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Mondal S, Bravaya KB. Complex potential energy surfaces with projected CAP technique: Vibrational excitation of N2. J Chem Phys 2024; 161:024106. [PMID: 38984953 DOI: 10.1063/5.0212647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/12/2024] [Indexed: 07/11/2024] Open
Abstract
The projected complex absorbing potential (CAP) technique is one of the methods that allow one to extend the bound state methods for computing resonances' energies and widths. Here, we explore the accuracy of the potential energy curves generated with different electronic structure theory methods in combination with the projected CAP technique by considering resonant vibrational excitation (RVE) of N2 by electron impact as a model process. We report RVE cross sections computed using the boomerang model with potential energy curves obtained with CAP-based extended multistate complete active space perturbation theory (XMS-CASPT2) and equation of motion coupled-cluster method for electron attachment with single and double substitution (EOM-EA-CCSD) methods. We also compare potential energy curves computed with several electronic structure methods, including XMS-CASPT2, EOM-EA-CCSD, multireference configuration interaction with singles (MR-CIS) and singles and doubles (MR-CISD). A good agreement is observed between the experiment and simulated RVE cross sections obtained with the potential energy curves generated with XMS-CASPT2 and EOM-EA-CCSD methods, thus highlighting the potential of the projected CAP technique combined with accurate electronic structure methods for dynamical simulations of the processes that proceed through metastable electronic states.
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Affiliation(s)
- Soubhik Mondal
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Ksenia B Bravaya
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
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2
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Maslyuk VT, Zavilopulo AN, Svatiuk NI, Bandurin YA. Peculiarities of Glucose Molecules Destruction under Irradiation at the M-30 Microtron (12.5 MeV): Mass Spectrometric Studies. Cell Biochem Biophys 2024; 82:203-211. [PMID: 37966623 DOI: 10.1007/s12013-023-01195-4] [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: 08/09/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023]
Abstract
The method of mass spectrometric studies was used to study the fragmentation of glucose in the gas phase upon collision with low-energy electrons (20-70 eV) before and after irradiation at the M-30 microtron (12.5 MeV) with doses of 14 and 164 kGy. The dose dependence of the transformation of glucose mass spectra was established. The results indicate the dominance in mass spectra of symmetric fission channels of the molecule itself and its fragments formed under the action of M-30 microtron radiation. The same ways of fragmentation of glucose one can expect under chemical, thermal, and biological processes at the cellular level. The dominant channels of fragmentizing the glucose molecule without and considering its radiation treatment are explained within the framework of the method of structural combinations. The obtained results are essential for understanding the processes of cellular biochemistry and biophysics involving glucose, the hierarchy of its fragmentation channels under the influence of terrestrial radiation factors, and metabolic processes.
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Affiliation(s)
- V T Maslyuk
- Institute of Electron Physics, National Academy of Sciences, Universitetska 21, Uzhhorod, 88017, Zakarpattia, Ukraine.
| | - A N Zavilopulo
- Institute of Electron Physics, National Academy of Sciences, Universitetska 21, Uzhhorod, 88017, Zakarpattia, Ukraine
| | - N I Svatiuk
- Institute of Electron Physics, National Academy of Sciences, Universitetska 21, Uzhhorod, 88017, Zakarpattia, Ukraine
| | - Y A Bandurin
- Institute of Electron Physics, National Academy of Sciences, Universitetska 21, Uzhhorod, 88017, Zakarpattia, Ukraine
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3
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Narayanan S J J, Tripathi D, Verma P, Adhikary A, Dutta AK. Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials. ACS OMEGA 2023; 8:10669-10689. [PMID: 37008102 PMCID: PMC10061531 DOI: 10.1021/acsomega.2c06776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.
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Affiliation(s)
- Jishnu Narayanan S J
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Pooja Verma
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Achintya Kumar Dutta
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
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4
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Verma P, Narayanan S J J, Dutta AK. Electron Attachment to DNA: The Protective Role of Amino Acids. J Phys Chem A 2023; 127:2215-2227. [PMID: 36881498 DOI: 10.1021/acs.jpca.2c06624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
We have studied the effect of amino acids on the electron attachment properties of a DNA nucleobase, with cytosine as a model system. The equation of motion coupled cluster theory with an extended basis set has been used to simulate the electron-attached state of the DNA model system. Arginine, alanine, lysine, and glycine are the four amino acids considered to investigate their role in electron attachment to a DNA nucleobase. The electron attachment to cytosine in all the four cytosine-amino acid gas-phase dimer complexes follows a doorway mechanism, where the electron gets transferred from the initial dipole-bound doorway state to the final nucleobase-bound state through the mixing of electronic and nuclear degrees of freedom. When cytosine is bulk-solvated with glycine, the glycine-bound state acts as the doorway state, where the initial electron density is localized on the bulk amino acid and away from the nucleobase, thus leading to the physical shielding of the nucleobase from the incoming electron. At the same time, the presence of amino acids can increase the stability of the nucleobase-bound anionic state, which can suppress the sugar-phosphate bond rupture caused by dissociative electron attachment to DNA.
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Affiliation(s)
- Pooja Verma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Jishnu Narayanan S J
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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5
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Das S, Samanta K. Recent Advances in the Study of Negative-Ion Resonances Using Multiconfigurational Propagator and a Complex Absorbing Potential. Chemphyschem 2023; 24:e202200546. [PMID: 36223261 DOI: 10.1002/cphc.202200546] [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: 07/25/2022] [Revised: 10/12/2022] [Indexed: 02/03/2023]
Abstract
The transient resonances are a challenge to bound state quantum mechanics. These states lie in the continuum part of the spectrum of the Hamiltonian. For this, one has to treat a continuum problem due to electron-molecule scattering and the many-electron correlation problem simultaneously. Moreover, the description of a resonance requires a wavefunction that bridges the part that resembles a bound state with another that resembles a continuum state such that the continuity of the wavefunction and its first derivative with respect to the distance between the incoming projectile and the target is maintained. A review of the recent advances in the theoretical investigation of the negative-ion resonances (NIR) is presented. The NIRs are ubiquitous in nature. They result from the scattering of electrons off of an atomic or molecular target. They are important for numerous chemical processes in upper atmosphere, space and even biological systems. A contextual background of the existing theoretical methods as well as the newly-developed multiconfigurational propagator tools based on a complex absorbing potential are discussed.
