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Radiation-Induced Damage to DNA 2.0
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Radiation-Induced Damage to DNA 2.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 17838

Special Issue Editors

Prof. Dr. Janusz Rak

E-Mail Website
Guest Editor
Department of Chemistry, University of Gdańsk, 80-233 Gdańsk, Poland
Interests: DNA damage; radiation chemistry; photochemistry; quantum-chemistry
Special Issues, Collections and Topics in MDPI journals
Dr. Anil Kumar

E-Mail Website
Co-Guest Editor
Department of Chemistry, Oakland University, Rochester, MI 48309, USA
Interests: theoretical chemistry; DNA radical; low energy electrons
Dr. Magdalena Zdrowowicz

E-Mail Website
Co-Guest Editor
Department of Chemistry, University of Gdańsk, 80-233 Gdańsk, Poland
Interests: radiosensitizers; photosensitizers; DNA damage; radiobiology; cellular studies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Since cancer is the third leading cause of death, radiation induced damage to DNA becomes a topic of a paramount importance. Indeed, radiotherapy and photodynamic therapy are common modalities for treating human cancers and efficient damage to the DNA of tumor cells is their main target. It is well known that cellular DNA, exposed to high energy or UV radiation, is damaged due to excitations as well as ionization of DNA bases resulting in various kinds of DNA lesions, such as DNA base ion radicals, double- and single-strand breaks, and a variety of inter- and intra-cross-linking reactions. Experimental tools including spectroscopy, pulse radiolysis and electron paramagnetic resonance (EPR) are conventionally used to unravel the complex nature of DNA damage.  On the other hand, with the advent of enormous computational power and availability of efficient quantum chemical methods properties such as spin distribution, redox potential, and proton transfer complement experimental results and provide an insight into the mechanism of radical formation and their reactions in DNA.

This Special issue will expose the reader to: the mechanisms of direct and indirect radiation-induced DNA damage, radiation damage to DNA-protein complexes, computational modeling of radiation damage to DNA, radio- and photosensitizers of DNA damage, repair of radiation-induced DNA damage, biological consequences of DNA damage, radiotherapy of cancer, photodynamic therapy, and cellular response to DNA damage.

The gathered in SI articles are expected to provide a reference for the recent development in this interdisciplinary and practical subject to organic and medicinal chemists, radiation and photochemists, molecular modeling chemists as well as to cellular biologists who are in the target audience.

Prof. Dr. Janusz Adam Rak
Guest Editors
Dr. Anil Kumar
Dr. Magdalena Zdrowowicz
Co-Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • Ionizing radiation
  • Low energy electrons (LEE)
  • Solvated electrons
  • DNA radio-/photodamage    
  • DNA ion radicals
  • DNA excited states
  • DNA crosslinks
  • Radiosensitizers
  • Antioxidants
  • Radical scavengers
  • Photosensitizers
  • Hypoxia
  • DNA repair
  • Protein–DNA complexes
  • Molecular modeling of DNA damage

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Published Papers (6 papers)

