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Ameixa J, Bald I. Unraveling the Complexity of DNA Radiation Damage Using DNA Nanotechnology. Acc Chem Res 2024; 57:1608-1619. [PMID: 38780304 PMCID: PMC11154965 DOI: 10.1021/acs.accounts.4c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Radiation cancer therapies use different ionizing radiation qualities that damage DNA molecules in tumor cells by a yet not completely understood plethora of mechanisms and processes. While the direct action of the radiation is significant, the byproducts of the water radiolysis, mainly secondary low-energy electrons (LEEs, <20 eV) and reactive oxygen species (ROS), can also efficiently cause DNA damage, in terms of DNA strand breakage or DNA interstrand cross-linking. As a result, these types of DNA damage evolve into mutations hindering DNA replication, leading to cancer cell death. Concomitant chemo-radiotherapy explores the addition of radiosensitizing therapeutics commonly targeting DNA, such as platinum derivatives and halogenated nucleosides, to enhance the harmful effects of ionizing radiation on the DNA molecule. Further complicating the landscape of DNA damage are secondary structures such as G-quadruplexes occurring in telomeric DNA. These structures protect DNA from radiation damage, rendering them as promising targets for new and more selective cancer radiation treatments, rather than targeting linear DNA. However, despite extensive research, there is no single paradigm approach to understanding the mysterious way in which ionizing radiation causes DNA damage. This is due to the multidisciplinary nature of the field of research, which deals with multiple levels of biological organization, from the molecular building blocks of life toward cells and organisms, as well as with complex multiscale radiation-induced effects. Also, intrinsic DNA features, such as DNA topology and specific oligonucleotide sequences, strongly influence its response to damage from ionizing radiation. In this Account, we present our studies focused on the absolute quantification of photon- and low-energy electron-induced DNA damage in strategically selected target DNA sequences. Our methodology involves using DNA origami nanostructures, specifically the Rothemund triangle, as a platform to expose DNA sequences to either low-energy electrons or vacuum-ultraviolet (VUV, <15 eV) photons and subsequent atomic force microscopy (AFM) analysis. Through this approach, the effects of the DNA sequence, incorporation of halogenated radiosensitizers, DNA topology, and the radiation quality on radiation-induced DNA strand breakage have been systematically assessed and correlated with fundamental photon- and electron-driven mechanisms underlying DNA radiation damage. At lower energies, these mechanisms include dissociative electron attachment (DEA), where electrons attach to DNA molecules causing strand breaks, and dissociative photoexcitation of DNA. Additionally, further dissociative processes such as photoionization and electron impact contribute to the complex cascade of DNA damage events induced by ionizing radiation. We expect that emerging DNA origami-based approaches will lead to a paradigm shift in research fields associated with DNA damage and suggest future directions, which can foster the development of technological applications in nanomedicine, e.g., optimized cancer treatments or the molecular design of optimized radiosensitizing therapeutics.
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Affiliation(s)
- João Ameixa
- Institute
of Chemistry, Hybrid Nanostructures, University
of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
- Centre
of Physics and Technological Research (CEFITEC), Department of Physics,
NOVA School of Science and Technology, University
NOVA of Lisbon, Campus de Caparica 2829-516, Portugal
| | - Ilko Bald
- Institute
of Chemistry, Hybrid Nanostructures, University
of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
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Saqib M, Izadi F, Isierhienrhien LU, Ončák M, Denifl S. Decomposition of triazole and 3-nitrotriazole upon low-energy electron attachment. Phys Chem Chem Phys 2023; 25:13892-13901. [PMID: 37183636 PMCID: PMC10207873 DOI: 10.1039/d3cp01162c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 04/26/2023] [Indexed: 05/16/2023]
Abstract
Compounds based on nitrotriazole have been studied for their application as potential radiosensitizers for the treatment of tumors and as energetic materials. In the former application, the initial reduction of the compounds may serve as a mechanism which leads to the formation of tumor-active species. In this study, we investigated the fundamental properties of anion formation in isolated 3-nitro-1,2,4-triazole (3NTR) molecules upon attachment of low-energy electrons. The resulting product anions formed were detected via mass spectrometry. Quantum chemical calculations were performed to study the dissociation pathways and to derive the threshold energies. We also studied the attachment of electrons to the native 1H-1,2,4-triazole (TR) molecule, revealing the influence of the nitro group on anion formation. Comparing the results for these two systems, we computationally observed a considerable more stable parent anion for 3NTR, which results in significantly more effective degradation of the molecule at lower electron energies. Although characteristic fragmentation reactions in the presence of the nitro group were observed (like formation of NO2- or the release of an OH radical), the main dissociation channel for the 3NTR anion turned out to be the direct dissociation of a hydrogen radical by a single bond cleavage, which we also observed for TR as the main channel. Thus, the triazole ring shows a pronounced stability against electron attachment-induced cleavage compared, for example, to the imidazole ring, which is found in common nitroimidazolic radiosensitizers.
