Real-time observation of a molecular reaction mechanism of aqueous 5-Halo-2'-deoxyuridines under UV/ionizing radiation

Interaction of low-energy electrons with radiosensitizers

We provide an experimentalist's perspective on the present state-of-the-art in the studies of low-energy electron interactions with common radiosensitizers, including compounds used in combined chemo-radiation therapy and their model systems. Low-energy electrons are important secondary species formed during the interaction of ionizing radiation with matter. Their role in the radiation chemistry of living organisms has become an important topic for more than 20 years. With the increasing number of works and reviews in the field, we would like to focus here on a very narrow area of compounds that have been shown to have radio-sensitizing properties on the one hand, and high reactivity towards low-energy electrons on the other hand. Gas phase experiments studying electron attachment to isolated molecules and environmental effects on reaction dynamics are reviewed for modified DNA components, nitroimidazoles, and organometallics. In the end, we provide a perspective on the future directions that may be important for transferring the fundamental knowledge about the processes induced by low-energy electrons into practice in the field of rational design of agents for concomitant chemo-radiation therapy.

Dissociative Electron Attachment to 5-Iodo-4-thio-2'-deoxyuridine: A Potential Radiosensitizer of Hypoxic Cells

In the search for effective radiosensitizers for tumor cells, halogenated uracils have attracted more attention due to their large cross section for dissociation upon the attachment of low-energy electrons. In this study, we investigated dissociative electron attachment (DEA) to 5-iodo-4-thio-2'-deoxyuridine, a potential radiosensitizer using a crossed electron-molecule beam experiment coupled with quadrupole mass spectrometry. The experimental results were supported by calculations on the threshold energies of formed anions and transition state calculations. We show that low-energy electrons with kinetic energies near 0 eV may effectively decompose the molecule upon DEA. The by far most abundant anion observed corresponds to the iodine anion (I-). Due to the associated bond cleavage, a radical site is formed at the C5 position, which may initiate strand break formation if the molecule is incorporated into a DNA strand. Our results reflect the conclusion from previous radiolysis studies with the title compound, suggesting its potential as a radiosensitizer.

Quasi-Free Electron-Mediated Radiation Sensitization by C5-Halopyrimidines

Substitution of the thymidine moiety in DNA by C5-substituted halogenated thymidine analogues causes significant augmentation of radiation damage in living cells. However, the molecular pathway involved in such radiosensitization process has not been clearly elucidated to date in solution at room temperature. So far, low-energy electrons (LEEs; 0-20 eV) under vacuum condition and solvated electrons (esol-) in solution are shown to produce the σ-type C5-centered pyrimidine base radical through dissociative electron attachment involving carbon-halogen bond breakage. Formation of this σ-type radical and its subsequent reactions are proposed to cause cellular radiosensitization. Here, we report time-resolved measurements at room temperature, showing that a radiation-produced quasi-free electron (eqf-) in solution promptly breaks the C5-halogen bond in halopyrimidines forming the σ-type C5 radical via an excited transient anion radical. These results demonstrate the importance of ultrafast reactions of eqf-, which are extremely important in chemistry, physics, and biology, including tumor radiochemotherapy.

Low-Energy Electron Damage to Condensed-Phase DNA and Its Constituents

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.

In situ monitoring of the influence of water on DNA radiation damage by near-ambient pressure X-ray photoelectron spectroscopy

Ionizing radiation damage to DNA plays a fundamental role in cancer therapy. X-ray photoelectron-spectroscopy (XPS) allows simultaneous irradiation and damage monitoring. Although water radiolysis is essential for radiation damage, all previous XPS studies were performed in vacuum. Here we present near-ambient-pressure XPS experiments to directly measure DNA damage under water atmosphere. They permit in-situ monitoring of the effects of radicals on fully hydrated double-stranded DNA. The results allow us to distinguish direct damage, by photons and secondary low-energy electrons (LEE), from damage by hydroxyl radicals or hydration induced modifications of damage pathways. The exposure of dry DNA to x-rays leads to strand-breaks at the sugar-phosphate backbone, while deoxyribose and nucleobases are less affected. In contrast, a strong increase of DNA damage is observed in water, where OH-radicals are produced. In consequence, base damage and base release become predominant, even though the number of strand-breaks increases further.