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Research

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14 pages, 7195 KiB  
Article
Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups
by Evangelos Balanikas, Lara Martinez-Fernandez, Gérard Baldacchino and Dimitra Markovitsi
Int. J. Mol. Sci. 2021, 22(24), 13436; https://doi.org/10.3390/ijms222413436 - 14 Dec 2021
Cited by 2 | Viewed by 2484
Abstract
The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine [...] Read more.
The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3′ or 5′ ends. This position also affects significantly the electronic absorption spectrum of (G+)● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)● radicals and, on the other, they give rise to a reaction product absorbing in the 300–500 nm spectral domain. Full article
(This article belongs to the Special Issue Radiation-Induced Damage to DNA 2.0)
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16 pages, 2133 KiB  
Article
Electron-Induced Repair of 2′-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study
by Michael Bell, Anil Kumar and Michael D. Sevilla
Int. J. Mol. Sci. 2021, 22(4), 1736; https://doi.org/10.3390/ijms22041736 - 9 Feb 2021
Cited by 5 | Viewed by 2705
Abstract
In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of [...] Read more.
In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′• > C1′• > C5′• > C3′• > C2′•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier. Full article
(This article belongs to the Special Issue Radiation-Induced Damage to DNA 2.0)
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14 pages, 3116 KiB  
Article
Electron Attachment Studies with the Potential Radiosensitizer 2-Nitrofuran
by Muhammad Saqib, Eugene Arthur-Baidoo, Milan Ončák and Stephan Denifl
Int. J. Mol. Sci. 2020, 21(23), 8906; https://doi.org/10.3390/ijms21238906 - 24 Nov 2020
Cited by 7 | Viewed by 2799
Abstract
Nitrofurans belong to the class of drugs typically used as antibiotics or antimicrobials. The defining structural component is a furan ring with a nitro group attached. In the present investigation, electron attachment to 2-nitrofuran (C4H3NO3), which is [...] Read more.
Nitrofurans belong to the class of drugs typically used as antibiotics or antimicrobials. The defining structural component is a furan ring with a nitro group attached. In the present investigation, electron attachment to 2-nitrofuran (C4H3NO3), which is considered as a potential radiosensitizer candidate for application in radiotherapy, has been studied in a crossed electron–molecular beams experiment. The present results indicate that low-energy electrons with kinetic energies of about 0–12 eV effectively decompose the molecule. In total, twelve fragment anions were detected within the detection limit of the apparatus, as well as the parent anion of 2-nitrofuran. One major resonance region of ≈0–5 eV is observed in which the most abundant anions NO2−, C4H3O−, and C4H3NO3− are detected. The experimental results are supported by ab initio calculations of electronic states in the resulting anion, thermochemical thresholds, connectivity between electronic states of the anion, and reactivity analysis in the hot ground state. Full article
(This article belongs to the Special Issue Radiation-Induced Damage to DNA 2.0)
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13 pages, 2201 KiB  
Article
5-Nitro-2,4-Dichloropyrimidine as an Universal Model for Low-Energy Electron Processes Relevant for Radiosensitization
by Thomas F. M. Luxford, Stanislav A. Pshenichnyuk, Nail L. Asfandiarov, Tomáš Perečko, Martin Falk and Jaroslav Kočišek
Int. J. Mol. Sci. 2020, 21(21), 8173; https://doi.org/10.3390/ijms21218173 - 31 Oct 2020
Cited by 5 | Viewed by 2464
Abstract
We report experimental results of low-energy electron interactions with 5-nitro-2,4-dichloropyrimidine isolated in the gas phase and hydrated in a cluster environment. The molecule exhibits a very rare combination of many so far hypothesized low-energy electron induced mechanisms, which may be responsible for synergism [...] Read more.
We report experimental results of low-energy electron interactions with 5-nitro-2,4-dichloropyrimidine isolated in the gas phase and hydrated in a cluster environment. The molecule exhibits a very rare combination of many so far hypothesized low-energy electron induced mechanisms, which may be responsible for synergism in concurrent chemo-radiation therapy of cancer. In contrast to many previous efforts to design an ideal radiosensitizer based on one mode of action, the present model molecule presents an alternative approach, where several modes of action are combined. With respect to the processes induced by the low-energy electrons, this is not a trivial task because of strong bond specificity of the dissociative electron attachment reaction, as it is discussed in the present paper. Unfortunately, low solubility and high toxicity of the molecule, as obtained from preliminary MTT assay tests, do not enable further studies of its activity in real biological systems but it can advantageously serve as a model or a base for rational design of radiosensitizers. Full article
(This article belongs to the Special Issue Radiation-Induced Damage to DNA 2.0)
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Review

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32 pages, 3070 KiB  
Review
Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents
by Yingxia Gao, Yi Zheng and Léon Sanche
Int. J. Mol. Sci. 2021, 22(15), 7879; https://doi.org/10.3390/ijms22157879 - 23 Jul 2021
Cited by 37 | Viewed by 3654
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Radiation-Induced Damage to DNA 2.0)
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11 pages, 1732 KiB  
Review
Excision of Oxidatively Generated Guanine Lesions by Competitive DNA Repair Pathways
by Vladimir Shafirovich and Nicholas E. Geacintov
Int. J. Mol. Sci. 2021, 22(5), 2698; https://doi.org/10.3390/ijms22052698 - 7 Mar 2021
Cited by 8 | Viewed by 2691
Abstract
The base and nucleotide excision repair pathways (BER and NER, respectively) are two major mechanisms that remove DNA lesions formed by the reactions of genotoxic intermediates with cellular DNA. It is generally believed that small non-bulky oxidatively generated DNA base modifications are removed [...] Read more.
The base and nucleotide excision repair pathways (BER and NER, respectively) are two major mechanisms that remove DNA lesions formed by the reactions of genotoxic intermediates with cellular DNA. It is generally believed that small non-bulky oxidatively generated DNA base modifications are removed by BER pathways, whereas DNA helix-distorting bulky lesions derived from the attack of chemical carcinogens or UV irradiation are repaired by the NER machinery. However, existing and growing experimental evidence indicates that oxidatively generated DNA lesions can be repaired by competitive BER and NER pathways in human cell extracts and intact human cells. Here, we focus on the interplay and competition of BER and NER pathways in excising oxidatively generated guanine lesions site-specifically positioned in plasmid DNA templates constructed by a gapped-vector technology. These experiments demonstrate a significant enhancement of the NER yields in covalently closed circular DNA plasmids (relative to the same, but linearized form of the same plasmid) harboring certain oxidatively generated guanine lesions. The interplay between the BER and NER pathways that remove oxidatively generated guanine lesions are reviewed and discussed in terms of competitive binding of the BER proteins and the DNA damage-sensing NER factor XPC-RAD23B to these lesions. Full article
(This article belongs to the Special Issue Radiation-Induced Damage to DNA 2.0)
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