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Affiliation(s)
- Subhasish Das
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Kansapada, Argul, 752050, India
| | - Kousik Samanta
- School of Basic Sciences, Indian Institute of Technology Bhubaneswar, Kansapada, Argul, 752050, India
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6
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Das S, Samanta K. Investigation of electron-induced scattering resonances using a multiconfigurational polarization propagator and a complex absorbing potential. Chem Phys 2023. [DOI: 10.1016/j.chemphys.2022.111712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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7
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Anstöter CS, Abou-Hatab S, Thodika M, Matsika S. Effective Fragment Potentials for Microsolvated Excited and Anionic States. J Phys Chem A 2022; 126:8508-8518. [DOI: 10.1021/acs.jpca.2c06122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Cate S. Anstöter
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania19122, United States
| | - Salsabil Abou-Hatab
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania19122, United States
| | - Mushir Thodika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania19122, United States
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Kumari B, Huwaidi A, Robert G, Cloutier P, Bass AD, Sanche L, Wagner JR. Shape Resonances in DNA: Nucleobase Release, Reduction, and Dideoxynucleoside Products Induced by 1.3 to 2.3 eV Electrons. J Phys Chem B 2022; 126:5175-5184. [PMID: 35793462 DOI: 10.1021/acs.jpcb.2c01851] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the details of DNA damage caused by high-energy particles or photons is complicated by the multitude of reactive species, arising from the ionization and dissociation of H2O, DNA, and protein. In this work, oligonucleotides (ODNs) are irradiated with a beam of low-energy electrons of 1.3 to 2.3 eV, which can only induce damage via the decay of shape resonances into various dissociative electron attachment channels. Using LC-MS/MS analysis, the major products are the release of nonmodified nucleobases (NB; Cyt ≫ Thy ∼ Ade > Gua). Additional damage includes 5,6-dihydropyrimidines (dHT > dHU) and eight nucleosides with modified sugar moieties consisting of 2',3'- and 2',5'-dideoxynucleosides (ddG > ddA ∼ ddC > ddT). The distribution of products is remarkably different in a 16-mer ODN compared to that observed previously with thymidylyl-(3'-5')-thymidine. This difference is explained by electron delocalization occurring within a sufficiently long strand, the DEA theory of O'Malley, and recent time-dependent density functional theory calculations.
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Affiliation(s)
- Bhavini Kumari
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Alaa Huwaidi
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Gabriel Robert
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Pierre Cloutier
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Andrew D Bass
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
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9
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Thodika M, Matsika S. Projected Complex Absorbing Potential Multireference Configuration Interaction Approach for Shape and Feshbach Resonances. J Chem Theory Comput 2022; 18:3377-3390. [PMID: 35622933 DOI: 10.1021/acs.jctc.1c01310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Anion resonances are formed as metastable intermediates in low-energy electron-induced reactions. Due to the finite lifetimes of resonances, applying standard Hermitian formalism for their characterization presents a vexing problem for computational chemists. Numerous modifications to conventional quantum chemical methods have enabled satisfactory characterization of resonances, but specific issues remain, especially in describing two-particle one-hole (2p-1h) resonances. An accurate description of these resonances and their coupling with single-particle resonances requires a multireference approach. We propose a projected complex absorbing potential (CAP) implementation within the multireference configuration interaction (MRCI) framework to characterize single-particle and 2p-1h resonances. As a first application, we use the projected-CAP-MRCI approach to characterize and benchmark the 2Πg shape resonance in N2-. We test its performance as a function of the size of the subspace and other parameters, and we compute the complex potential energy surface of the 2Πg shape resonance to show that a smooth curve is obtained. One key benefit of MRCI is that it can describe Feshbach resonances (most common examples of 2p-1h resonances) at the same footing as shape resonances. Therefore, it is uniquely positioned to describe mixing between the different channels. To test these additional capabilities, we compute Feshbach resonances in H2O- and anions of dicyanoethylene isomers. We find that CAP-MRCI can efficiently capture the mixing between the Feshbach and shape resonances in dicyanoethylene isomers, which has significant consequences for their lifetimes.
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Affiliation(s)
- Mushir Thodika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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10
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Sala L, Lyshchuk H, Šáchová J, Chvátil D, Kočišek J. Different Mechanisms of DNA Radiosensitization by 8-Bromoadenosine and 2'-Deoxy-2'-fluorocytidine Observed on DNA Origami Nanoframe Supports. J Phys Chem Lett 2022; 13:3922-3928. [PMID: 35472278 PMCID: PMC9083549 DOI: 10.1021/acs.jpclett.2c00584] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/15/2022] [Indexed: 06/14/2023]
Abstract
DNA origami nanoframes with two parallel DNA sequences are used to evaluate the effect of nucleoside substituents on radiation-induced DNA damage. Double strand breaks (DSB) of DNA are counted using atomic force microscopy (AFM), and total number of lesions is evaluated using real-time polymerase chain reaction (RT-PCR). Enhanced AT or GC content does not increase the number of DNA strand breaks. Incorporation of 8-bromoadenosine results in the highest enhancement in total number of lesions; however, the highest enhancement in DSB is observed for 2'-deoxy-2'-fluorocytidine, indicating different mechanisms of radiosensitization by nucleoside analogues with the halogen substituent on base or sugar moieties, respectively. "Bystander" effects are observed, when the number of DSB in a sequence is enhanced by a substituent in the parallel DNA sequence. The present approach eliminates limitations of previously developed methods and motivates detailed studies of poorly understood conformation or bystander effects in radiation induced damage to DNA.
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Affiliation(s)
- Leo Sala
- J.
Heyrovský Institute of Physical Chemistry of CAS, Dolejškova 3, 18223 Prague, Czech Republic
| | - Hlib Lyshchuk
- J.
Heyrovský Institute of Physical Chemistry of CAS, Dolejškova 3, 18223 Prague, Czech Republic
| | - Jana Šáchová
- Laboratory
of Genomics and Bioinformatics, Institute
of Molecular Genetics of the CAS, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - David Chvátil
- Nuclear
Physics Institute of the CAS, Řež 130, 250 68 Řež, Czech
Republic
| | - Jaroslav Kočišek
- J.
Heyrovský Institute of Physical Chemistry of CAS, Dolejškova 3, 18223 Prague, Czech Republic
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11
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Liu C, Zheng Y, Sanche L. Damage Induced to DNA and Its Constituents by 0-3 eV UV Photoelectrons †. Photochem Photobiol 2021; 98:546-563. [PMID: 34767635 DOI: 10.1111/php.13559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 11/07/2021] [Indexed: 11/28/2022]
Abstract
The complex physical and chemical interactions between DNA and 0-3 eV electrons released by UV photoionization can lead to the formation of various lesions such as base modifications and cleavage, crosslinks and single strand breaks. Furthermore, in the presence of platinum chemotherapeutic agents, these electrons can cause clustered lesions, including double strand breaks. We explain the mechanisms responsible for these damages via the production 0-3 eV electrons by UVC radiation, and by UV photons of any wavelengths, when they are produced by photoemission from nanoparticles lying within about 10 nm from DNA. We review experimental evidence showing that a single 0-3 eV electron can produce these damages. The foreseen benefits UV-irradiation of nanoparticles targeted to the cell nucleus are mentioned in the context of cancer therapy, as well as the potential hazards to human health when they are present in cells.
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Affiliation(s)
- Chaochao Liu
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, China
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou, China
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC, Canada
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12
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Narayanan S J J, Tripathi D, Dutta AK. Doorway Mechanism for Electron Attachment Induced DNA Strand Breaks. J Phys Chem Lett 2021; 12:10380-10387. [PMID: 34669407 DOI: 10.1021/acs.jpclett.1c02735] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report a new doorway mechanism for the dissociative electron attachment to genetic materials. The dipole-bound state of the nucleotide anion acts as the doorway for electron capture in the genetic material. The electron gets subsequently transferred to a dissociative σ*-type anionic state localized on a sugar-phosphate or a sugar-nucleobase bond, leading to their cleavage. The electron transfer is mediated by the mixing of electronic and nuclear degrees of freedom. The cleavage rate of the sugar-phosphate bond predicted by this new mechanism is higher than that of the sugar-nucleobase bond breaking, and both processes are considerably slower than the formation of a stable valence-bound anion. The new mechanism can explain the relative rates of electron attachment induced bond cleavages in genetic materials.
