1
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Lucia-Tamudo J, Nogueira JJ, Díaz-Tendero S. Charge Transfer Mechanism in Guanine-Based Self-Assembled Monolayers on a Gold Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:15129-15139. [PMID: 38984413 PMCID: PMC11270990 DOI: 10.1021/acs.langmuir.4c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
In this work, we have theoretically determined the one-electron oxidation potentials and charge transfer mechanisms in complex systems based on a self-assembled monolayer of guanine molecules adsorbed on a gold surface through different organic linkers. Classical molecular dynamics simulations were carried out to sample the conformational space of both the neutral and the cationic species. Thus, the redox potentials were determined for the ensembles of geometries through multiscale quantum-mechanics/molecular-mechanics/continuum solvation model calculations in the framework of the Marcus theory and in combination with an additive scheme previously developed. In this context, conformational sampling, description of the environment, and effects caused by the linker have been considered. Applying this methodology, we unravel the phenomena of electric current transport by evaluating the different stages in which charge transfer could occur. The results revealed how the positive charge migrates from the organic layer to the gold surface. Specifically, the transport mechanism seems to take place mainly along a single ligand and driven with the help of the electrostatic interactions of the surrounding molecules. Aside, several self-assembled monolayers with different linkers have been analyzed to understand how the nature of that moiety can tune the redox properties and the efficiency of the transport. We have found that the conjugation between the guanine and the linker, at the same time conjugated to the gold surface, gives rise to a more efficient transport. In conclusion, the established computational protocol sheds light on the mechanism behind charge transport in electrochemical DNA-based biosensor nanodevices.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
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2
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches. J Chem Inf Model 2024; 64:4802-4810. [PMID: 38856665 PMCID: PMC11200263 DOI: 10.1021/acs.jcim.4c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The number of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge-transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes, and the Marcus theory. One-electron oxidation potential and hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by clustering analysis provides accurate results when compared with those obtained from sampling, reducing considerably the computational cost.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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3
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Somseemee O, Siriwong K, Sae-Oui P, Harnchana V, Appamato I, Prada T, Siriwong C. Preparation of UV-cured cellulose nanocrystal-filled epoxidized natural rubber and its application in a triboelectric nanogenerator. Int J Biol Macromol 2024; 262:130109. [PMID: 38346626 DOI: 10.1016/j.ijbiomac.2024.130109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/11/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
Cellulose nanocrystal (CNC) is an abundant biopolymer possessing high strength and biodegradability. In the present work, the extraction of CNCs from Napier grass stems was carried out. The CNCs were subsequently modified by maleic anhydride, called M-CNC, before being incorporated into the epoxidized natural rubber (ENR). The compounds were later cured by ultraviolet (UV) irradiation under various conditions. The obtained optimum condition was then used to fabricate the biocomposites filled with various CNC and M-CNC loadings for triboelectric nanogenerator (TENG) performance measurements. Output voltage and current increased continuously with increasing filler loading. Regardless of the filler type, an increase in filler loading enhanced TENG output. ENR/M-CNC exhibited a superior TENG output to ENR/CNC due to the greater electron transfer capability of the biocomposites, as proven by the reduction in the ionization potential (IP) value obtained from the quantum calculation. In this study, ENR/M-CNC5 exhibited the maximum output voltage (80.3 V), current (7.4 μA), and power density (1.32 W/m2) at a load resistance of 9 MΩ.
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Affiliation(s)
- Oranooch Somseemee
- Materials Chemistry Research Center (MCRC), Department of Chemistry and Center of excellence for innovation in Chemistry (PERCH-CIC), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; Department of Chemistry, Faculty of Engineering, Rajamangala University of Technology Isan, Khon Kaen Campus, Khon Kaen 40000, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Center (MCRC), Department of Chemistry and Center of excellence for innovation in Chemistry (PERCH-CIC), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Pongdhorn Sae-Oui
- MTEC, National Science and Technology Development Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
| | - Viyada Harnchana
- Institute of Nanomaterials Research and Innovation for Energy (IN-RIE), NANOTEC-KKU RNN on Nanomaterials Research and Innovation for Energy, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Intuorn Appamato
- Materials Science and Nanotechnology Program, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Teerayut Prada
- Materials Science and Nanotechnology Program, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Chomsri Siriwong
- Materials Chemistry Research Center (MCRC), Department of Chemistry and Center of excellence for innovation in Chemistry (PERCH-CIC), Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.
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4
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Zhou Q, Guo W, Hu Z, Yan S, Jie J, Su H. Can methylated purine bases act as photoionization hotspots? Photochem Photobiol 2024; 100:368-379. [PMID: 37792888 DOI: 10.1111/php.13862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
The direct photoionization of DNA canonical bases under ultraviolet radiation is difficult due to the high ionization potentials. According to previous quantum chemical calculations, methylation can have great influence on the ionization potential. Are methylated nucleobases prone to photoionization and cause DNA damage? As an important epigenetic modification in transcription, expression, and regulation of genes, it is of great biological significance to explore the effect of methylation on base photoionization from the experimental perspective. Herein, we study the photoionization behavior of methylated purines 6 mA and 6mG at 266 nm using a nanosecond transient UV-Vis spectroscopy. The hydrated electron and methylated base radicals are observed, indicating the occurrence of photoionization for both 6mG and 6 mA. We measured one-photon ionization yields to be (5.0 ± 0.2) × 10-3 and (1.4 ± 0.2) × 10-3 for 6mG and 6 mA, respectively. These are higher than those of (dA)20 and (dA20 )·(dT20 ) previously reported, indicating that methylation significantly promotes base photoionization with a stronger effect than base stacking, consistent with calculations in literature. Given that the hydrated electrons and methylated base radicals from photoionization can trigger a cascade of deleterious reactions, the methylated purine bases may act as hotspots of DNA photoionization damage of living organisms.
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Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Wenwen Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuyi Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing, China
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5
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Kılıç M, Diamantis P, Johnson SK, Toth O, Rothlisberger U. Redox-Based Defect Detection in Packed DNA: Insights from Hybrid Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2023; 19:8434-8445. [PMID: 37963372 PMCID: PMC10687876 DOI: 10.1021/acs.jctc.3c01013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/16/2023]
Abstract
The impact of an 8-oxoguanine (8oxoG) defect on the redox properties of DNA within the nucleosome core particle (NCP) was investigated employing hybrid quantum mechanical/molecular mechanics (QM/MM) molecular dynamics simulations of native and 8oxoG-containing NCP systems with an explicit representation of a biologically relevant environment. Two distinct NCP positions with varying solvent accessibility were considered for 8oxoG insertion. In both cases, it is found that the presence of 8oxoG drastically decreases the redox free energy of oxidation by roughly 1 eV, which is very similar to what was recently reported for free native and 8oxoG-containing DNA. In contrast, the effect of 8oxoG on the reorganization free energy is even smaller for packed DNA (decrease of 0.13 and 0.01 eV for defect-free and defect-containing systems, respectively) compared to the one for free DNA (0.25 eV), consistent with the increased rigidity of the NCP as compared to free DNA. Furthermore, the presence of an 8oxoG defect does not yield any significant changes in the packed DNA structure. Such a conclusion favors the idea that in the case of chromatin, defect-induced changes in DNA redox chemistry can also be exploited to detect damaged bases via DNA-mediated hole transfer.