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Affiliation(s)
- Muhammad Saqib
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria.
- Center for Biomolecular Sciences Innsbruck, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Farhad Izadi
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria.
- Center for Biomolecular Sciences Innsbruck, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Leon U Isierhienrhien
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria.
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria.
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria.
- Center for Biomolecular Sciences Innsbruck, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
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Ferreira da Silva F. Electron and Photon Interactions with Bio (Related) Molecules. Int J Mol Sci 2022; 23:ijms232415491. [PMID: 36555138 PMCID: PMC9779049 DOI: 10.3390/ijms232415491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Part of the energy deposited in biological tissue by high-energy radiation is converted to secondary electrons. The knowledge at the molecular level on radiation interaction with biological species has increased due to the contributions of many different scientists working on radiation physics and radiation chemistry. The intention of this Special Issue on electron and photon interactions with (bio) molecules is to bring together different areas of knowledge that focus on radiation interactions with matter.
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Affiliation(s)
- Filipe Ferreira da Silva
- Centre of Physics and Technological Research (CEFITEC), Department of Physics, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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4
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Arthur-Baidoo E, Ončák M, Denifl S. Electron attachment to fluorodeoxyglucose: Dissociation dynamics in a molecule of near-zero electron affinity. J Chem Phys 2022; 157:074301. [PMID: 35987575 DOI: 10.1063/5.0101726] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fluorodeoxyglucose (FDG) is a glucose derivative with fluorine at the C2 position. The molecule containing the radioactive F-18 isotope is well known from its application in positron emission tomography as a radiotracer in tumor examination. In the stable form with the F-19 isotope, FDG was proposed as a potential radiosensitizer. Since reduction processes may be relevant in radiosensitization, we investigated low-energy electron attachment to FDG with a crossed electron-molecule beam experiment and with quantum chemical calculations as well as molecular dynamics at elevated temperatures to reveal statistical dissociation. We experimentally find that the susceptibility of FDG to low-energy electrons is relatively low. The calculations indicate that upon attachment of an electron with a kinetic energy of ∼0 eV, only dipole-bound states are accessible, which agrees with the weak ion yields observed in the experiment. The temporary negative ions formed upon electron attachment to FDG may decay by a large variety of dissociation reactions. The major fragmentation channels include H2O, HF, and H2 dissociation, accompanied by ring opening.
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Affiliation(s)
- Eugene Arthur-Baidoo
- Institut fücr Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Milan Ončák
- Institut fücr Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
| | - Stephan Denifl
- Institut fücr Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstrasse 25, A-6020 Innsbruck, Austria
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Arthur-Baidoo E, Schöpfer G, Ončák M, Chomicz-Mańka L, Rak J, Denifl S. Electron Attachment to 5-Fluorouracil: The Role of Hydrogen Fluoride in Dissociation Chemistry. Int J Mol Sci 2022; 23:8325. [PMID: 35955461 PMCID: PMC9369043 DOI: 10.3390/ijms23158325] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/03/2022] Open
Abstract
We investigate dissociative electron attachment to 5-fluorouracil (5-FU) employing a crossed electron-molecular beam experiment and quantum chemical calculations. Upon the formation of the 5-FU- anion, 12 different fragmentation products are observed, the most probable dissociation channel being H loss. The parent anion, 5-FU-, is not stable on the experimental timescale (~140 µs), most probably due to the low electron affinity of FU; simple HF loss and F- formation are seen only with a rather weak abundance. The initial dynamics upon electron attachment seems to be governed by hydrogen atom pre-dissociation followed by either its full dissociation or roaming in the vicinity of the molecule, recombining eventually into the HF molecule. When the HF molecule is formed, the released energy might be used for various ring cleavage reactions. Our results show that higher yields of the fluorine anion are most probably prevented through both faster dissociation of an H atom and recombination of F- with a proton to form HF. Resonance calculations indicate that F- is formed upon shape as well as core-excited resonances.
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Affiliation(s)
- Eugene Arthur-Baidoo
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria; (E.A.-B.); (G.S.)
- Center for Molecular Biosciences Innsbruck, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
| | - Gabriel Schöpfer
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria; (E.A.-B.); (G.S.)
| | - Milan Ončák
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria; (E.A.-B.); (G.S.)
| | - Lidia Chomicz-Mańka
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (L.C.-M.); (J.R.)
| | - Janusz Rak
- Laboratory of Biological Sensitizers, Physical Chemistry Department, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland; (L.C.-M.); (J.R.)
| | - Stephan Denifl
- Institut für Ionenphysik und Angewandte Physik, Leopold-Franzens Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria; (E.A.-B.); (G.S.)