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Affiliation(s)
- Jishnu Narayanan S J
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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13
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Huwaidi A, Kumari B, Robert G, Guérin B, Sanche L, Wagner JR. Profiling DNA Damage Induced by the Irradiation of DNA with Gold Nanoparticles. J Phys Chem Lett 2021; 12:9947-9954. [PMID: 34617774 DOI: 10.1021/acs.jpclett.1c02598] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The presence of gold nanoparticles (AuNPs) greatly enhances the formation of DNA damage when exposed to therapeutic X-rays. Three types of DNA damage are assessed in irradiated DNA by enzymatic digestion coupled to liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. The major type of damage is release of the four nonmodified nucleobases, with a bias toward the release of cytosine and thymine. The second most important pathway involves the formation of several common reduction and oxidation products of DNA. Lastly, eight unique modifications of the 2-deoxyribose moiety are formed, which includes the 2',3'- and 2',5'-dideoxynucleosides (ddNs) of the four canonical nucleosides. The yield of ddNs decreases in the following order: ddG > ddA > ddC > ddT. From the yield and distribution of products, most of the damage is considered to arise from the generation of Auger/low-energy electrons (LEEs) and their reaction with DNA.
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Affiliation(s)
- Alaa Huwaidi
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Bhavini Kumari
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Gabriel Robert
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Brigitte Guérin
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
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14
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Gao Y, Zheng Y, Sanche L. Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents. Int J Mol Sci 2021; 22:7879. [PMID: 34360644 PMCID: PMC8345953 DOI: 10.3390/ijms22157879] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 11/18/2022] Open
Abstract
The complex physical and chemical reactions between the large number of low-energy (0-30 eV) electrons (LEEs) released by high energy radiation interacting with genetic material can lead to the formation of various DNA lesions such as crosslinks, single strand breaks, base modifications, and cleavage, as well as double strand breaks and other cluster damages. When crosslinks and cluster damages cannot be repaired by the cell, they can cause genetic loss of information, mutations, apoptosis, and promote genomic instability. Through the efforts of many research groups in the past two decades, the study of the interaction between LEEs and DNA under different experimental conditions has unveiled some of the main mechanisms responsible for these damages. In the present review, we focus on experimental investigations in the condensed phase that range from fundamental DNA constituents to oligonucleotides, synthetic duplex DNA, and bacterial (i.e., plasmid) DNA. These targets were irradiated either with LEEs from a monoenergetic-electron or photoelectron source, as sub-monolayer, monolayer, or multilayer films and within clusters or water solutions. Each type of experiment is briefly described, and the observed DNA damages are reported, along with the proposed mechanisms. Defining the role of LEEs within the sequence of events leading to radiobiological lesions contributes to our understanding of the action of radiation on living organisms, over a wide range of initial radiation energies. Applications of the interaction of LEEs with DNA to radiotherapy are briefly summarized.
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Affiliation(s)
- Yingxia Gao
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, China;
| | - Yi Zheng
- State Key Laboratory of Photocatalysis on Energy and Environment, Fuzhou University, Fuzhou 350116, China;
| | - Léon Sanche
- Département de Médecine Nucléaire et Radiobiologie et Centre de Recherche Clinique, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada;
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15
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Castellani ME, Verlet JRR. Intramolecular Photo-Oxidation as a Potential Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study. Molecules 2021; 26:2877. [PMID: 34067988 PMCID: PMC8152231 DOI: 10.3390/molecules26102877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
A carboxylated adenosine analog (C-Ado-) has been synthesized and probed via time-resolved photoelectron spectroscopy in order to induce intra-molecular charge transfer from the carboxylic acid moiety to the nucleobase. Intra-molecular charge transfer can be exploited as starting point to probe low-energy electron (LEE) damage in DNA and its derivatives. Time-dependent density functional theory (TD-DFT) calculations at the B3LYP-6311G level of theory have been performed to verify that the highest occupied molecular orbital (HOMO) was located on carboxylic acid and that the lowest occupied molecular orbital (LUMO) was on the nucleobase. Hence, the carboxylic acid could work as electron source, whilst the nucleobase could serve the purpose of electron acceptor. The dynamics following excitation at 4.66 eV (266 nm) were probed using time-resolved photoelectron spectroscopy using probes at 1.55 eV (800 nm) and 3.10 eV (400 nm). The data show rapid decay of the excited state population and, based on the similarity of the overall dynamics to deoxy-adenosine monophosphate (dAMP-), it appears that the dominant decay mechanism is internal conversion following 1ππ* excitation of the nucleobase, rather than charge-transfer from the carboxylic acid to the nucleobase.
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16
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Thodika M, Mackouse N, Matsika S. Description of Two-Particle One-Hole Electronic Resonances Using Orbital Stabilization Methods. J Phys Chem A 2020; 124:9011-9020. [DOI: 10.1021/acs.jpca.0c07904] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Mushir Thodika
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Nathan Mackouse
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, 1901 N 13th Street, Philadelphia, Pennsylvania 19122, United States
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17
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Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA. Int J Mol Sci 2019; 21:ijms21010111. [PMID: 31877939 PMCID: PMC6981450 DOI: 10.3390/ijms21010111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/10/2019] [Accepted: 12/19/2019] [Indexed: 12/27/2022] Open
Abstract
The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A4), d(A8), d(A12), d(A16), and d(A20)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A4) to d(A16), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A20), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA20 sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.
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18
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Khorsandgolchin G, Sanche L, Cloutier P, Wagner JR. Strand Breaks Induced by Very Low Energy Electrons: Product Analysis and Mechanistic Insight into the Reaction with TpT. J Am Chem Soc 2019; 141:10315-10323. [PMID: 31244176 DOI: 10.1021/jacs.9b03295] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Numerous experimental studies show that 5-15 eV electrons induce strand breaks in DNA at energies below the ionization threshold of DNA components. In this energy range, DNA damage arises principally by the formation of transient negative ions, decaying into dissociative electron attachment (DEA) and electronic excitation of dissociative states. Here, we carried out LC-MS/MS analysis of the degradation products arising from bombardment of TpT, a DNA model compound, irradiated with very low energy electrons (vLEEs; ∼1.8 eV). The formation of thymidine 5'-monophosphate (TMP5') together with 2',3'-dideoxythymidine (ddT3') can be explained by cleavage of the C3'-O bond of TpT, whereas thymidine 3'-monophosphate (TMP3') and 2',5'-dideoxythymidine (ddT5') are formed by cleavage of the C5'-O bond. The formation of ddT3' and ddT5' decreased upon irradiation of either TMP5' or TMP3', and even further in the case of thymidine, underlining the critical role of the phosphate group. Interestingly, the yield of TMP5' and TMP3' was higher than that of the corresponding ddT3' and ddT5' products, suggesting alternative fates of C3' and C5'-centered sugar radicals. In contrast, the release of thymine from TpT was minor (<20%) and did not result in the formation of expected products from DEA-mediated cleavage at the N-glycosidic bond. Lastly, vLEE induced the conversion of thymine to 5,6-dihydrothymine (5,6-dhT) within TpT, a reaction likely involving thymine anion radicals. In summary, we show that a major pathway of vLEEs involves DEA-mediated cleavage of the C3'-O and C5'-O bonds of TpT, resulting in the formation of specific fragments, which represent a prompt single strand break in DNA.
