding molecular cross sections. The latter follow from the former within the independent atom model accompanied by the Bragg additivity rule. The investigated atomic targets are from the backbone of DNA and/or RNA molecules. These are atomic hydrogen, carbon, nitrogen and oxygen (H, C, N, O). Neon is also added to this sequence of targets as an isoelectronic atomic counterpart of water vapor, methane and ammonia molecules. The studied molecular targets are H2O (water vapor), CO (carbon-monoxide), CO2 (carbon-dioxide), CH4 (methane), C2H4 (ethylene), C2H6 (ethane), C4H10 (butane) as well as the DNA/RNA nucleobases C4H4N2O2 (uracil), C5H5N5 (adenine), C5H5N5O (guanine), C5H6N2O2 (thymine) and C4H5N3O (cytosine). The obtained total cross sections for any electronic target shell are compared with the available experimental data and overall favorable agreement is recorded at intermediate and high impact energies, which is the validity domain of the CDW method.
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Affiliation(s)
- Dževad Belkić
- Karolinska Institute, Department of Oncology-Pathology, P.O. Box 260, SE-171 76 Stockholm, Sweden; Karolinska University Hospital, Radiation Physics and Nuclear Medicine, SE-171 76 Stockholm, Sweden.
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8
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Yonetani Y, Nakagawa H. Understanding water-mediated DNA damage production by molecular dynamics calculation of solvent accessibility. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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9
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Biswas PK, Chakraborty S. Targeted DNA oxidation and trajectory of radical DNA using DFT based QM/MM dynamics. Nucleic Acids Res 2019; 47:2757-2765. [PMID: 30773597 PMCID: PMC6451130 DOI: 10.1093/nar/gkz089] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/27/2019] [Accepted: 02/04/2019] [Indexed: 01/06/2023] Open
Abstract
Molecular insight into electronic rearrangements and structural trajectories arising from oxidative damages to DNA backbone is of crucial importance in understanding the effect of ionizing radiation, developing DNA biosensors and designing effective DNA cleaving molecules. Employing a Density Functional Theory based multi-scale Quantum-Mechanical-Molecular-Mechanical (QM/MM) simulation and a suitable partitioning of the Hamiltonian on solvated nucleotide, and single-, and double-stranded DNA, we mimic hydrogen transfer reactions from the backbone by OH radicals and report structural trajectories arising from on-the-fly electronic charge- and spin-density redistribution in these three different structural topologies of DNA. Trajectories reveal that H4′ abstraction can disrupt the deoxyribose moiety through the formation of C4′=O4′ ketone and a π-bond with base at C1′-N9 in a nucleotide versus only partial ketone formation in single- and double-stranded DNA, where the orientation of the base is topologically restrained. However, H5′ abstraction can lead DNA cleavage at 5′ end through the formation of C5′=O5′ ketone and breakage of P-O5′ bond. Results demonstrate that structural damages from oxidative reactions are restrained by base stacking and base-pair hydrogen bonding. The methodology can be suitably used to study targeted DNA and RNA damages from radicals and radiomimetic drugs to design DNA cleaving molecules for chemotherapy.
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Affiliation(s)
- Pradip K Biswas
- Laboratory of Computational Biophysics and Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174, USA
| | - Sandipan Chakraborty
- Laboratory of Computational Biophysics and Bioengineering, Department of Physics, Tougaloo College, Tougaloo, MS 39174, USA
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10
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Plasma for cancer treatment: How can RONS penetrate through the cell membrane? Answers from computer modeling. Front Chem Sci Eng 2019. [DOI: 10.1007/s11705-018-1786-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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11
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Liu P, Wang Q, Niu M, Wang D. Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution. Sci Rep 2017; 7:7798. [PMID: 28798372 PMCID: PMC5552687 DOI: 10.1038/s41598-017-08219-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.
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Affiliation(s)
- Peng Liu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Qiong Wang
- College of Chemistry, Shandong Normal University, Jinan, 250014, China
| | - Meixing Niu
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China
| | - Dunyou Wang
- College of Physics and Electronics, Shandong Normal University, Jinan, 250014, China.