- Center for Molecular Biosciences Innsbruck, Universität Innsbruck, Technikerstraße 25, A-6020 Innsbruck, Austria
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Gomes ER, Franco MS. Combining Nanocarrier-Assisted Delivery of Molecules and Radiotherapy. Pharmaceutics 2022; 14:pharmaceutics14010105. [PMID: 35057001 PMCID: PMC8781448 DOI: 10.3390/pharmaceutics14010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/23/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Cancer is responsible for a significant proportion of death all over the world. Therefore, strategies to improve its treatment are highly desired. The use of nanocarriers to deliver anticancer treatments has been extensively investigated and improved since the approval of the first liposomal formulation for cancer treatment in 1995. Radiotherapy (RT) is present in the disease management strategy of around 50% of cancer patients. In the present review, we bring the state-of-the-art information on the combination of nanocarrier-assisted delivery of molecules and RT. We start with formulations designed to encapsulate single or multiple molecules that, once delivered to the tumor site, act directly on the cells to improve the effects of RT. Then, we describe formulations designed to modulate the tumor microenvironment by delivering oxygen or to boost the abscopal effect. Finally, we present how RT can be employed to trigger molecule delivery from nanocarriers or to modulate the EPR effect.
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Affiliation(s)
- Eliza Rocha Gomes
- Department of Pharmaceutical Products, Faculty of Pharmacy, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil;
| | - Marina Santiago Franco
- Department of Radiation Sciences (DRS), Institute of Radiation Medicine (IRM), 85764 München, Germany
- Correspondence: ; Tel.: +49-89-3187-48767
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Mikhailov OV. The Physical Chemistry and Chemical Physics (PCCP) Section of the International Journal of Molecular Sciences in Its Publications: The First 300 Thematic Articles in the First 3 Years. Int J Mol Sci 2021; 23:241. [PMID: 35008667 PMCID: PMC8745423 DOI: 10.3390/ijms23010241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
The Physical Chemistry and Chemical Physics Section (PCCP Section) is one of the youngest among the sections of the International Journal of Molecular Sciences (IJMS)-the year 2021 will only mark three years since its inception [...].
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Affiliation(s)
- Oleg V Mikhailov
- Department of Analytical Chemistry, Certification and Quality Management, Kazan National Research Technological University, K. Marx Street 68, 420015 Kazan, Russia
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Ziegler P, Pelc A, Arthur-Baidoo E, Ameixa J, Ončák M, Denifl S. Negative ion formation and fragmentation upon dissociative electron attachment to the nicotinamide molecule. RSC Adv 2021; 11:32425-32434. [PMID: 35495526 PMCID: PMC9041917 DOI: 10.1039/d1ra06083j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/13/2021] [Indexed: 12/20/2022] Open
Abstract
Nicotinamide (C6H6N2O) is a biologically relevant molecule. This compound has several important roles related to the anabolic and metabolic processes that take place in living organisms. It is also used as a radiosensitizer in tumor therapy. As a result of the interaction of high-energy radiation with matter, low-energy electrons are also released, which can also interact with other molecules, forming several types of ions. In the present investigation, dissociative electron attachment to C6H6N2O has been studied in a crossed electron-molecular beams experiment in the electron energy range of about 0-15 eV. In the experiment, six anionic species were detected: C6H5N2O-, C5H4N-, NCO-, O-/NH2 -, and CN-, with NCO- being the most prominent anion. We also provide detailed computational results regarding the energetic thresholds and pathways of the respective dissociative electron attachment (DEA) channels. The experimental results are compared with the theoretical ones and on this basis, the possible DEA reactions for the formation of anions at a given resonance energy were assigned as well as the generation of neutrals fragments such as pyridine and its several derivatives and radicals are predicted. The pyridine ring seems to stay intact during the DEA process.
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Affiliation(s)
- Patrick Ziegler
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Andrzej Pelc
- Maria Curie-Skłodowska University, Department of Biophysics, Mass Spectrometry Laboratory Pl. M. C.-Skłodowskiej 1 20-031 Lublin Poland
| | - Eugene Arthur-Baidoo
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Joao Ameixa
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
- Centre of Physics and Technological Research, Departamento de Física, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa 2829-516 Caparica Portugal
| | - Milan Ončák
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
| | - Stephan Denifl
- Institute for Ion Physics and Applied Physics, University of Innsbruck Technikerstrasse 25 6020 Innsbruck Austria
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