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Affiliation(s)
- Ghazal Khorsandgolchin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences , Université de Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
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19
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McKee AD, Schaible MJ, Rosenberg RA, Kundu S, Orlando TM. Low energy secondary electron induced damage of condensed nucleotides. J Chem Phys 2019; 150:204709. [PMID: 31153208 DOI: 10.1063/1.5090491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Radiation damage and stimulated desorption of nucleotides 2'-deoxyadenosine 5'-monophosphate (dAMP), adenosine 5'-monophosphate (rAMP), 2'-deoxycytidine 5'-monophosphate (dCMP), and cytidine 5'-monophosphate (rCMP) deposited on Au have been measured using x-rays as both the probe and source of low energy secondary electrons. The fluence dependent behavior of the O-1s, C-1s, and N-1s photoelectron transitions was analyzed to obtain phosphate, sugar, and nucleobase damage cross sections. Although x-ray induced reactions in nucleotides involve both direct ionization and excitation, the observed bonding changes were likely dominated by the inelastic energy-loss channels associated with secondary electron capture and transient negative ion decay. Growth of the integrated peak area for the O-1s component at 531.3 eV, corresponding to cleavage of the C-O-P phosphodiester bond, yielded effective damage cross sections of about 23 Mb and 32 Mb (1 Mb = 10-18 cm2) for AMP and CMP molecules, respectively. The cross sections for sugar damage, as determined from the decay of the C-1s component at 286.4 eV and the glycosidic carbon at 289.0 eV, were slightly lower (about 20 Mb) and statistically similar for the r- and d- forms of the nucleotides. The C-1s component at 287.6 eV, corresponding to carbons in the nucleobase ring, showed a small initial increase and then decayed slowly, yielding a low damage cross section (∼5 Mb). Although there is no statistical difference between the sugar forms, changing the nucleobase from adenine to cytidine has a slight effect on the damage cross section, possibly due to differing electron capture and transfer probabilities.
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Affiliation(s)
- A D McKee
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - M J Schaible
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - R A Rosenberg
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - S Kundu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - T M Orlando
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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20
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Vogel S, Ebel K, Schürmann RM, Heck C, Meiling T, Milosavljevic AR, Giuliani A, Bald I. Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks - Influence of the DNA Sequence and Substrate. Chemphyschem 2019; 20:823-830. [PMID: 30719805 DOI: 10.1002/cphc.201801152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/01/2019] [Indexed: 12/28/2022]
Abstract
DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3×10-16 cm2 . The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.
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Affiliation(s)
- Stefanie Vogel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Germany
| | - Kenny Ebel
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Robin M Schürmann
- Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Christian Heck
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Germany
| | - Till Meiling
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | | | - Alexandre Giuliani
- Synchrotron SOLEIL, 91192, Gif-sur-Yvette, France.,UAR 1008 CEPIA, INRA, 44316, Nantes, France
| | - Ilko Bald
- Institute of Chemistry - Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1 - Analytical Chemistry and Reference Materials, BAM Federal Institute of Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
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21
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Schürmann R, Vogel S, Ebel K, Bald I. The Physico-Chemical Basis of DNA Radiosensitization: Implications for Cancer Radiation Therapy. Chemistry 2018. [PMID: 29522244 DOI: 10.1002/chem.201800804] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
High-energy radiation is used in combination with radiosensitizing therapeutics to treat cancer. The most common radiosensitizers are halogenated nucleosides and cisplatin derivatives, and recently also metal nanoparticles have been suggested as potential radiosensitizing agents. The radiosensitizing action of these compounds can at least partly be ascribed to an enhanced reactivity towards secondary low-energy electrons generated along the radiation track of the high-energy primary radiation, or to an additional emission of secondary reactive electrons close to the tumor tissue. This is referred to as physico-chemical radiosensitization. In this Concept article we present current experimental methods used to study fundamental processes of physico-chemical radiosensitization and discuss the most relevant classes of radiosensitizers. Open questions in the current discussions are identified and future directions outlined, which can lead to optimized treatment protocols or even novel therapeutic concepts.
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Affiliation(s)
- Robin Schürmann
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Stefanie Vogel
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany.,School of Analytical Sciences Adlershof, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany
| | - Kenny Ebel
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
| | - Ilko Bald
- Institute of Chemistry-Physical Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany.,Department 1-Analytical Chemistry and Reference Materials, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter Str. 11, 12489, Berlin, Germany
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22
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Piroozfar B, Raisali G, Alirezapour B, Mirzaii M. The effect of 111In radionuclide distance and auger electron energy on direct induction of DNA double-strand breaks: a Monte Carlo study using Geant4 toolkit. Int J Radiat Biol 2018; 94:385-393. [DOI: 10.1080/09553002.2018.1440329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Behnaz Piroozfar
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Gholamreza Raisali
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Behrouz Alirezapour
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
| | - Mohammad Mirzaii
- Radiation Applications Research School, Nuclear Science and Technology Research Institute, Tehran, Iran
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23
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Kohanoff J, McAllister M, Tribello GA, Gu B. Interactions between low energy electrons and DNA: a perspective from first-principles simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383001. [PMID: 28617676 DOI: 10.1088/1361-648x/aa79e3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts with the interaction of radiation-either photons or swift ions-and the biological medium, which causes electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, and strand breaks in plasmid DNA in particular (Boudaiffa et al 2000 Science 287 1658-60). These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage. In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.
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Affiliation(s)
- Jorge Kohanoff
- Atomistic Simulation Centre, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
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24
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Choofong S, Cloutier P, Sanche L, Wagner JR. Base Release and Modification in Solid-Phase DNA Exposed to Low-Energy Electrons. Radiat Res 2016; 186:520-530. [PMID: 27802110 DOI: 10.1667/rr14476.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ionization generates a large number of secondary low-energy electrons (LEEs) with a most probable energy of approximately 10 eV, which can break DNA bonds by dissociative electron attachment (DEA) and lead to DNA damage. In this study, we investigated radiation damage to dry DNA induced by X rays (1.5 keV) alone on a glass substrate or X rays combined with extra LEEs (average energy of 5.8 eV) emitted from a tantalum (Ta) substrate under an atmosphere of N2 and standard ambient conditions of temperature and pressure. The targets included calf-thymus DNA and double-stranded synthetic oligonucleotides. We developed analytical methods to measure the release of non-modified DNA bases from DNA and the formation of several base modifications by LC-MS/MS with isotopic dilution for precise quantification. The results show that the yield of non-modified bases as well as base modifications increase by 20-30% when DNA is deposited on a Ta substrate compared to that on a glass substrate. The order of base release (Gua > Ade > Thy ∼ Cyt) agrees well with several theoretical studies indicating that Gua is the most susceptible site toward sugar-phosphate cleavage. The formation of DNA damage by LEEs is explained by DEA leading to the release of non-modified bases involving the initial cleavage of N1-C1', C3'-O3' or C5'-O5' bonds. The yield of base modifications was lower than the release of non-modified bases. The main LEE-induced base modifications include 5,6-dihydrothymine (5,6-dHT), 5,6-dihydrouracil (5-dHU), 5-hydroxymethyluracil (5-HmU) and 5-formyluracil (5-ForU). The formation of base modifications by LEEs can be explained by DEA and cleavage of the C-H bond of the methyl group of Thy (giving 5-HmU and 5-ForU) and by secondary reactions of H atoms and hydride anions that are generated by primary LEE reactions followed by subsequent reaction with Cyt and Thy (giving 5,6-dHU and 5,6-dHT).