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12
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Grüber R, Aranda J, Bellili A, Tuñón I, Dumont E. Free energy profiles for two ubiquitous damaging agents: methylation and hydroxylation of guanine in B-DNA. Phys Chem Chem Phys 2017; 19:14695-14701. [PMID: 28537602 DOI: 10.1039/c6cp07966k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA methylation and hydroxylation are two ubiquitous reactions in DNA damage induction, yet insights are scarce concerning the free energy of activation within B-DNA. We resort to multiscale simulations to investigate the attack of a hydroxyl radical and of the primary diazonium onto a guanine embedded in a solvated dodecamer. Reaction free energy profiles characterize two strongly exergonic processes, yet allow unprecedented quantification of the barrier towards this damage reaction, not higher than 6 kcal mol-1 and sometimes inexistent, and of the exergonicities. In the case of the [G(C8)-OH]˙ intermediate, we challenge the functional dependence of such simulations: recently-proposed functionals, such as M06-2X and LC-BLYP, agree on a ∼4 kcal mol-1 barrier, whereas the hybrid GGA B3LYP functional predicts a barrier-less pathway. In the long term, multiscale approaches can help build up a unified panorama of DNA lesion induction. These results stress the importance of DFT/MM-MD simulations involving new functionals towards the sound modelling of biomolecule damage even in the ground state.
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Affiliation(s)
- R Grüber
- Univ. Lyon, Ens de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F-69342 Lyon, France.
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13
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Milhøj BO, Sauer SPA. The Effect of Solvation on the Radiation Damage Rate Constants for Adenine. Chemphyschem 2016; 17:3086-3095. [DOI: 10.1002/cphc.201600533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Birgitte O. Milhøj
- Department of Chemistry; University of Copenhagen; DK-2100 Copenhagen Ø Denmark
| | - Stephan P. A. Sauer
- Department of Chemistry; University of Copenhagen; DK-2100 Copenhagen Ø Denmark
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14
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Influence of solvating water molecules on the attacking mechanisms of OH-radical to DNA base pairs: DFT calculations in explicit waters. Struct Chem 2016. [DOI: 10.1007/s11224-016-0800-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Liang Y, Yang G, Liu F, Wang Y. Monte Carlo simulation of ionizing radiation induced DNA strand breaks utilizing coarse grained high-order chromatin structures. Phys Med Biol 2015; 61:445-60. [DOI: 10.1088/0031-9155/61/1/445] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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16
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Dumont E, Monari A. Understanding DNA under oxidative stress and sensitization: the role of molecular modeling. Front Chem 2015; 3:43. [PMID: 26236706 PMCID: PMC4500984 DOI: 10.3389/fchem.2015.00043] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/29/2015] [Indexed: 12/12/2022] Open
Abstract
DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
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Affiliation(s)
- Elise Dumont
- Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon Lyon, France
| | - Antonio Monari
- Université de Lorraine - Nancy, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France ; Centre National de la Recherche Scientifique, Theory-Modeling-Simulation, Structure et Réactivité des Systèmes Moléculaires Complexes (SRSMC) Vandoeuvre-les-Nancy, France
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17
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Grüber R, Dumont É. DFT investigation of the formation of linear aminols as the first step toward the induction of oxidatively generated interstrand cross-link DNA lesions. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1631-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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18
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Attri P, Kumar N, Park JH, Yadav DK, Choi S, Uhm HS, Kim IT, Choi EH, Lee W. Influence of reactive species on the modification of biomolecules generated from the soft plasma. Sci Rep 2015; 5:8221. [PMID: 25649786 PMCID: PMC4316168 DOI: 10.1038/srep08221] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/05/2015] [Indexed: 12/26/2022] Open
Abstract
Plasma medicine is an upcoming research area that has attracted the scientists to explore more deeply the utility of plasma. So, apart from the treating biomaterials and tissues with plasma, we have studied the effect of soft plasma with different feeding gases such as Air, N2 and Ar on modification of biomolecules. Hence, in this work we have used the soft plasma on biomolecules such as proteins ((Hemoglobin (Hb) and Myoglobin (Mb)), calf thymus DNA and amino acids. The structural changes or structural modification of proteins and DNA have been studied using circular dichroism (CD), fluorescence spectroscopy, protein oxidation test, gel electrophoresis, UV-vis spectroscopy, dynamic light scattering (DLS) and 1D NMR, while Liquid Chromatograph/Capillary Electrophoresis-Mass Spectrometer (LC/CE-MS) based on qualitative and quantitative bio-analysis have been used to study the modification of amino acids. Further, the thermal analysis of the protein has been studied with differential scanning calorimetry (DSC) and CD. Additionally, we have performed docking studies of H2O2 with Hb and Mb, which reveals that H2O2 molecules preferably attack the amino acids near heme group. We have also shown that N2 gas plasma has strong deformation action on biomolecules and compared to other gases plasma.