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Affiliation(s)
| | | | - Sophia K. Johnson
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Oliver Toth
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry
and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale
de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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6
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Lucia-Tamudo J, Alcamí M, Díaz-Tendero S, Nogueira JJ. One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA. Biochemistry 2023; 62:3312-3322. [PMID: 37923303 PMCID: PMC10666269 DOI: 10.1021/acs.biochem.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
| | - Manuel Alcamí
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Sergio Díaz-Tendero
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
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7
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Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA. Phys Chem Chem Phys 2023; 25:14578-14589. [PMID: 37191244 DOI: 10.1039/d3cp00884c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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8
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Lucia-Tamudo J, Nogueira JJ, Díaz-Tendero S. An Efficient Multilayer Approach to Model DNA-Based Nanobiosensors. J Phys Chem B 2023; 127:1513-1525. [PMID: 36779932 PMCID: PMC9969517 DOI: 10.1021/acs.jpcb.2c07225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
In this work, we present a full computational protocol to successfully obtain the one-electron reduction potential of nanobiosensors based on a self-assembled monolayer of DNA nucleobases linked to a gold substrate. The model is able to account for conformational sampling and environmental effects at a quantum mechanical (QM) level efficiently, by combining molecular mechanics (MM) molecular dynamics and multilayer QM/MM/continuum calculations within the framework of Marcus theory. The theoretical model shows that a guanine-based biosensor is more prone to be oxidized than the isolated nucleobase in water due to the electrostatic interactions between the assembled guanine molecules. In addition, the redox properties of the biosensor can be tuned by modifying the nature of the linker that anchor the nucleobases to the metal support.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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9
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Lee W, Matsika S. Mechanistic Aspects of the Effect of Flanking Nucleotide Sequence on CPD Formation and CPD Self-Repair in DNA. J Phys Chem B 2023; 127:18-25. [PMID: 36574488 DOI: 10.1021/acs.jpcb.2c06680] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A cyclobutane pyrimidine dimer (CPD) is a photolesion which is produced by a cycloaddition reaction between two stacked pyrimidine bases upon UV light absorption. Because of its harmful effect on important cellular processes involving DNA and especially its relevance to skin cancer, the mechanisms of how a CPD is formed or repaired have been studied extensively, and it has been demonstrated that flanking nucleotide sequences play a crucial role in CPD formation or self-repair. Understanding the mechanisms behind this sequence dependence of CPD formation or self-repair is of great importance because it can give us valuable information on which sequence will be vulnerable to this DNA photodamage. This Perspective focuses on the mechanisms of how flanking nucleotide sequences affect CPD formation or self-repair, especially highlighting the role of computational studies in this field.
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Affiliation(s)
- Wook Lee
- Department of Biochemistry, Kangwon National University, Chuncheon 24341, Korea
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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10
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Beheshti A, Pourbasheer E, Ganjali MR. Density function theory calculation to study the oxidation potential of electron-donating compounds; affirming the oxidation mechanism by NICS calculations. J Mol Model 2023; 29:32. [PMID: 36609766 DOI: 10.1007/s00894-022-05431-1] [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: 02/16/2022] [Accepted: 12/18/2022] [Indexed: 01/09/2023]
Abstract
The manuscript describes a method for understanding the correlation of structural features and first oxidation potentials [Formula: see text] of electron-donating compounds (EDCs) with tetrathiafulvalene (TTF), dithiadiazafulvalenes (DTDAF), and tetraazafulvalene (TAF) frameworks. The density functional theory (DFT) procedure at B3LYP (6-31 + g(d)) was used for geometric optimization, given the large dimensions of the molecules studied, and their high structural similarity. First of all, the correlation between the oxidation potential and the highest occupied molecular orbital (HOMO) energy level as an effective quantum chemical descriptor was examined. Then, nucleus-independent chemical shifts (NICSs) calculation was applied to affirm the oxidation mechanism and interpret the effect of replacing the sulfur atoms by nitrogen, on the oxidation process. Finally, a more comprehensive investigation of structural features that affect the oxidation potential, topological, geometrical, constitutional, as well as, electrostatic, charged partial surface area, quantum-chemical, molecular orbital, and thermodynamic descriptors was calculated. A predictive model was developed based on the genetic algorithm multivariate linear regression (GA-MLR). There was an outstanding agreement between the theoretical and the experimental values obtained for the first oxidation potentials of the test set (Q2Ext = 0.981).
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Affiliation(s)
- Abolghasem Beheshti
- Department of Chemistry, Payame Noor University (PNU), P.O. Box, 19395-3697, Tehran, Iran.
| | - Eslam Pourbasheer
- Department of Chemistry, Faculty of Science, University of Mohaghegh Ardabili, P.O. Box 179, Ardabil, Iran
| | - Mohammad Reza Ganjali
- Center of Excellence in Electrochemistry, Faculty of Chemistry, University of Tehran, Tehran, Iran.,National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
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11
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Study of the Electrochemical Behavior of N-Substituted-4-Piperidones Curcumin Analogs: A Combined Experimental and Theoretical Approach. Int J Mol Sci 2022; 23:ijms232315043. [PMID: 36499370 PMCID: PMC9736124 DOI: 10.3390/ijms232315043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/20/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
The electrochemical behavior of N-methyl- and N-benzyl-4-piperidone curcumin analogs were studied experimentally and theoretically. The studied compounds present different substituents at the para position in the phenyl rings (-H, -Br, -Cl, -CF3, and -OCH3). We assessed their electrochemical behavior by differential pulse and cyclic voltammetry, while we employed density functional theory (DFT) M06 and M06-2x functionals along with 6-311+G(d,p) basis set calculations to study them theoretically. The results showed that compounds suffer a two-electron irreversible oxidation in the range of 0.72 to 0.86 V, with surface concentrations ranging from 1.72 × 10-7 to 5.01 × 10-7 mol/cm2. The results also suggested that the process is diffusion-controlled for all compounds. M06 DFT calculations showed a better performance than M06-2x to obtain oxidation potentials. We found a good correlation between the experimental and theoretical oxidation potential for N-benzyl-4-piperidones (R2 = 0.9846), while the correlation was poor for N-methyl-4-piperidones (R2 = 0.3786), suggesting that the latter suffer a more complex oxidation process. Calculations of the BDEs for labile C-H bonds in the compounds suggested that neither of the two series of compounds has a different tendency for a proton-coupled electron transfer (PCET) oxidation process. It is proposed that irreversible behavior is due to possible dimerization of the compounds by Shono-type oxidation.
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12
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Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA. Sci Rep 2022; 12:14803. [PMID: 36045146 PMCID: PMC9428881 DOI: 10.1038/s41598-022-19069-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Fluorescence is an ideal tool to see and manipulate nucleic acids, and engage in their rich and complex biophysical properties. Labeling is the preferred approach to track and quantify fluorescence with nucleic acids and cyanine dyes are emblematic in this context. The fluorescent properties of cyanine dyes are known to be sequence-dependent, with purines in the immediate vicinity increasing the fluorescence intensity of Cy3 and Cy5 dyes, and the ability of nucleobases to modulate the photophysical properties of common fluorophores may influence fluorescence measurements in critical assays such as FISH, qPCR or high-throughput sequencing. In this paper, we comprehensively map the sequence-dependence of Cy3 and Cy5 dyes in 3ʹ-fluorescently labeled single-stranded DNA by preparing the complete permutation library of the 5 consecutive nucleotides immediately adjacent to the dye, or 1024 sequences. G-rich motifs dominate the high fluorescence range, while C-rich motifs lead to significant quenching, an observation consistent with 5ʹ-labeled systems. We also uncover GCGC patterns in the extreme top range of fluorescence, a feature specific to 3ʹ-Cy3 and Cy5 oligonucleotides. This study represents the final piece in linking nucleotide identity to fluorescence changes for Cy3, Cy5 and fluorescein in all 3ʹ, 5ʹ, single-stranded and double-stranded DNA formats.