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Affiliation(s)
- Surakarn Choofong
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Pierre Cloutier
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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25
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Wang S, Zhao P, Zhang C, Bu Y. The Equally Important Role of Adenine Derivatives to That of Pyrimidine Derivatives in Near‐0 eV Electron‐Induced DNA Lesions. Chemphyschem 2016; 17:1669-77. [DOI: 10.1002/cphc.201600002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Indexed: 01/27/2023]
Affiliation(s)
- Shoushan Wang
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Peiwen Zhao
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Changzhe Zhang
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
| | - Yuxiang Bu
- Institute of Theoretical Chemistry School of Chemistry and Chemical Engineering Shandong University Jinan 250100 P. R. China
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26
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Wang S, Zhao P, Zhang C, Bu Y. Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines. J Phys Chem B 2016; 120:2649-57. [PMID: 26913546 DOI: 10.1021/acs.jpcb.5b11432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental studies showed that high energy radiation induced base release and DNA backbone breaks mainly occur at the neighboring 5' nucleotide when a single-stranded DNA is modified by radiosensitizing 5-halogenated deoxyuridines. However, no mechanism can be used to interpret these experimental observations. To better understand the radiosensitivity of 5-halogenated deoxyuridines, mechanisms involving hydrogen abstraction by the uracil-5-yl radical from the C2' and C3' positions of an adjacent nucleotide separately followed by the C3'-O3' or N-glycosidic bond rupture and the P-O3' bond breakage are investigated in the DNA sequence 5'-TU(•)-3' employing density functional theory calculations in the present study. It is found that hydrogen abstractions from both positions are comparable with the one from the C2' site slightly more favorable. The N-glycosidic bond cleavage in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is estimated to have the lowest activation free energies, indicating that the adjacent 5' base release dominates electron induced damage to single-stranded DNA incorporated by 5-halogenated deoxyuridines. Relative to the P-O3' bond breakage after the internucleotide C3'-H abstraction, the C3'-O3' bond rupture in the neighboring 5' nucleotide following the internucleotide C2'-Ha abstraction is predicted to have a lower activation free energy, implying that single-stranded DNA backbone breaks are prone to occur at the C3'-O3' bond site. The 5'-TU(•)-3' species has substantial electron affinity and can even capture a hydrated electron, forming the 5'-TU(-)-3' anion. However, the electron induced C3'-O3' bond rupture in 5'-TU(-)-3' anion via a pathway of internucleotide proton abstraction is only minor in both the gas phase and aqueous solution. The present theoretical predictions can interpret rationally experimental observations, thereby demonstrating that the mechanisms proposed here are responsible for high energy radiation induced damage to single-stranded DNA incorporated by radiosensitizing 5-halogenated deoxyuridines. By comparing with previous results, our work proves that the radiosensitizing action of 5-bromo-2-deoxyuridine is not weaker but stronger than its isomer 6-bromo-2-deoxyuridine on the basis of the available data.
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Affiliation(s)
- Shoushan Wang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Peiwen Zhao
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Changzhe Zhang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan 250100, P. R. China
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27
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Vogel S, Rackwitz J, Schürman R, Prinz J, Milosavljević AR, Réfrégiers M, Giuliani A, Bald I. Using DNA origami nanostructures to determine absolute cross sections for UV photon-induced DNA strand breakage. J Phys Chem Lett 2015; 6:4589-93. [PMID: 26536162 DOI: 10.1021/acs.jpclett.5b02238] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We have characterized ultraviolet (UV) photon-induced DNA strand break processes by determination of absolute cross sections for photoabsorption and for sequence-specific DNA single strand breakage induced by photons in an energy range from 6.50 to 8.94 eV. These represent the lowest-energy photons able to induce DNA strand breaks. Oligonucleotide targets are immobilized on a UV transparent substrate in controlled quantities through attachment to DNA origami templates. Photon-induced dissociation of single DNA strands is visualized and quantified using atomic force microscopy. The obtained quantum yields for strand breakage vary between 0.06 and 0.5, indicating highly efficient DNA strand breakage by UV photons, which is clearly dependent on the photon energy. Above the ionization threshold strand breakage becomes clearly the dominant form of DNA radiation damage, which is then also dependent on the nucleotide sequence.
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Affiliation(s)
- Stefanie Vogel
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
| | - Jenny Rackwitz
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
| | - Robin Schürman
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
- BAM Federal Institute for Materials Research and Testing , Richard-Willstätter Str. 11, 12489 Berlin, Germany
| | - Julia Prinz
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
| | | | | | - Alexandre Giuliani
- Synchrotron SOLEIL , 91192 Gif-sur-Yvette, France
- UAR 1008 CEPIA, INRA, 44316 Nantes, France
| | - Ilko Bald
- Institute of Chemistry, University of Potsdam , Karl-Liebknecht-Str. 24-25, 14469 Potsdam, Germany
- BAM Federal Institute for Materials Research and Testing , Richard-Willstätter Str. 11, 12489 Berlin, Germany
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28
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Wang S, Zhang C, Zhao P, Bu Y. Efficient and Substantial DNA Lesions From Near 0 eV Electron-Induced Decay of the O4-Hydrogenated Thymine Nucleotides: A DFT Study. J Phys Chem B 2015; 119:13971-9. [PMID: 26441346 DOI: 10.1021/acs.jpcb.5b06195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Possible electron-induced ruptures of C3'-O3', C5'-O5', and N1-C1' bonds in O4-hydrogenated 2'-deoxythymidine-3'-monophosphate (3'-dT(O4H)MPH) and 2'-deoxythymidine-5'-monophosphate (5'-dT(O4H)MPH) are investigated using density functional theory calculations, and efficient pathways are proposed. Electron attachment causes remarkable structural relaxation in the thymine C6 site. A concerted process of intramolecular proton transfer (IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3'-O3' bond rupture is observed in [3'-dT(O4H)MPH](-). A low activation barrier (9.32 kcal/mol) indicates that this pathway is the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3'-end thymine, which prevents the N1-C1' bond cleavage in [3'-dT(O4H)MPH](-). However, essentially spontaneous N1-C1' bond cleavage following similar IPT is predicted in [5'-dT(O4H)MPH](-). A moderate activation barrier (13.02 kcal/mol) for the rate-controlling IPT step suggests that base release from the N1-C1' cleavage arises readily at the 3'-end of single strand DNA with the strand ended by a thymine. The C5'-O5' bond has only an insignificant change in the IPT process. Solvent effects are found to increase slightly the energy requirements for either bond ruptures (11.23 kcal/mol (C3'-O3') vs 16.18 kcal/mol (N1-C1')), but not change their relative efficiencies.
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Affiliation(s)
- Shoushan Wang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| | - Changzhe Zhang
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| | - Peiwen Zhao
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Institute of Theoretical Chemistry, Shandong University , Jinan, 250100 P. R. China
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Champion C, Quinto MA, Monti JM, Galassi ME, Weck PF, Fojón OA, Hanssen J, Rivarola RD. Water versus DNA: new insights into proton track-structure modelling in radiobiology and radiotherapy. Phys Med Biol 2015; 60:7805-28. [PMID: 26406277 DOI: 10.1088/0031-9155/60/20/7805] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Water is a common surrogate of DNA for modelling the charged particle-induced ionizing processes in living tissue exposed to radiations. The present study aims at scrutinizing the validity of this approximation and then revealing new insights into proton-induced energy transfers by a comparative analysis between water and realistic biological medium. In this context, a self-consistent quantum mechanical modelling of the ionization and electron capture processes is reported within the continuum distorted wave-eikonal initial state framework for both isolated water molecules and DNA components impacted by proton beams. Their respective probability of occurrence-expressed in terms of total cross sections-as well as their energetic signature (potential and kinetic) are assessed in order to clearly emphasize the differences existing between realistic building blocks of living matter and the controverted water-medium surrogate. Consequences in radiobiology and radiotherapy will be discussed in particular in view of treatment planning refinement aiming at better radiotherapy strategies.