5-Nitro-2,4-Dichloropyrimidine as an Universal Model for Low-Energy Electron Processes Relevant for Radiosensitization

We report experimental results of low-energy electron interactions with.

Reaction Cycles of Halogen Species in the Immune Defense: Implications for Human Health and Diseases and the Pathology and Treatment of COVID-19

There is no vaccine or specific antiviral treatment for COVID-19, which is causing a global pandemic. One current focus is drug repurposing research, but those drugs have limited therapeutic efficacies and known adverse effects. The pathology of COVID-19 is essentially unknown. Without this understanding, it is challenging to discover a successful treatment to be approved for clinical use. This paper addresses several key biological processes of reactive oxygen, halogen and nitrogen species (ROS, RHS and RNS) that play crucial physiological roles in organisms from plants to humans. These include why superoxide dismutases, the enzymes to catalyze the formation of H₂O₂, are required for protecting ROS-induced injury in cell metabolism, why the amount of ROS/RNS produced by ionizing radiation at clinically relevant doses is ~1000 fold lower than the endogenous ROS/RNS level routinely produced in the cell and why a low level of endogenous RHS plays a crucial role in phagocytosis for immune defense. Herein we propose a plausible amplification mechanism in immune defense: ozone-depleting-like halogen cyclic reactions enhancing RHS effects are responsible for all the mentioned physiological functions, which are activated by H₂O₂ and deactivated by NO signaling molecule. Our results show that the reaction cycles can be repeated thousands of times and amplify the RHS pathogen-killing (defense) effects by 100,000 fold in phagocytosis, resembling the cyclic ozone-depleting reactions in the stratosphere. It is unraveled that H₂O₂ is a required protective signaling molecule (angel) in the defense system for human health and its dysfunction can cause many diseases or conditions such as autoimmune disorders, aging and cancer. We also identify a class of potent drugs for effective treatment of invading pathogens such as HIV and SARS-CoV-2 (COVID-19), cancer and other diseases, and provide a molecular mechanism of action of the drugs or candidates.

Direct electron irradiation of DNA in a fully aqueous environment. Damage determination in combination with Monte Carlo simulations

We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si₃N₄ membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D_1/2 = 1.7 ± 0.3 Gy was found to be much smaller as compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of the DSBs to SSBs was found to be 1 : 12 as compared to 1 : 88 found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, co-solutes) for an electron energy range which is difficult to probe by standard methods.

Electronic Excited State Lifetimes of Anionic Water Clusters: Dependence on Charge Solvation Motif

An ongoing controversy about water cluster anions concerns the electron-binding motif, whether the charge center is localized at the surface or within the cluster interior. Here, mixed quantum-classical dynamics simulations have been carried out for a wide range of cluster sizes (n ≤ 1000) for (H₂O)_n^- and (D₂O)_n^-, based on a nonequilibrium first-order rate constant approach. The computed data are in good general agreement with time-resolved photoelectron imaging results (n ≤ 200). The analysis reveals that, for surface state electrons, the cluster size dependence of the excited state electronic energy gap and the magnitude of the nonadiabatic couplings have compensating influences on the excited state lifetimes: the excited state lifetime for surface states reaches a minimum for n ∼ 150 and then increases for larger clusters. It is concluded that the electron resides in a surface-localized motif in all of these measured clusters, dominating at least up to n = 200.

Excess electron reactivity in amino acid aqueous solution revealed by ab initio molecular dynamics simulation: anion-centered localization and anion-relayed electron transfer dissociation