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13
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Takakado A, Iwata K. Sequence-dependent thymine dimerization and lifetimes of the photoexcited state of oligonucleotides. Chem Commun (Camb) 2022; 58:10198-10201. [PMID: 36000476 DOI: 10.1039/d2cc03902h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-sequence-dependent thymine-thymine (TT) dimerization was investigated from the perspective of the UV-induced charge transfer state. Steady-state and transient absorption measurements suggest that the relatively small oxidation potential and long-lived charge transfer state at the neighboring nucleobases of the TT site may reduce DNA lesion accumulation.
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Affiliation(s)
- Akira Takakado
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
| | - Koichi Iwata
- Department of Chemistry, Faculty of Science, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo 171-8588, Japan.
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14
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Lucia-Tamudo J, Cárdenas G, Anguita-Ortiz N, Díaz-Tendero S, Nogueira JJ. Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches. J Chem Inf Model 2022; 62:3365-3380. [PMID: 35771991 PMCID: PMC9326891 DOI: 10.1021/acs.jcim.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The determination
of the redox properties of nucleobases is of
paramount importance to get insight into the charge-transfer processes
in which they are involved, such as those occurring in DNA-inspired
biosensors. Although many theoretical and experimental studies have
been conducted, the value of the one-electron oxidation potentials
of nucleobases is not well-defined. Moreover, the most appropriate
theoretical protocol to model the redox properties has not been established
yet. In this work, we have implemented and evaluated different static
and dynamic approaches to compute the one-electron oxidation potentials
of solvated nucleobases. In the static framework, two thermodynamic
cycles have been tested to assess their accuracy against the direct
determination of oxidation potentials from the adiabatic ionization
energies. Then, the introduction of vibrational sampling, the effect
of implicit and explicit solvation models, and the application of
the Marcus theory have been analyzed through dynamic methods. The
results revealed that the static direct determination provides more
accurate results than thermodynamic cycles. Moreover, the effect of
sampling has not shown to be relevant, and the results are improved
within the dynamic framework when the Marcus theory is applied, especially
in explicit solvent, with respect to the direct approach. Finally,
the presence of different tautomers in water does not affect significantly
the one-electron oxidation potentials.
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Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Gustavo Cárdenas
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Nuria Anguita-Ortiz
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
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15
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Nardi AN, Olivieri A, D'Abramo M. Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations. J Phys Chem B 2022; 126:5017-5023. [PMID: 35671051 PMCID: PMC9289878 DOI: 10.1021/acs.jpcb.2c02391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
![]()
The effect of the
environment on the guanine redox potential is
studied by means of a theoretical–computational approach. Our
data, in agreement with previous experimental findings, clearly show
that the presence of consecutive guanine bases in both single- and
double-stranded DNA oligomers lowers their reduction potential. Such
an effect is even more marked when a G-rich quadruplex is considered,
where the oxidized form of guanine is particularly stabilized. To
the best of our knowledge, this is the first computational study reporting
on a quantitative estimate of the dependence of the guanine redox
potential on sequence and conformational effects in complex DNA molecules,
ranging from single-stranded DNA to G-quadruplex.
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Affiliation(s)
| | - Alessio Olivieri
- Department of Chemistry, Sapienza University of Rome, Rome, Italy 00185
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome, Italy 00185
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16
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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:1077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
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17
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Lietard J, Ameur D, Somoza MM. Sequence-dependent quenching of fluorescein fluorescence on single-stranded and double-stranded DNA. RSC Adv 2022; 12:5629-5637. [PMID: 35425544 PMCID: PMC8982050 DOI: 10.1039/d2ra00534d] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 02/10/2022] [Indexed: 02/01/2023] Open
Abstract
Fluorescein is commonly used to label macromolecules, particularly proteins and nucleic acids, but its fluorescence is known to be strongly dependent on its direct chemical environment.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Dominik Ameur
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Mark M. Somoza
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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18
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Fudickar W, Bauch M, Ihmels H, Linker T. DNA-Triggered Enhancement of Singlet Oxygen Production by Pyridinium Alkynylanthracenes. Chemistry 2021; 27:13591-13604. [PMID: 34263955 DOI: 10.1002/chem.202101918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/23/2022]
Abstract
There is an ongoing interest in 1 O2 sensitizers, whose activity is selectively controlled by their interaction with DNA. To this end, we synthesized three isomeric pyridinium alkynylanthracenes 2 o-p and a water-soluble trapping reagent for 1 O2 . In water and in the absence of DNA, these dyes show a poor efficiency to sensitize the photooxygenation of the trapping reagent as they decompose due to electron transfer processes. In contrast, in the presence of DNA 1 O2 is generated from the excited DNA-bound ligand. The interactions of 2 o-p with DNA were investigated by thermal DNA melting studies, UV/vis and fluorescence spectroscopy, and linear and circular dichroism spectroscopy. Our studies revealed an intercalative binding with an orientation of the long pyridyl-alkynyl axis parallel to the main axis of the DNA base pairs. In the presence of poly(dA : dT), all three isomers show an enhanced formation of singlet oxygen, as indicated by the reaction of the latter with the trapping reagent. With green light irradiation of isomer 2 o in poly(dA : dT), the conversion rate of the trapping reagent is enhanced by a factor >10. The formation of 1 O2 was confirmed by control experiments under anaerobic conditions, in deuterated solvents, or by addition of 1 O2 quenchers. When bound to poly(dG : dC), the opposite effect was observed only for isomers 2 o and 2 m, namely the trapping reagent reacted significantly slower. Overall, we showed that pyridinium alkynylanthracenes are very useful intercalators, that exhibit an enhanced photochemical 1 O2 generation in the DNA-bound state.
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Affiliation(s)
- Werner Fudickar
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Marcel Bauch
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Torsten Linker
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
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19
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Kato D, Kamata T, Sumimoto M. Electrochemical Detection of Tryptophan Metabolites via Kynurenine Pathway by Using Nanocarbon Films. ELECTROANAL 2021. [DOI: 10.1002/elan.202100241] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Dai Kato
- Health and Medical Institute National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
| | - Tomoyuki Kamata
- Health and Medical Institute National Institute of Advanced Industrial Science and Technology (AIST) 1-1-1 Higashi Tsukuba Ibaraki 305-8566 Japan
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20
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D'Annibale V, Nardi AN, Amadei A, D'Abramo M. Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution. J Chem Theory Comput 2021; 17:1301-1307. [PMID: 33621084 PMCID: PMC8028051 DOI: 10.1021/acs.jctc.0c00728] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here, we present the theoretical-computational modeling of the oxidation properties of four DNA nucleosides and nucleotides and a set of dinucleotides in solutions. Our estimates of the vertical ionization energies and reduction potentials, close to the corresponding experimental data, show that an accurate calculation of the molecular electronic properties in solutions requires a proper treatment of the effect of the environment. In particular, we found that the effect of the environment is to stabilize the oxidized state of the nucleobases resulting in a remarkable reduction-up to 6.6 eV-of the energy with respect to the gas phase. Our estimates of the aqueous and gas-phase vertical ionization energies, in good agreement with photoelectron spectroscopy experiments, also show that the effect on the reduction potential of the phosphate group and of the additional nucleotide in dinucleotides is rather limited.