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Affiliation(s)
- C Champion
- Université de Bordeaux, CNRS/IN2P3, Centre d'Etudes Nucléaires de Bordeaux Gradignan, Gradignan, France
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McAllister M, Smyth M, Gu B, Tribello GA, Kohanoff J. Understanding the Interaction between Low-Energy Electrons and DNA Nucleotides in Aqueous Solution. J Phys Chem Lett 2015; 6:3091-3097. [PMID: 26267207 DOI: 10.1021/acs.jpclett.5b01011] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Reactions that can damage DNA have been simulated using a combination of molecular dynamics and density functional theory. In particular, the damage caused by the attachment of a low energy electron to the nucleobase. Simulations of anionic single nucleotides of DNA in an aqueous environment that was modeled explicitly have been performed. This has allowed us to examine the role played by the water molecules that surround the DNA in radiation damage mechanisms. Our simulations show that hydrogen bonding and protonation of the nucleotide by the water can have a significant effect on the barriers to strand breaking reactions. Furthermore, these effects are not the same for all four of the bases.
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Affiliation(s)
- Maeve McAllister
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Maeve Smyth
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Bin Gu
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
- ‡Department of Physics, Nanjing University of Information Science and Technology, Nanjing 21004, China
| | - Gareth A Tribello
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
| | - Jorge Kohanoff
- †Atomistic Simulation Centre, School of Mathematics and Physics, Queen's University Belfast, Belfast BT7 1NN, United Kingdom
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Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays. Sci Rep 2014; 4:7391. [PMID: 25487346 PMCID: PMC4260214 DOI: 10.1038/srep07391] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/20/2014] [Indexed: 01/18/2023] Open
Abstract
The electronic structure of DNA is determined by its nucleotide sequence, which is for instance exploited in molecular electronics. Here we demonstrate that also the DNA strand breakage induced by low-energy electrons (18 eV) depends on the nucleotide sequence. To determine the absolute cross sections for electron induced single strand breaks in specific 13 mer oligonucleotides we used atomic force microscopy analysis of DNA origami based DNA nanoarrays. We investigated the DNA sequences 5′-TT(XYX)3TT with X = A, G, C and Y = T, BrU 5-bromouracil and found absolute strand break cross sections between 2.66 · 10−14 cm2 and 7.06 · 10−14 cm2. The highest cross section was found for 5′-TT(ATA)3TT and 5′-TT(ABrUA)3TT, respectively. BrU is a radiosensitizer, which was discussed to be used in cancer radiation therapy. The replacement of T by BrU into the investigated DNA sequences leads to a slight increase of the absolute strand break cross sections resulting in sequence-dependent enhancement factors between 1.14 and 1.66. Nevertheless, the variation of strand break cross sections due to the specific nucleotide sequence is considerably higher. Thus, the present results suggest the development of targeted radiosensitizers for cancer radiation therapy.
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Chen HY, Yang PY, Chen HF, Kao CL, Liao LW. DFT reinvestigation of DNA strand breaks induced by electron attachment. J Phys Chem B 2014; 118:11137-44. [PMID: 25184499 DOI: 10.1021/jp506679b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The benchmark study of DFT methods on the activation energies of phosphodiester C3'-O and C5'-O bond ruptures and glycosidic C1'-N bond ruptures induced by electron attachment was performed. While conventional pure and hybrid functionals provide a relatively reasonable description for the C1'-N bond rupture, they significantly underestimate the energy barriers of the C-O bond ruptures. This is because the transition states of the later reactions, which are characterized by an electron distribution delocalized from the nucleobase to sugar-phosphate backbone, suffer from a severe self-interaction error in common DFT methods. CAM-B3LYP, M06-2X, and ωB97XD are the top three methods that emerged from the benchmark study; the mean absolute errors relative to the CCSD(T) values are 1.7, 1.9, and 2.2 kcal/mol, respectively. The C-O bond cleavages of 3'- and 5'-dXMP(•-), where X represents four nucleobases, were then recalculated at the M06-2X/6-31++G**//M06-2X/6-31+G* level, and it turned out that the C-O bond cleavages do not proceed as easily as previously predicted by the B3LYP calculations. Our calculations revealed that the C-O bonds of purine nucleotides are more susceptible than pyrimidine nucleotides to the electron attachment. The energies of electron attachment to nucleotides were calculated and discussed as well.
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Affiliation(s)
- Hsing-Yin Chen
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University , Kaohsiung 807, Taiwan
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33
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Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy. Molecules 2014; 19:13803-23. [PMID: 25191873 PMCID: PMC6271098 DOI: 10.3390/molecules190913803] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 08/21/2014] [Accepted: 08/29/2014] [Indexed: 12/26/2022] Open
Abstract
DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.
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Falcetta MF, DiFalco LA, Ackerman DS, Barlow JC, Jordan KD. Assessment of Various Electronic Structure Methods for Characterizing Temporary Anion States: Application to the Ground State Anions of N2, C2H2, C2H4, and C6H6. J Phys Chem A 2014; 118:7489-97. [DOI: 10.1021/jp5003287] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Laura A. DiFalco
- Grove City College, Grove City, Pennsylvania 16127, United States
| | | | - John C. Barlow
- Grove City College, Grove City, Pennsylvania 16127, United States
| | - Kenneth D. Jordan
- University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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36
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Park Y, Peoples AR, Madugundu GS, Sanche L, Wagner JR. Side-by-side comparison of DNA damage induced by low-energy electrons and high-energy photons with solid TpTpT trinucleotide. J Phys Chem B 2013; 117:10122-31. [PMID: 23909580 PMCID: PMC3817083 DOI: 10.1021/jp405397m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The genotoxic effects of high-energy ionizing radiation have been largely attributed to the ionization of H2O leading to hydroxyl radicals and the ionization of DNA leading mostly to damage through base radical cations. However, the contribution of low-energy electrons (LEEs; ≤ 10 eV), which involves subionization events, has been considered to be less important than that of hydroxyl radicals and base radical cations. Here, we compare the ability of LEEs and high-energy X-ray photons to induce DNA damage using dried thin films of TpTpT trinucleotide as a simple and representative model for DNA damage. The main radiation-induced damage of TpTpT as measured by high-performance liquid chromatography (HPLC) with UV detection and HPLC coupled to tandem mass spectrometry analyses included thymine release (-Thy), strand breaks (pT, Tp, pTpT, TpTp, and TpT), and the formation of base modifications [5,6-dihydrothymine (5,6-dhT), 5-hydroxymethyluracil (5-hmU), and 5-formyluracil (5-fU)]. The global profile of products was very similar for both types of radiation indicating converging pathways of formation. The percent damage of thymine release, fragmentation, and base modification was 20, 19, and 61 for high-energy X-rays, respectively, compared to 35, 13, and 51 for LEEs (10 eV). Base release was significantly lower for X-rays. In both cases, phosphodiester bond cleavage gave mononucleotides (pT and Tp) and dinucleotides (pTpT and TpTp) containing a terminal phosphate as the major fragments. For base modifications, the ratio of reductive (5,6-dhT) to oxidative products (5-hmU plus 5-fU) was 0.9 for high-energy X-rays compared to 1.7 for LEEs. These results indicate that LEEs give a similar profile of products compared to ionizing radiation.