Studies on the structure, states, and reactivity of excess electrons (EEs) in biological media are of great significance. Although there is information about EE interaction with desolvated biological molecules, solution effects are hardly explored. In this work, we present an ab initio molecular dynamics simulation study on the interaction and reactivity of an EE with glycine in solution. Our simulations reveal two striking results. Firstly, a pre-solvated EE partially localizes on the negatively charged -COO(-) group of the zwitterionic glycine and the remaining part delocalizes over solvent water molecules, forming an anion-centered quasi-localized structure, due to relative alignment of the lowest unoccupied molecular orbital energy levels of potential sites for EE residence in the aqueous solution. Secondly, after a period of anion-centered localization of an EE, the zwitterionic glycine is induced to spontaneously fragment through the cleavage of the N-Cα bond, losing ammonia (deamination), and leaving a ˙CH2-COO(-) anion radical, in good agreement with experimental observations. Introduction of the same groups (-COO(-) or -NH3(+)) in the side chain (taking lysine and aspartic acid as examples) can affect EE localization, with the fragmentation of the backbone part of these amino acids dependent on the properties of the side chain groups. These findings provide insights into EE interaction mechanisms with the backbone parts of amino acids and low energy EE induced fragmentation of amino acids and even peptides and proteins.

Hydrated Electrons in Water Clusters: Inside or Outside, Cavity or Noncavity?

In this work, we compare the applicability of three electron–water molecule pseudopotentials in modeling the physical properties of hydrated electrons. Quantum model calculations illustrate that the recently suggested Larsen–Glover–Schwartz (LGS) model and its modified m-LGS version have a too-attractive potential in the vicinity of the oxygen. As a result, LGS models predict a noncavity hydrated electron structure in clusters at room temperature, as seen from mixed one-electron quantum–classical molecular dynamics simulations of water cluster anions, with the electron localizing exclusively in the interior of the clusters. Comparative calculations using the cavity-preferring Turi–Borgis (TB) model predict interior-state and surface-state cluster isomers. The computed associated physical properties are also analyzed and compared to available experimental data. We find that the LGS and m-LGS potentials provide results that appear to be inconsistent with the size dependence of the experimental data. The simulated TB tendencies are qualitatively correct. Furthermore, ab initio calculations on static LGS noncavity structures indicate weak stabilization of the excess electron in regions where the LGS potential preferably and strongly binds the electron. TB calculations give stabilization energies that are in line with the ab initio results. In conclusion, we observe that the cavity-preferring pseudopotential model predicts cluster physical properties in better agreement with experimental data and ab initio calculations than the models predicting noncavity structures for the hydrated electron.

Mechanisms Responsible for High Energy Radiation Induced Damage to Single-Stranded DNA Modified by Radiosensitizing 5-Halogenated Deoxyuridines

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.

In Vitro and In Vivo Studies of a New Class of Anticancer Molecules for Targeted Radiotherapy of Cancer

There is a compelling need to develop anticancer therapies that target cancer cells and tissues. Arising from innovative femtomedicine studies, a new class of non-platinum-based halogenated molecules (called FMD molecules) that selectively kill cancer cells and protect normal cells in treatments of multiple cancers has been discovered. This article reports the first observation of the radiosensitizing effects of such compounds in combination with ionizing radiation for targeted radiotherapy of a variety of cancers. We present in vitro and in vivo studies focused on combination with radiotherapy of cervical, ovarian, head and neck, and lung cancers. Our results demonstrate that treatments of various cancer cells in vitro and in vivo mouse xenograft models with such compounds led to enhanced efficiencies in radiotherapy, while the compounds themselves induced no or little radiotoxicity toward normal cells or tissues. These compounds are therefore effective radiosensitizers that can be translated into clinical trials for targeted radiotherapy of multiple types of cancer. This study also shows the potential of femtomedicine to bring breakthroughs in understanding fundamental biologic processes and to accelerate the discovery of novel drugs for effective treatment or prevention of a variety of cancers. Mol Cancer Ther; 15(4); 640-50. ©2016 AACR.

In Vitro and In Vivo Studies of Non-Platinum-Based Halogenated Compounds as Potent Antitumor Agents for Natural Targeted Chemotherapy of Cancers

Based on a molecular-mechanism-based anticancer drug discovery program enabled by an innovative femtomedicine approach, we have found a previously unknown class of non-platinum-based halogenated molecules (called FMD compounds) as potent antitumor agents for effective treatment of cancers. Here, we present in vitro and in vivo studies of the compounds for targeted chemotherapy of cervical, breast, ovarian, and lung cancers. Our results show that these FMD agents led to DNA damage, cell cycle arrest in the S phase, and apoptosis in cancer cells. We also observed that such a FMD compound caused an increase of reduced glutathione (GSH, an endogenous antioxidant) levels in human normal cells, while it largely depleted GSH in cancer cells. We correspondingly found that these FMD agents exhibited no or little toxicity toward normal cells/tissues, while causing significant cytotoxicity against cancer cells, as well as suppression and delay in tumor growth in mouse xenograft models of cervical, ovarian, breast and lung cancers. These compounds are therefore a previously undiscovered class of potent antitumor agents that can be translated into clinical trials for natural targeted chemotherapy of multiple cancers.