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Affiliation(s)
| | | | - Andrea Amadei
- Department of Chemical Sciences and Technology, Tor Vergata University, Rome 00133, Italy
| | - Marco D'Abramo
- Department of Chemistry, Sapienza University of Rome, Rome 00185, Italy
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21
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Mukherjee M, Tripathi D, Brehm M, Riplinger C, Dutta AK. Efficient EOM-CC-based Protocol for the Calculation of Electron Affinity of Solvated Nucleobases: Uracil as a Case Study. J Chem Theory Comput 2020; 17:105-116. [DOI: 10.1021/acs.jctc.0c00655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Divya Tripathi
- Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Martin Brehm
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
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22
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Sobek J, Schlapbach R. Dependence of Fluorescence Quenching of CY3 Oligonucleotide Conjugates on the Oxidation Potential of the Stacking Base Pair. Molecules 2020; 25:molecules25225369. [PMID: 33212871 PMCID: PMC7698394 DOI: 10.3390/molecules25225369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 01/02/2023] Open
Abstract
To understand the complex fluorescence properties of astraphloxin (CY3)-labelled oligonucleotides, it is necessary to take into account the redox properties of the nucleobases. In oligonucleotide hybrids, we observed a dependence of the fluorescence intensity on the oxidation potential of the neighbouring base pair. For the series I < A < G < 8-oxoG, the extent of fluorescence quenching follows the trend of decreasing oxidation potentials. In a series of 7 nt hybrids, stacking interactions of CY3 with perfect match and mismatch base pairs were found to stabilise the hybrid by 7–8 kJ/mol. The fluorescence measurements can be explained by complex formation resulting in fluorescence quenching that prevails over the steric effect of a reduced excited state trans-cis isomerisation, which was expected to increase the fluorescence efficiency of the dye when stacking to a base pair. This can be explained by the fact that, in a double strand, base pairing and stacking cause a dramatic change in the oxidation potential of the nucleobases. In single-molecule fluorescence measurements, the oxidation of G to 8-oxoG was observed as a result of photoinduced electron transfer and subsequent chemical reactions. Our results demonstrate that covalently linked CY3 is a potent oxidant towards dsDNA. Sulfonated derivatives should be used instead.
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23
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Piccinni V, Reiter S, Keefer D, de Vivie-Riedle R. Multiscale Conformational Sampling Reveals Excited-State Locality in DNA Self-Repair Mechanism. J Phys Chem A 2020; 124:9133-9140. [PMID: 33089694 DOI: 10.1021/acs.jpca.0c07207] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet (UV) irradiation is known to be responsible for DNA damage. However, experimental studies in DNA oligonucleotides have shown that UV light can also induce sequence-specific self-repair. Following charge transfer from a guanine adenine sequence adjacent to a cyclobutane pyrimidine dimer (CPD), the covalent bond between the two thymines could be cleaved, recovering the intact base sequence. Mechanistic details promoting the self-repair remained unclear, however. In our theoretical study, we investigated whether optical excitation could directly lead to a charge-transfer state, thereby initiating the repair, or whether the initial excited state remains localized on a single nucleobase. We performed conformational sampling of 200 geometries of the damaged DNA double strand solvated in water and used a hybrid quantum and molecular mechanics approach to compute excited states at the complete active space perturbation level of theory. Analysis of the conformational data set clearly revealed that the excited-state properties are uniformly distributed across the fluctuations of the nucleotide in its natural environment. From the electronic wavefunction, we learned that the electronic transitions remained predominantly local on either adenine or guanine, and no direct charge transfer occurred in the experimentally accessed energy range. The investigated base sequence is not only specific to the CPD repair mechanism but ubiquitously occurs in nucleic acids. Our results therefore give a very general insight into the charge locality of UV-excited DNA, a property that is regarded to have determining relevance in the structural consequences following absorption of UV photons.
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Affiliation(s)
- Viviana Piccinni
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | - Sebastian Reiter
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
| | - Daniel Keefer
- Department Chemie, Ludwig-Maximilians-Universität München, München D-81377, Germany
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24
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Diamantis P, Tavernelli I, Rothlisberger U. Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations. J Chem Theory Comput 2020; 16:6690-6701. [PMID: 32926773 DOI: 10.1021/acs.jctc.0c00568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations. The quantum region of the native fragment comprised 3 G-C base pairs, while one G was replaced by an 8oxoG in the defect fragment. The calculated values for the redox free energy are 6.55 ± 0.28 eV and 5.62 ± 0.30 eV for the native and the 8oxoG-containing fragment, respectively. The respective estimates for the reorganization free energy are 1.25 ± 0.18 eV and 1.00 ± 0.18 eV. Both reactions follow the Marcus theory for electron transfer. The large difference in redox potential between the two fragments shows that replacement of a G by an 8oxoG renders the DNA more easily oxidizable. This finding is in agreement with the suggestion that DNA fragments containing an 8oxoG defect can act as sinks of oxidative damage that protect the rest of the genome from assault. In addition, the difference in redox potential between the native and the defect DNA fragment indicates that a charge transfer-based mechanism for the recognition of DNA defects might be feasible, in line with recent suggestions based on experimental observations.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne, Swiss Federal Institute of Technology, CH-1015 Lausanne, Switzerland
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25
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Kufner CL, Zinth W, Bucher DB. UV-Induced Charge-Transfer States in Short Guanosine-Containing DNA Oligonucleotides. Chembiochem 2020; 21:2306-2310. [PMID: 32239789 PMCID: PMC7496882 DOI: 10.1002/cbic.202000103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Indexed: 11/24/2022]
Abstract
Charge transfer has proven to be an important mechanism in DNA photochemistry. In particular, guanine (dG) plays a major role as an electron donor, but the photophysical dynamics of dG-containing charge-transfer states have not been extensively investigated so far. Here, we use UV pump (266 nm) and picosecond IR probe (∼5-7 μm) spectroscopy to study ultrafast dynamics in dG-containing short oligonucleotides as a function of sequence and length. For the pure purine oligomers, we observed lifetimes for the charge-transfer states of the order of several hundreds of picoseconds, regardless of the oligonucleotide length. In contrast, pyrimidine-containing dinucleotides d(GT) and d(GC) show much faster relaxation dynamics in the 10 to 30 ps range. In all studied nucleotides, the charge-transfer states are formed with an efficiency of the order of ∼50 %. These photophysical characteristics will lead to an improved understanding of DNA damage and repair processes.
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Affiliation(s)
- Corinna L. Kufner
- Biomolecular Optics and Center for Integrated Protein ScienceLudwig-Maximilians-University MunichOettingenstr. 6780538MunichGermany
- present affiliation: Harvard-Smithsonian Center for Astrophysics Department of AstronomyHarvard University60 Garden StreetCambridgeMA 02138USA
| | - Wolfgang Zinth
- Biomolecular Optics and Center for Integrated Protein ScienceLudwig-Maximilians-University MunichOettingenstr. 6780538MunichGermany
| | - Dominik B. Bucher
- Biomolecular Optics and Center for Integrated Protein ScienceLudwig-Maximilians-University MunichOettingenstr. 6780538MunichGermany
- present affiliation: Department of ChemistryTechnical University of MunichLichtenbergstr. 485748MunichGermany
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26
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Sobek J, Schmidt M, Grossmann J, Rehrauer H, Schmidt L, Schlapbach R. Single-molecule chemistry. Part I: monitoring oxidation of G in oligonucleotides using CY3 fluorescence. Methods Appl Fluoresc 2020; 8:035010. [PMID: 32428873 DOI: 10.1088/2050-6120/ab947d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-molecule hybridisation of CY3 dye labelled short oligonucleotides to surface immobilised probes was investigated in zero-mode waveguide nanostructures using a modified DNA sequencer. At longer measuring times, we observed changes of the initial hybridisation fluorescence pulse pattern which we attribute to products created by chemical reactions at the nucleobases. The origin is a charge separated state created by a photoinduced electron transfer from nucleobases to the dye followed by secondary reactions with oxygen and water, respectively. The positive charge can migrate through the hybrid resulting in base modifications at distant sites. Static fluorescence spectra were recorded in order to determine the properties of CY3 stacking to different base pairs, and compared to pulse intensities. A characteristic pulse pattern change was assigned to the oxidation of G to 8-oG besides the formation of a number of secondary products that are not yet identified. Further, we present a method to visualise the degree of chemical reactions to gain an overview of ongoing processes. Our study demonstrates that CY3 is able to oxidise nucleobases in ds DNA, and also in ss overhangs. An important finding is the correlation between nucleobase oxidation potential and fluorescence quenching which explains the intensity changes observed in single molecule measurements. The analysis of fluorescence traces provides the opportunity to track complete and coherent reaction sequences enabling to follow the fate of a single molecule over a long period of time, and to observe chemical reactions in real-time. This opens up the opportunity to analyse reaction pathways, to detect new products and short-lived intermediates, and to investigate rare events due to the large number of single molecules observed in parallel.