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Affiliation(s)
- Yeunsoo Park
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Heath Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
- Fundamental Technology Division, Plasma Technology Research Center, National Fusion Research Institute, Gunsan, Jeollabuk-do, South Korea 573-540
| | - Anita R. Peoples
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - Guru S. Madugundu
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Heath Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Heath Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
| | - J. Richard Wagner
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Heath Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada J1H 5N4
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Cauët E, Bogatko S, Liévin J, De Proft F, Geerlings P. Electron-Attachment-Induced DNA Damage: Instantaneous Strand Breaks. J Phys Chem B 2013; 117:9669-76. [DOI: 10.1021/jp406320g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emilie Cauët
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
- Service de Chimie Quantique
et Photophysique, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, CPi160/09, B-1050 Brussels, Belgium
| | - Stuart Bogatko
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
| | - Jacques Liévin
- Service de Chimie Quantique
et Photophysique, Université Libre de Bruxelles, Avenue F.D. Roosevelt 50, CPi160/09, B-1050 Brussels, Belgium
| | - Frank De Proft
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
| | - Paul Geerlings
- General Chemistry - Algemene
Chemie, Vrije Universiteit Brussel, Pleinlaan
2, B-1050 Brussels, Belgium
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38
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Boulanouar O, Fromm M, Mavon C, Cloutier P, Sanche L. Dissociative electron attachment to DNA-diamine thin films: impact of the DNA close environment on the OH- and O- decay channels. J Chem Phys 2013; 139:055101. [PMID: 23927286 PMCID: PMC3813476 DOI: 10.1063/1.4815967] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We measure the desorption of anions stimulated by the impact of 0-20 eV electrons on highly uniform thin films of plasmid DNA-diaminopropane. The results are accurately correlated with film thickness and composition by AFM and XPS measurements, respectively. Resonant structures in the H(-), O(-), and OH(-) yield functions are attributed to the decay of transient anions into the dissociative electron attachment (DEA) channel. The diamine induces ammonium-phosphate bridges along the DNA backbone, which suppresses the DEA O(-) channel and in counter-part increases considerably the desorption of OH(-). The close environment of the phosphate groups may therefore play an important role in modulating the rate and type of DNA damages induced by low energy electrons.
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Affiliation(s)
- Omar Boulanouar
- UMR CNRS 6249 Chrono-Environnement, Laboratoire de Chimie Physique et Rayonnements – Alain Chambaudet, LRC CEA, Université de Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Michel Fromm
- UMR CNRS 6249 Chrono-Environnement, Laboratoire de Chimie Physique et Rayonnements – Alain Chambaudet, LRC CEA, Université de Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Christophe Mavon
- UMR CNRS 6249 Chrono-Environnement, Laboratoire de Chimie Physique et Rayonnements – Alain Chambaudet, LRC CEA, Université de Franche-Comté, 16 route de Gray, F-25030 Besançon cedex, France
| | - Pierre Cloutier
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et de Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Québec J1H 5N4, Canada
| | - Léon Sanche
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et de Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Québec J1H 5N4, Canada
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Alizadeh E, Sanche L. The Role of Humidity and Oxygen Level on Damage to DNA Induced by Soft X-rays and Low-Energy Electrons. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2013; 117:22445-22453. [PMID: 24976877 PMCID: PMC4072655 DOI: 10.1021/jp403350j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Single- and double-strand breaks induced by soft X-rays (1.5 keV) and photo-emitted LEEs (0-30 eV) were measured in dry and humid thin films of plasmid DNA irradiated under different controllable levels of oxygen at standard ambient temperature and pressure (SATP). G values derived from these experiments shows that the presence of H2O and changing the atmosphere from N2 to O2, while keeping all other experimental parameters constant, increases the formation of DSBs by factors of 4.5 and 11.8 for X-rays and LEEs, respectively. Under an oxygenated environment in humid DNA films, the additional LEE-induced damage resulting from the combination of water and oxygen exhibits a supper-additive effect, which leads to the formation of DSBs with a G value almost 7 times higher than that obtained by X-ray photons. These results indicate that O2, H2O and LEEs effectively contribute synergistically to enhance the formation of DSBs.
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Affiliation(s)
- Elahe Alizadeh
- Group of Radiation Sciences, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada J1H5N4
| | - Léon Sanche
- Group of Radiation Sciences, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, University of Sherbrooke, Sherbrooke, Québec, Canada J1H5N4
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40
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Madugundu GS, Park Y, Sanche L, Wagner JR. Radiation-induced formation of 2',3'-dideoxyribonucleosides in DNA: a potential signature of low-energy electrons. J Am Chem Soc 2012; 134:17366-8. [PMID: 23057636 DOI: 10.1021/ja306810w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have identified a series of modifications of the 2'-deoxyribose moiety of DNA arising from the exposure of isolated and cellular DNA to ionizing radiation. The modifications consist of 2',3'-dideoxyribonucleoside derivatives of T, C, A, and G, as identified by enzymatic digestion and LC-MS/MS. Under dry conditions, the yield of these products was 6- to 44-fold lower than the yield of 8-oxo-7,8-dihydroguanine. We propose that 2',3'-dideoxyribonucleosides are generated from the reaction of low-energy electrons with DNA, leading to cleavage of the C3'-O bond and formation of the corresponding C3'-deoxyribose radical.
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Affiliation(s)
- Guru S Madugundu
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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41
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Park Y, Polska K, Rak J, Wagner JR, Sanche L. Fundamental mechanisms of DNA radiosensitization: damage induced by low-energy electrons in brominated oligonucleotide trimers. J Phys Chem B 2012; 116:9676-82. [PMID: 22812492 DOI: 10.1021/jp304964r] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The replacement of nucleobases with brominated analogs enhances DNA radiosensitivity. We examine the chemistry of low-energy electrons (LEEs) in this sensitization process by experiments with thin films of the oligonucleotide trimers TBrXT, where BrX = 5-BrU (5-bromouracil), 5-BrC (5-bromocytosine), 8-BrA (8-bromoadenine), or 8-BrG (8-bromoguanine). The products induced from irradiation of thin (∼ 2.5 nm) oligonucleotide films, with 10 eV electrons, under ultrahigh vacuum (UHV) are analyzed by HPLC-UV. The number of damaged brominated trimers ranges from about 12 to 15 × 10(-3) molecules per incident electron, whereas under the identical conditions, these numbers drop to 4-7 × 10(-3) for the same, but nonbrominated oligonucleotides. The results of HPLC analysis show that the main degradation pathway of trinucleotides containing brominated bases involve debromination (i.e., loss of the bromine atom and its replacement with a hydrogen atom). The electron-induced sum of products upon bromination increases by factors of 2.1 for the pyrimidines and 3.2 for the purines. Thus, substitution of any native nucleobase with a brominated one in simple models of DNA increases LEE-induced damage to DNA and hence its radiosensitivity. Furthermore, besides the brominated pyrimidines that have already been tested in clinical trials, brominated purines not only appear to be promising sensitizers for radiotherapy, but could provide a higher degree of radiosensitization.