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Affiliation(s)
- Pankaj Attri
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea 139-701
| | - Naresh Kumar
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea 139-701
| | - Ji Hoon Park
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea 139-701
| | - Dharmendra Kumar Yadav
- Laboratory of Nanoscale Characterization &Environmental Chemistry, Department of Chemistry, College of Natural Sciences, Hanyang University, Seoul 133-791, Korea
| | - Sooho Choi
- Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea
| | - Han S Uhm
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea 139-701
| | - In Tae Kim
- Department of Chemistry, Kwangwoon University, Seoul, Korea 139-701
| | - Eun Ha Choi
- Plasma Bioscience Research Center/Department of Electrical and Biological Physics, Kwangwoon University, Seoul, Korea 139-701
| | - Weontae Lee
- Department of Biochemistry, College of Life Science &Biotechnology, Yonsei University, Seoul 120-749, Korea
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19
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Chaban GM, Wang D, Huo WM. Ab Initio Study of Guanine Damage by Hydroxyl Radical. J Phys Chem A 2015; 119:377-82. [DOI: 10.1021/jp508771g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Galina M. Chaban
- NASA Ames Research Center, Mail Stop 258-1, P.O.
Box 1, Moffett Field, California 94035-0001, United States
| | - Dunyou Wang
- Shandong Normal University, 88
E. Wenhua Road, Jinan, Shangdong 250014, P. R. China
| | - Winifred M. Huo
- NASA Ames Research Center, Mail Stop 258-1, Moffett
Field, California 94035-0001, United States
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20
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Park JH, Kumar N, Uhm HS, Lee W, Choi EH, Attri P. Effect of nanosecond-pulsed plasma on the structural modification of biomolecules. RSC Adv 2015. [DOI: 10.1039/c5ra04993h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Nanosecond-pulsed plasma (NPP) action on biomolecules modification.
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Affiliation(s)
- Ji Hoon Park
- Plasma Bioscience Research Center
- Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul
- Korea 139-701
| | - Naresh Kumar
- Plasma Bioscience Research Center
- Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul
- Korea 139-701
| | - Han Sup Uhm
- Plasma Bioscience Research Center
- Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul
- Korea 139-701
| | - Weontae Lee
- Department of Biochemistry
- College of Life Science & Biotechnology
- Yonsei University
- Seoul
- Korea
| | - Eun Ha Choi
- Plasma Bioscience Research Center
- Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul
- Korea 139-701
| | - Pankaj Attri
- Plasma Bioscience Research Center
- Department of Electrical and Biological Physics
- Kwangwoon University
- Seoul
- Korea 139-701
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21
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Shimizu E, Tokuyama Y, Okutsu N, Nomura K, Danilov VI, Kurita N. Attacking mechanism of hydroxyl radical to DNA base-pair: density functional study in vacuum and in water. J Biomol Struct Dyn 2014; 33:158-66. [PMID: 24460544 DOI: 10.1080/07391102.2013.864572] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Recently, the influence of radiation on human body has been recognized as a serious problem. In particular, highly reactive hydroxyl radicals *OH produced by the radiation react with DNA, resulting in a great damage on its structure and electronic properties. It is thus important to investigate the reaction mechanism of *OH to DNA for elucidating the initial damage in DNA induced by the radiation. In the present study, we search for transition states (TS) of the reaction between G-C/A-T base-pair and [Formula: see text] in vacuum and in water, by the density functional theory (DFT) calculations. At first, we obtain the stable structures for the dehydrogenated G-C and A-T, in which the hydrogen atom of NH2 group of G or A base is abstracted by [Formula: see text]. From the structures of the dehydrogenated as well as the natural base-pairs, the TS between these structures is searched for and the activation free energy (AFE) is estimated for the reaction. In vacuum, AFEs for the G-C and A-T are almost the same each other, while the stabilization energy by the reaction for G-C is about 4.9 kcal/mol larger than that for A-T, indicating that the population of the dehydrogenated G-C is remarkably larger than that of the dehydrogenated A-T in vacuum. On the other hand, in water approximated by the continuum solvation model, the AFE for A-T is 2.6 kcal/mol smaller than that for G-C, indicating that the reaction dehydrogenated by [Formula: see text] occurs more frequently for the solvated A-T base-pair than G-C.