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Affiliation(s)
- Jens Sobek
- Functional Genomics Center Zurich, Eidgenössische Technische Hochschule (ETH) Zurich and University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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27
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Hesabi N, Ebrahimi A. The electrochemical properties and PIM1 kinase enzyme inhibition of some 2-(hydroxy phenyl amino) naphthalene-1,4-dione derivatives. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112874] [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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28
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Wang J, Yang S, Zhang Y. One-electron oxidation and redox potential of nucleobases and deoxyribonucleosides computed by QM/MM simulations. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136948] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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29
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Lee W, Matsika S. Role of charge transfer states into the formation of cyclobutane pyrimidine dimers in DNA. Faraday Discuss 2019; 216:507-519. [PMID: 31025669 DOI: 10.1039/c8fd00184g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Photoinduced charge transfer between neighboring bases plays an important role in DNA. One of its important effects is shown in its ability to affect the photochemical yields of the formation of cyclobutane pyrimidine dimer (CPD) products between adjacent pyrimidine bases. In this work we examine how the energies of charge transfer states depend on the sequences of oligonucleotides using a hybrid quantum and molecular mechanics (QM/MM) methodology combined with the algebraic diagrammatic construction through a second order electronic structure method for excited states. Specifically, we examine 10 sequences with guanine being on the 5' or 3' position of two pyrimidine bases. The results show that the energies of charge transfer states are affected by the nature of the donor acceptor pair, by the distance between them, and by other electrostatic effects created by the surrounding environment.
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Affiliation(s)
- Wook Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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30
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Liu C, Niazi MR, Perepichka DF. Strong Enhancement of π‐Electron Donor/Acceptor Ability by Complementary DD/AA Hydrogen Bonding. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201910288] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Cheng‐Hao Liu
- Department of ChemistryMcGill University 801 Sherbrooke Street W Quebec H3A 0B1 Canada
| | - Muhammad Rizwan Niazi
- Department of ChemistryMcGill University 801 Sherbrooke Street W Quebec H3A 0B1 Canada
| | - Dmitrii F. Perepichka
- Department of ChemistryMcGill University 801 Sherbrooke Street W Quebec H3A 0B1 Canada
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31
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Liu CH, Niazi MR, Perepichka DF. Strong Enhancement of π-Electron Donor/Acceptor Ability by Complementary DD/AA Hydrogen Bonding. Angew Chem Int Ed Engl 2019; 58:17312-17321. [PMID: 31560447 DOI: 10.1002/anie.201910288] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Indexed: 11/11/2022]
Abstract
π-Conjugated organic materials possess a wide range of tunable optoelectronic properties which are dictated by their molecular structure and supramolecular arrangement. While many efforts have been put into tuning the molecular structure to achieve the desired properties, rational supramolecular control remains a challenge. Here, we report a novel series of supramolecular materials formed by the co-assembly of weak π-electron donor (indolo[2,3-a]carbazole) and acceptor (aromatic o-quinones) molecules via complementary hydrogen bonding. The resulting polarization creates a drastic perturbation of the molecular energy levels, causing strong charge transfer in the weak donor-acceptor pairs. This leads to a significant lowering (up to 1.5 eV) of the band gaps, intense absorption in the near-IR region, very short π-stacking distances (≥3.15 Å), and strong ESR signals in the co-crystals. By varying the strength of the acceptor, the characteristics of the complexes can be tuned between intrinsic, gate-, or light-induced semiconductivity with a p-type or ambipolar transport mechanism.
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Affiliation(s)
- Cheng-Hao Liu
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Quebec, H3A 0B1, Canada
| | - Muhammad Rizwan Niazi
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Quebec, H3A 0B1, Canada
| | - Dmitrii F Perepichka
- Department of Chemistry, McGill University, 801 Sherbrooke Street W, Quebec, H3A 0B1, Canada
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32
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Kamata T, Sumimoto M, Shiba S, Kurita R, Niwa O, Kato D. Increased electrode activity during geosmin oxidation provided by Pt nanoparticle-embedded nanocarbon film. NANOSCALE 2019; 11:8845-8854. [PMID: 31012904 DOI: 10.1039/c9nr00793h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The musty odor compound geosmin was electrochemically detected by using Pt nanoparticle (PtNP)-embedded nanocarbon (Pt-C) films formed with unbalanced magnetron (UBM) co-sputtering. The sputtered Pt components formed NPs (typically 1.53-4.75 nm in diameter) spontaneously in the carbon films, owing to the poor intermiscibility of Pt with carbon. The surface concentrations of PtNPs embedded in the nanocarbon film were widely controllable (Pt = 4.8-35.9 at%) by regulating the target powers of the Pt and carbon individually. The obtained film had a flat surface (Ra = 0.17-0.18 nm) despite the fact the PtNPs were partially exposed at the surface. Compared with a Pt film electrode, some Pt-C films exhibited higher electrode activity against geosmin although the surface Pt concentrations of these Pt-C films were much lower than that of the Pt film electrode, thanks to the wider potential window and lower background current that resulted from the ultraflat and stable carbon-based film prepared by UBM co-sputtering. Computational experiments revealed that the theoretical oxidation potential (Eox) value for geosmin was relatively similar to that obtained in electrochemical experiments using our Pt-C film electrode. Moreover, we also theoretically estimated the possible oxidation site of geosmin molecules and the advantage of the NP shape of the electroactive Pt parts as regards the electrochemical oxidation of geosmin. We successfully used the Pt-C film (10.6 at%) electrode to detect geosmin in combination with HPLC at a low detection limit of 100 ng L-1.
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Affiliation(s)
- Tomoyuki Kamata
- National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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Diamantis P, Tavernelli I, Rothlisberger U. Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair. J Chem Theory Comput 2019; 15:2042-2052. [PMID: 30681847 DOI: 10.1021/acs.jctc.8b00645] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as for larger fragments containing one or multiple pairs. Absolute values of VIE and VEA under implicit solvation did not converge as a function of model size even up to the largest systems taken into consideration (3 base pairs/2 nucleotide pairs). Nonetheless, a consistent trend was observed for the relative difference in the VIE of native and damaged DNA showing that the defect was lowering the VIE by -0.1 eV for the largest fragments. This strongly suggests that the presence of 8OG makes the DNA more easily oxidizable and is in line with experimental evidence that a defect region can act as a sink of oxidative damage. In contrast, relative differences in VEA were very small and varied inconsistently around 0.01 eV. This seems to indicate that insertion of 8OG has a negligible effect on the electron capturing properties of DNA. Similar conclusions can be drawn by the adiabatic IEs and EAs computed for some of the larger fragments. Analysis of the hole and excess electron distributions was consistent with the above trends. The findings presented here support the possibility that a mechanism based on hole transport through DNA may be efficiently employed by the cell for the detection of defect bases.