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Affiliation(s)
- Yeunsoo Park
- Center for Radiobiology and Radiotherapy, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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42
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Kumar SVK, Pota T, Peri D, Dongre AD, Rao BJ. Low energy electron induced damage to plasmid DNA pQE30. J Chem Phys 2012; 137:045101. [DOI: 10.1063/1.4737182] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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43
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Alizadeh E, Sanche L. Precursors of solvated electrons in radiobiological physics and chemistry. Chem Rev 2012; 112:5578-602. [PMID: 22724633 DOI: 10.1021/cr300063r] [Citation(s) in RCA: 232] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elahe Alizadeh
- Groupe en Sciences des Radiations, Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Canada
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Keller A, Bald I, Rotaru A, Cauët E, Gothelf KV, Besenbacher F. Probing electron-induced bond cleavage at the single-molecule level using DNA origami templates. ACS NANO 2012; 6:4392-9. [PMID: 22510060 DOI: 10.1021/nn3010747] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Low-energy electrons (LEEs) play an important role in nanolithography, atmospheric chemistry, and DNA radiation damage. Previously, the cleavage of specific chemical bonds triggered by LEEs has been demonstrated in a variety of small organic molecules such as halogenated benzenes and DNA nucleobases. Here we present a strategy that allows for the first time to visualize the electron-induced dissociation of single chemical bonds within complex, but well-defined self-assembled DNA nanostructures. We employ atomic force microscopy to image and quantify LEE-induced bond dissociations within specifically designed oligonucleotide targets that are attached to DNA origami templates. In this way, we use a highly selective approach to compare the efficiency of the electron-induced dissociation of a single disulfide bond with the more complex cleavage of the DNA backbone within a TT dinucleotide sequence. This novel technique enables the fast and parallel determination of DNA strand break yields with unprecedented control over the DNA's primary and secondary structure. Thus the detailed investigation of DNA radiation damage in its most natural environment, e.g., DNA nucleosomes constituting the chromatin, now becomes feasible.
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Affiliation(s)
- Adrian Keller
- Interdisciplinary Nanoscience Center (iNANO) and Danish National Research Foundation: Centre for DNA Nanotechnology (CDNA), Aarhus University, 8000 Aarhus C, Denmark.
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Liu Z, Guo X, Tan C, Li J, Kao YT, Wang L, Sancar A, Zhong D. Electron tunneling pathways and role of adenine in repair of cyclobutane pyrimidine dimer by DNA photolyase. J Am Chem Soc 2012; 134:8104-14. [PMID: 22533849 DOI: 10.1021/ja2105009] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Electron tunneling pathways in enzymes are critical to their catalytic efficiency. Through electron tunneling, photolyase, a photoenzyme, splits UV-induced cyclobutane pyrimidine dimer into two normal bases. Here, we report our systematic characterization and analyses of photoinitiated three electron transfer processes and cyclobutane ring splitting by following the entire dynamical evolution during enzymatic repair with femtosecond resolution. We observed the complete dynamics of the reactants, all intermediates and final products, and determined their reaction time scales. Using (deoxy)uracil and thymine as dimer substrates, we unambiguously determined the electron tunneling pathways for the forward electron transfer to initiate repair and for the final electron return to restore the active cofactor and complete the catalytic photocycle. Significantly, we found that the adenine moiety of the unusual bent flavin cofactor is essential to mediating all electron-transfer dynamics through a superexchange mechanism, leading to a delicate balance of time scales. The cyclobutane ring splitting takes tens of picoseconds, while electron-transfer dynamics all occur on a longer time scale. The active-site structural integrity, unique electron tunneling pathways, and the critical role of adenine ensure the synergy of these elementary steps in this complex photorepair machinery to achieve maximum repair efficiency which is close to unity. Finally, we used the Marcus electron-transfer theory to evaluate all three electron-transfer processes and thus obtained their reaction driving forces (free energies), reorganization energies, and electronic coupling constants, concluding that the forward and futile back-electron transfer is in the normal region and that the final electron return of the catalytic cycle is in the inverted region.
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Affiliation(s)
- Zheyun Liu
- Department of Physics, The Ohio State University, Columbus, Ohio 43210, United States
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Li Z, Cloutier P, Sanche L, Wagner JR. Low-energy electron-induced damage in a trinucleotide containing 5-bromouracil. J Phys Chem B 2011; 115:13668-73. [PMID: 21902215 PMCID: PMC3818159 DOI: 10.1021/jp205194g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The reaction of low-energy electrons (LEEs; 10 eV) with 5'-TpXpT-3' (TXT), where X is uracil (U), thymine (T), and 5-bromouracil (5BrU), was examined by HPLC-UV analysis. The presence of 5BrU increased total damage by >50%. The radiation products of T5BrUT included TUT (40%), free U, T, 5BrU (23%), and fragments (13%). These products may be explained by initial capture of LEEs by the nucleobase to form a transient anion, followed by transfer of the electron within the molecule and cleavage of susceptible bonds by dissociative electron attachment (C-Br, C-N, or C-O bonds). In addition, these products may arise from the uracilyl-5-yl (U-5-yl) radicals that undergo H-atom abstraction from the sugar moiety. Interestingly, several products contained two sites of cleavage (U, pUT, and TUp). The formation of these products was linear with dose, and thus, they arise from the single-electron reactions. To explain these products, we propose that the reaction of LEEs (10 eV) involves the coupling of two dissociative processes in the same molecule (for example, dissociative excitation and dissociative electron attachment). The latter reactions may contribute to the formation of clustered damage, which is the most deleterious damage induced by ionizing radiation.
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Affiliation(s)
- Zejun Li
- Center for Radiobiology and Radiotherapy, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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Smyth M, Kohanoff J. Excess electron localization in solvated DNA bases. PHYSICAL REVIEW LETTERS 2011; 106:238108. [PMID: 21770551 DOI: 10.1103/physrevlett.106.238108] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 05/02/2011] [Indexed: 05/31/2023]
Abstract
We present a first-principles molecular dynamics study of an excess electron in condensed phase models of solvated DNA bases. Calculations on increasingly large microsolvated clusters taken from liquid phase simulations show that adiabatic electron affinities increase systematically upon solvation, as for optimized gas-phase geometries. Dynamical simulations after vertical attachment indicate that the excess electron, which is initially found delocalized, localizes around the nucleobases within a 15 fs time scale. This transition requires small rearrangements in the geometry of the bases.
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Affiliation(s)
- Maeve Smyth
- Atomistic Simulation Centre, Queen's University Belfast, Belfast, Northern Ireland, United Kingdom
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Park Y, Li Z, Cloutier P, Sanche L, Wagner JR. DNA damage induced by low-energy electrons: conversion of thymine to 5,6-dihydrothymine in the oligonucleotide trimer TpTpT. Radiat Res 2010; 175:240-6. [PMID: 21268718 DOI: 10.1667/rr2381.1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Low-energy electrons (LEE) induce single- and double-strand breaks in DNA. To investigate the mechanism of LEE-induced DNA damage, nucleotides and short oligonucleotide were irradiated with monoenergetic electrons in the solid state and the modifications were observed by chemical analyses. With 10 eV electrons and TpTpT as the target, approximately one-third of the total damage of TpTpT involves cleavage of the phosphodiester-sugar bond (C-O) and the N-glycosidic bond (C-N). Here we focus on the remaining two-thirds of the damage. The major products were observed to elute between TpT and TpTpT on the HPLC chromatogram. Of these products, three modifications were identified as XpTpT, TpXpT and TpTpX, where X = 5,6-dihydrothymine, on the basis of comparison with standard compounds using HPLC and mass spectrometry. These results suggest that 5,6-dihydrothymine is a major product of the reaction of LEE with DNA.
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Affiliation(s)
- Yeunsoo Park
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Heath Sciences, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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