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Affiliation(s)
- Eisuke Shimizu
- a Department of Computer Science and Engineering , Toyohashi University of Technology , Tempaku-cho, Toyohashi, Aichi 441 8580 , Japan
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Cerón-Carrasco JP, Jacquemin D, Dumont E. Impact of DNA Environment on the Intrastrand Cross-Link Lesions: Hydrogen Atom Release as the Last Step of Formation of G[8-5m]T. J Phys Chem B 2013; 117:16397-404. [DOI: 10.1021/jp408947u] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- José Pedro Cerón-Carrasco
- Departamento
de Quı́mica Fı́sica, Universidad de Murcia, 30100 Murcia, Spain
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2 Rue de la Houssinière, 44322 Nantes, Cedex 3, France
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2 Rue de la Houssinière, 44322 Nantes, Cedex 3, France
- Institut Universitaire de France, 103 bd St Michel, 75005 Paris, Cedex 5, France
| | - Elise Dumont
- Laboratoire de Chimie, UMR 5182 CNRS, École Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon, Cedex 07, France
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Bergonzo C, Galindo-Murillo R, Cheatham TE. Molecular modeling of nucleic acid structure: energy and sampling. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; 54:7.8.1-7.8.21. [PMID: 24510800 DOI: 10.1002/0471142700.nc0708s54] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.
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Affiliation(s)
- Christina Bergonzo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah
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24
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Abolfath RM, Carlson DJ, Chen ZJ, Nath R. A molecular dynamics simulation of DNA damage induction by ionizing radiation. Phys Med Biol 2013; 58:7143-57. [DOI: 10.1088/0031-9155/58/20/7143] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Kobori T, Sodeyama K, Otsuka T, Tateyama Y, Tsuneyuki S. Trimer effects in fragment molecular orbital-linear combination of molecular orbitals calculation of one-electron orbitals for biomolecules. J Chem Phys 2013; 139:094113. [DOI: 10.1063/1.4818599] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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26
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Jovanović V, Miyazaki Y, Ebata T, Petković M. Vibrational Spectroscopy of Picolinamide and Water: From Dimers to Condensed Phase. J Phys Chem A 2013; 117:6474-82. [DOI: 10.1021/jp402033c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Vladimir Jovanović
- Institute of Theoretical and
Computational Chemistry, Heinrich-Heine-University Düsseldorf, Universitätsstraβe 1, 40225 Düsseldorf, Germany
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12, 11 158 Belgrade,
Serbia
| | - Yasunori Miyazaki
- Department of Chemistry, Graduate
School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Takayuki Ebata
- Department of Chemistry, Graduate
School of Science, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Milena Petković
- Faculty of Physical Chemistry, University of Belgrade, Studentski trg 12, 11 158 Belgrade,
Serbia
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Chakraborty S, Biswas PK. Elucidation of the Mechanistic Pathways of the Hydroxyl Radical Scavenging Reaction by Daidzein Using Hybrid QM/MM Dynamics. J Phys Chem A 2012; 116:8775-85. [DOI: 10.1021/jp303543z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Sandipan Chakraborty
- Laboratory of Computational Biophysics & Bioengineering Department of Physics, Tougaloo College, Tougaloo Mississippi 39174, United States
| | - P. K. Biswas
- Laboratory of Computational Biophysics & Bioengineering Department of Physics, Tougaloo College, Tougaloo Mississippi 39174, United States
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28
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Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: energy and sampling. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2001; Chapter 7:Unit-7.8. [PMID: 18428876 PMCID: PMC4029503 DOI: 10.1002/0471142700.nc0708s04] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit expands an accompanying overview unit (UNIT 7.5) by discussing methods used to treat the energy and sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields.
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