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Affiliation(s)
- Polydefkis Diamantis
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland
| | - Ivano Tavernelli
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry , École Polytechnique Fédérale de Lausanne , Swiss Federal Institute of Technology, CH-1015 Lausanne , Switzerland
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Cadet J, Douki T. Formation of UV-induced DNA damage contributing to skin cancer development. Photochem Photobiol Sci 2018; 17:1816-1841. [PMID: 29405222 DOI: 10.1039/c7pp00395a] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
UV-induced DNA damage plays a key role in the initiation phase of skin cancer. When left unrepaired or when damaged cells are not eliminated by apoptosis, DNA lesions express their mutagneic properties, leading to the activation of proto-oncogene or the inactivation of tumor suppression genes. The chemical nature and the amount of DNA damage strongly depend on the wavelength of the incident photons. The most energetic part of the solar spectrum at the Earth's surface (UVB, 280-320 nm) leads to the formation of cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (64PPs). Less energetic but 20-times more intense UVA (320-400 nm) also induces the formation of CPDs together with a wide variety of oxidatively generated lesions such as single strand breaks and oxidized bases. Among those, 8-oxo-7,8-dihydroguanine (8-oxoGua) is the most frequent since it can be produced by several mechanisms. Data available on the respective yield of DNA photoproducts in cells and skin show that exposure to sunlight mostly induces pyrimidine dimers, which explains the mutational signature found in skin tumors, with lower amounts of 8-oxoGua and strand breaks. The present review aims at describing the basic photochemistry of DNA and discussing the quantitative formation of the different UV-induced DNA lesions reported in the literature. Additional information on mutagenesis, repair and photoprotection is briefly provided.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, 3001 12e Avenue Nord, Université de Sherbrooke, Sherbrooke, Québec JIH 5N4, Canada.
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Cadet J, Wagner JR, Angelov D. Biphotonic Ionization of DNA: From Model Studies to Cell. Photochem Photobiol 2018; 95:59-72. [PMID: 30380156 DOI: 10.1111/php.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.
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Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule LBMC, CNRS-UMR 5239, Université de Lyon, École Normale Supérieure de Lyon, Lyon, France
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36
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Reina M, Martínez A. A new free radical scavenging cascade involving melatonin and three of its metabolites (3OHM, AFMK and AMK). COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Limpanuparb T, Roongruangsree P, Areekul C. A DFT investigation of the blue bottle experiment: E∘half-cell analysis of autoxidation catalysed by redox indicators. ROYAL SOCIETY OPEN SCIENCE 2017; 4:170708. [PMID: 29291061 PMCID: PMC5717635 DOI: 10.1098/rsos.170708] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/05/2017] [Indexed: 06/07/2023]
Abstract
The blue bottle experiment is a collective term for autoxidation reactions catalysed by redox indicators. The reactions are characterized by their repeatable cycle of colour changes when shaken/left to stand and intricate chemical pattern formation. The blue bottle experiment is studied based on calculated solution-phase half-cell reduction potential of related reactions. Our investigation confirms that the reaction in various versions of the blue bottle experiment published to date is mainly the oxidation of an acyloin to a 1,2-dicarbonyl structure. In the light of the calculations, we also propose new non-acyloin reducing agents for the experiment. These results can help guide future experimental studies on the blue bottle experiment.
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Affiliation(s)
- Taweetham Limpanuparb
- Science Division, Mahidol University International College, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
| | - Pakpong Roongruangsree
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand
- Department of Chemical Engineering, McGill University, Quebec H3A 0C5, Canada
| | - Cherprang Areekul
- Science Division, Mahidol University International College, Mahidol University, Salaya, Nakhon Pathom 73170, Thailand
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38
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Aydemir N, Chan E, Baek P, Barker D, Williams DE, Travas-Sejdic J. New immobilisation method for oligonucleotides on electrodes enables highly-sensitive, electrochemical label-free gene sensing. Biosens Bioelectron 2017; 97:128-135. [DOI: 10.1016/j.bios.2017.05.049] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 05/16/2017] [Accepted: 05/27/2017] [Indexed: 01/02/2023]
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Chakraborty R, Ghosh D. The effect of sequence on the ionization of guanine in DNA. Phys Chem Chem Phys 2016; 18:6526-33. [PMID: 26864778 DOI: 10.1039/c5cp07804k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The accurate estimation of the ionization energies and understanding the nature of the ionized states of the nucleic acid bases (NABs) are crucial to the understanding of the DNA damage mechanism. The vertical ionization energy (VIE) of guanine is the lowest among the NABs and the ionization energies are strongly affected by the environment, such as solvation and characteristics of nearby NABs. Therefore, we investigate the sequence dependence of the VIEs of guanine in B-DNA. We use the equation of motion coupled cluster method for the estimation of ionization potential with single and double excitations (EOM-IP-CCSD) and density functional theory with dispersion corrected ωB97x-D for the estimation of VIEs. A significant amount of non-additivity or cooperativity, directly proportional to charge delocalization, is noticed in the change in VIE due to the interaction with the nearby NABs. While the change in VIE due to base pairing originates predominantly from charge-dipole interactions, stacking between base pairs is a more complicated balance of dispersion and charge-dipole interactions as well as stabilization due to the delocalization of the positive charge. The long range interactions are however dominated by 1/r(3) distance dependence which shows the major role played by charge-dipole interactions. The extent of localization of positive holes on guanine is also estimated for various sequences.
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Affiliation(s)
- Rahul Chakraborty
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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40
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Black HT, Yee N, Zems Y, Perepichka DF. Complementary Hydrogen Bonding Modulates Electronic Properties and Controls Self-Assembly of Donor/Acceptor Semiconductors. Chemistry 2016; 22:17251-17261. [DOI: 10.1002/chem.201602543] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Indexed: 11/09/2022]
Affiliation(s)
- H. T. Black
- Department of Chemistry and Centre for Self-Assembled Chemical Structures; McGill University; Montreal Qc H3A 0B8 Canada
- Organic Materials Department; Sandia National Laboratories; Albuquerque NM 87185 USA
| | - N. Yee
- Department of Chemistry and Centre for Self-Assembled Chemical Structures; McGill University; Montreal Qc H3A 0B8 Canada
| | - Y. Zems
- Department of Chemistry and Centre for Self-Assembled Chemical Structures; McGill University; Montreal Qc H3A 0B8 Canada
| | - D. F. Perepichka
- Department of Chemistry and Centre for Self-Assembled Chemical Structures; McGill University; Montreal Qc H3A 0B8 Canada
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41
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Abstract
Biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. Duplex DNA is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. Increasingly, [4Fe4S] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in DNA processing. DNA-binding enzymes containing [4Fe4S] clusters can thus utilize DNA charge transport (DNA CT) for redox signaling to coordinate reactions over long molecular distances. In particular, DNA CT signaling may represent the first step in the search for DNA lesions by proteins containing [4Fe4S] clusters that are involved in DNA repair. Here we describe research carried out to examine the chemical characteristics and biological consequences of DNA CT. We are finding that DNA CT among metalloproteins represents powerful chemistry for redox signaling at long range within the cell.
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Affiliation(s)
- Elizabeth O’Brien
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Rebekah M.B. Silva
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena CA 91125
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42
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Reina M, Martínez A. Is Silybin the Best Free Radical Scavenger Compound in Silymarin? J Phys Chem B 2016; 120:4568-78. [PMID: 27149000 DOI: 10.1021/acs.jpcb.6b02807] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Silymarin is a natural mixture with beneficial properties for health, specifically due to its antiradical characteristics. The major components of this mixture are silybin (SIL), silychristin (SILYC), isosilybin (ISOSIL), silydianin (SILYD), and taxifolin (TAX). In this report, the electronic properties of these substances are investigated using density functional theory calculations, mainly in order to fully understand the free radical scavenger properties of these compounds. Optimized geometries and Raman spectra are reported. These results could be experimentally useful for identifying some of the major components of the mixture. The relative abundance of deprotonated species under physiological conditions is also included. The free radical scavenger capacity is studied in relation to three mechanisms: the single electron transfer (SET), the radical adduct formation (RAF), and the hydrogen atom transfer (HAT). According to this investigation, the HAT mechanism is the most efficient mechanism for scavenging free radicals for these compounds followed by the RAF mechanism where intramolecular hydrogen bonds are formed in order to stabilize the (•)OOH free radical. A particularly important factor is that none of the compounds being studied showed an outstanding antiradical capacity performance compared to the others. In this sense, silymarin is an interesting mixture with antiradical properties and we now know that one single component should be as effective as the mixture.
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Affiliation(s)
- Miguel Reina
- Departamento de Materiales de Baja Dimensionalidad Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México , Circuito Exterior s/n, CU, P.O. Box 70-360, Coyoacán, 04510 Ciudad de México, México
| | - Ana Martínez
- Departamento de Materiales de Baja Dimensionalidad Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México , Circuito Exterior s/n, CU, P.O. Box 70-360, Coyoacán, 04510 Ciudad de México, México
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43
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Guerard JJ, Tentscher PR, Seijo M, Samuel Arey J. Explicit solvent simulations of the aqueous oxidation potential and reorganization energy for neutral molecules: gas phase, linear solvent response, and non-linear response contributions. Phys Chem Chem Phys 2016; 17:14811-26. [PMID: 25978135 DOI: 10.1039/c4cp04760e] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
First principles simulations were used to predict aqueous one-electron oxidation potentials (Eox) and associated half-cell reorganization energies (λaq) for aniline, phenol, methoxybenzene, imidazole, and dimethylsulfide. We employed quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations of the oxidized and reduced species in an explicit aqueous solvent, followed by EOM-IP-CCSD computations with effective fragment potentials for diabatic energy gaps of solvated clusters, and finally thermodynamic integration of the non-linear solvent response contribution using classical MD. A priori predicted Eox and λaq values exhibit mean absolute errors of 0.17 V and 0.06 eV, respectively, compared to experiment. We also disaggregate Eox into several well-defined free energy properties, including the gas phase adiabatic free energy of ionization (7.73 to 8.82 eV), the solvent-induced shift in the free energy of ionization due to linear solvent response (-2.01 to -2.73 eV), and the contribution from non-linear solvent response (-0.07 to -0.14 eV). The linear solvent response component is further apportioned into contributions from the solvent-induced shift in vertical ionization energy of the reduced species (ΔVIEaq) and the solvent-induced shift in negative vertical electron affinity of the ionized species (ΔNVEAaq). The simulated ΔVIEaq and ΔNVEAaq are found to contribute the principal sources of uncertainty in computational estimates of Eox and λaq. Trends in the magnitudes of disaggregated solvation properties are found to correlate with trends in structural and electronic features of the solute. Finally, conflicting approaches for evaluating the aqueous reorganization energy are contrasted and discussed, and concluding recommendations are given.
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Affiliation(s)
- Jennifer J Guerard
- Environmental Chemistry Modeling Laboratory, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.
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44
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Bucher DB, Kufner CL, Schlueter A, Carell T, Zinth W. UV-Induced Charge Transfer States in DNA Promote Sequence Selective Self-Repair. J Am Chem Soc 2015; 138:186-90. [PMID: 26651219 DOI: 10.1021/jacs.5b09753] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Absorption of UV-radiation in nucleotides initiates a number of photophysical and photochemical processes, which may finally cause DNA damage. One major decay channel of photoexcited DNA leads to reactive charge transfer states. This study shows that these states trigger self-repair of DNA photolesions. The experiments were performed by UV spectroscopy and HPLC on different single and double stranded oligonucleotides containing a cyclobutane pyrimidine dimer (CPD) lesion. In a first experiment we show that photoexcitation of adenine adjacent to a CPD has no influence on this lesion. However, excitation of a guanine (G) adenine (A) sequence leads to reformation of the intact thymine (T) bases. The involvement of two bases for the repair points to a long-living charge transfer state between G and A to be responsible for the repair. The negatively charged A radical anion donates an electron to the CPD, inducing ring splitting and repair. In contrast, a TA sequence, having an inverted charge distribution (T radical anion, A radical cation), is not able to repair the CPD lesion. The investigations show that the presence of an adjacent radical ion is not sufficient for repair. More likely it is the driving power represented by the oxidation potential of the radical ion, which controls the repair. Thus, repair capacities are strongly sequence-dependent, creating DNA regions with different tendencies of self-repair. This self-healing activity represents the simplest sequence-dependent DNA repair system.
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Affiliation(s)
- Dominik Benjamin Bucher
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany.,Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13, 81377 München, Germany
| | - Corinna Lucia Kufner
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany
| | - Alexander Schlueter
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany
| | - Thomas Carell
- Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München , Butenandtstrasse 5-13, 81377 München, Germany
| | - Wolfgang Zinth
- BioMolecular Optics and Center for Integrated Protein Science, Ludwigs-Maximilians-Universität München , Oettingenstrasse 67, 80538 München, Germany
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45
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Fröbel S, Levi L, Ulamec SM, Gilch P. Photoinduced Electron Transfer between Psoralens and DNA: Influence of DNA Sequence and Substitution. Chemphyschem 2015; 17:1377-86. [PMID: 26607751 DOI: 10.1002/cphc.201500889] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Indexed: 01/24/2023]
Abstract
Psoralens are heterocyclic compounds which are, among other uses, used to treat skin deseases in the framework of PUVA therapy. In the dark, they intercalate into DNA and can form photoadducts with thymines upon UV-A excitation, which harms the affected cells. We have recently discovered that after excitation of intercalated psoralens, an efficient photoinduced electron transfer (PET) from DNA occurs. Here, the PET is studied in detail by means of femtosecond transient absorption spectroscopy. Using DNA samples that contain either only GC or AT base pairs, we show that only guanine donates the electrons. Additionally, the substituent effects on PET are studied relying on three different psoralen derivatives. The substitution alters spectroscopic and electrochemical properties of the psoralens, which are determined by cyclic voltammetry and steady state spectroscopy. These experiments allow us to estimate the PET energetics, which are in line with the measured kinetics. Implications for the applications of psoralens are discussed.
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Affiliation(s)
- Sascha Fröbel
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Lucilla Levi
- Institut für Organische Chemie und Makromolekulare Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Sabine M Ulamec
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Peter Gilch
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany.
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46
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Karabıyık H, Sevinçek R, Karabıyık H. π-Cooperativity effect on the base stacking interactions in DNA: is there a novel stabilization factor coupled with base pairing H-bonds? Phys Chem Chem Phys 2015; 16:15527-38. [PMID: 24953339 DOI: 10.1039/c4cp00997e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The results from absolutely localized molecular orbital (ALMO)-energy decomposition analysis (EDA) and ALMO-charge transfer analysis (CTA) at M06-2X/cc-pVTZ level reveal that double-proton transfer (DPT) reactions through base pairing H-bonds have nonignorable effects on the stacking energies of dinucleotide steps, which introduces us to a novel stabilization (or destabilization) factor in the DNA duplex. Thus, intra- and inter-strand base stacking interactions are coalesced with each other mediated by H-bridged quasirings between base pairs. Changes in stacking energies of dinucleotide steps depending on the positions of H atoms are due to variations in local aromaticities of individual nucleobases, manifesting π-cooperativity effects. CT analyses show that dispersion forces in dinucleotide steps can lead to radical changes in the redox properties of nucleobases, in particular those of adenine and guanine stacked dimers in a strand. Besides Watson-Crick rules, novel base pairing rules were propounded by considering CT results. According to these, additional base pairing through π-stacks of nucleobases in dinucleotide steps does not cause any intrinsic oxidative damage to the associated nucleobases throughout DPT.
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Affiliation(s)
- Hande Karabıyık
- Department of Physics, Dokuz Eylül University, 35160-Tınaztepe, İzmir, Turkey.
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47
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Reina M, Martínez A. Silybin and 2,3-Dehydrosilybin Flavonolignans as Free Radical Scavengers. J Phys Chem B 2015; 119:11597-606. [PMID: 26259041 DOI: 10.1021/acs.jpcb.5b06448] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The electronic properties of six derivatives of silybin (characterized by the absence of the 2,3 double bond) and six derivatives of 2,3-dehydrosilybin (characterized by the presence of the 2,3 double bond) have been studied by applying density functional theory to fully understand the free radical scavenger's mechanism for action and the relationship between reactivity and chemical structure. Optimized geometries, Raman spectra, and λmax values are reported, enabling us to characterize the systems. These spectra may be useful for monitoring the oxidation between silybin and 2,3-dehydrosilybin, thus providing important experimental information. The relative abundance of deprotonated species under physiological conditions is also reported. Under physiological conditions (pH 7.4), ∼70% of silybin is protonated, but 60% of 2,3-dehydrosilybin is deprotonated. The free radical scavenger capacity is analyzed in terms of two mechanisms: electron transfer and adduct formation. Deprotonated molecules are better electron donors and worse electron acceptors than non-deprotonated species. The conclusions derived from this investigation completely concur with previous experimental results. The free radical scavenging activity of 2,3-dehydrosilybin derivatives is higher than that for silybin derivatives. What was not previously considered was the importance of the deprotonated species, which is remarkable and may be important for future experiments.
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Affiliation(s)
- Miguel Reina
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México , Circuito Exterior SN, Ciudad Universitaria, CP 04510 Coyoacán, México DF, México
| | - Ana Martínez
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México , Circuito Exterior SN, Ciudad Universitaria, CP 04510 Coyoacán, México DF, México
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48
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Karwowski BT. The influence of phosphorothioate on charge migration in single and double stranded DNA: a theoretical approach. Phys Chem Chem Phys 2015. [PMID: 26219639 DOI: 10.1039/c5cp01382h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study the influence of the phosphorothioate internucleotide bond on the electronic properties of single and double-stranded short nucleotides has been investigated at the M06-2X/6-31+G** level of theory in the gaseous phase. Due to the chirality of the phosphorus atom in a phosphorothioate (PT) internucleotide diester bond, the adiabatic/vertical mode of electron affinity/ionization potential, spin density and molecular orbital distribution, as well as structural analysis were taken under consideration for the single stranded (ss) R(P) and S(P) diastereomers of d[G(PS)G] and for double stranded (ds) d[G(PS)G]*d[C(PO)C], in comparison with the corresponding parent phosphate compounds. Moreover, the excitation states, HOMO and LUMO energies were calculated using a TD-DFT methodology at the M06-2X/6-31+G**//M06-2X/6-31++G** level of theory in the aqueous phase. The obtained results show that the PT plays a significant role in the case of ss-oligonucleotides, and to a much smaller extent in ds-oligomers.
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Affiliation(s)
- Boleslaw T Karwowski
- Food Science Department, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland.
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49
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Pluhařová E, Slavíček P, Jungwirth P. Modeling photoionization of aqueous DNA and its components. Acc Chem Res 2015; 48:1209-17. [PMID: 25738773 DOI: 10.1021/ar500366z] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Radiation damage to DNA is usually considered in terms of UVA and UVB radiation. These ultraviolet rays, which are part of the solar spectrum, can indeed cause chemical lesions in DNA, triggered by photoexcitation particularly in the UVB range. Damage can, however, be also caused by higher energy radiation, which can ionize directly the DNA or its immediate surroundings, leading to indirect damage. Thanks to absorption in the atmosphere, the intensity of such ionizing radiation is negligible in the solar spectrum at the surface of Earth. Nevertheless, such an ionizing scenario can become dangerously plausible for astronauts or flight personnel, as well as for persons present at nuclear power plant accidents. On the beneficial side, ionizing radiation is employed as means for destroying the DNA of cancer cells during radiation therapy. Quantitative information about ionization of DNA and its components is important not only for DNA radiation damage, but also for understanding redox properties of DNA in redox sensing or labeling, as well as charge migration along the double helix in nanoelectronics applications. Until recently, the vast majority of experimental and computational data on DNA ionization was pertinent to its components in the gas phase, which is far from its native aqueous environment. The situation has, however, changed for the better due to the advent of photoelectron spectroscopy in liquid microjets and its most recent application to photoionization of aqueous nucleosides, nucleotides, and larger DNA fragments. Here, we present a consistent and efficient computational methodology, which allows to accurately evaluate ionization energies and model photoelectron spectra of aqueous DNA and its individual components. After careful benchmarking, the method based on density functional theory and its time-dependent variant with properly chosen hybrid functionals and polarizable continuum solvent model provides ionization energies with accuracy of 0.2-0.3 eV, allowing for faithful modeling and interpretation of DNA photoionization. The key finding is that the aqueous medium is remarkably efficient in screening the interactions within DNA such that, unlike in the gas phase, ionization of a base, nucleoside, or nucleotide depends only very weakly on the particular DNA context. An exception is the electronic interaction between neighboring bases which can lead to sequence-specific effects, such as a partial delocalization of the cationic hole upon ionization enabled by presence of adjacent bases of the same type.
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Affiliation(s)
- Eva Pluhařová
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Petr Slavíček
- University of Chemistry and Technology, Department
of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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Sun W, Ren H, Tao Y, Xiao D, Qin X, Deng L, Shao M, Gao J, Chen X. Two Aromatic Rings Coupled a Sulfur-Containing Group to Favor Protein Electron Transfer by Instantaneous Formations of π∴S:π↔π:S∴π or π∴π:S↔π:π∴S Five-Electron Bindings. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2015; 119:9149-9158. [PMID: 26120374 PMCID: PMC4479289 DOI: 10.1021/acs.jpcc.5b01740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The cooperative interactions among two aromatic rings with a S-containing group are described, which may participate in electron hole transport in proteins. Ab initio calculations reveal the possibility for the formations of the π∴S:π↔π:S∴π and π∴π:S↔π:π∴S five-electron bindings in the corresponding microsurrounding structures in proteins, both facilitating electron hole transport as efficient relay stations. The relay functionality of these two special structures comes from their low local ionization energies and proper binding energies, which varies with the different aromatic amino acids, S-containing residues, and the arrangements of the same aromatic rings according to the local microsurroundings in proteins.
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Affiliation(s)
- Weichao Sun
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Haisheng Ren
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ye Tao
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Dong Xiao
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Xin Qin
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Li Deng
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Mengyao Shao
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Xiaohua Chen
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing, 400030, People's Republic of China
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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