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Femtomedicine may accelerate drug discovery for effective treatment of cancer.

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A previously undiscovered class of non-platinum-based halogenated compounds is found to have potent antitumor effects.

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FMD agents can be used for natural targeted chemotherapy of multiple types of cancer while inducing minimal toxicity.

Excess electron interaction with radiosensitive 5-bromopyrimidine in aqueous solution: a combined ab initio molecular dynamics and time-dependent wave-packet study

Radiation-generated secondary electrons can induce resonance processes in a target molecule and fragment it via different pathways.

Glucose-Promoted Localization Dynamics of Excess Electrons in Aqueous Glucose Solution Revealed by Ab Initio Molecular Dynamics Simulation

Ab initio molecular dynamics simulations reveal that an excess electron (EE) can be more efficiently localized as a cavity-shaped state in aqueous glucose solution (AGS) than in water. Compared with that (∼1.5 ps) in water, the localization time is shortened by ∼0.7-1.2 ps in three AGSs (0.56, 1.12, and 2.87 M). Although the radii of gyration of the solvated EEs are all close to 2.6 Å in the four solutions, the solvated EE cavities in the AGSs become more compact and can localize ∼80% of an EE, which is considerably larger than that (∼40-60% and occasionally ∼80%) in water. These observations are attributed to a modification of the hydrogen-bonded network by the introduction of glucose molecules into water. The water acts as a promoter and stabilizer, by forming voids around glucose molecules and, in this fashion, favoring the localization of an EE with high efficiency. This study provides important information about EEs in physiological AGSs and suggests a new strategy to efficiently localize an EE in a stable cavity for further exploration of biological function.

Antioxidant induces DNA damage, cell death and mutagenicity in human lung and skin normal cells

Clinical trials have shown that antioxidant supplementation increased the risk of lung and skin cancers, but the underlying molecular mechanism is unknown. Here, we show that epigallocatechin gallate (EGCG) as an exemplary antioxidant induced significant death and DNA damage in human lung and skin normal cells through a reductive mechanism. Our results show direct evidence of reductive DNA damage in the cells. We found that EGCG was much more toxic against normal cells than H₂O₂ and cisplatin as toxic and cancer-causing agents, while EGCG at low concentrations (≤100 μM) increased slightly the lung cancer cell viability. EGCG induced DNA double-strand breaks and apoptosis in normal cells and enhanced the mutation frequency. These results provide a compelling explanation for the clinical results and unravel a new reductive damaging mechanism in cellular processes. This study therefore provides a fresh understanding of aging and diseases, and may lead to effective prevention and therapies.

Crystal structures, UV spectra of solid iodide anionic water clusters I(-)(H2O)(1-4), and electrochemical reaction of I(-)(H2O)(1-4) → I· + e(-)(H2O)(1-4)

Four iodide anionic water clusters of I(-)(H2O)1-4 in two supramolecular complexes of [Fe(phen)3][I2(H2O)3] (1) and [Zn(phen)3][I2(H2O)4.5] (2) have been determined by single-crystal X-ray diffraction analysis. The diffuse reflectance spectra for the solid iodide anionic water clusters of I(-)(H2O)1-4 were investigated, and their absorption bands were demonstrated by denisty functional theory calculation. The electrochemical reaction of I(-)(H2O)1-4 → I· + e(-)(H2O)1-4 with the oxidation potential of Ep = 0.61 eV was first found and reported in two aqueous solutions (1 mmol·dm(-3)) of 1 and 2.

Electron transfer-based combination therapy of cisplatin with tetramethyl-p-phenylenediamine for ovarian, cervical, and lung cancers

The platinum-based chemotherapy is the standard treatment for several types of cancer. However, cancer cells often become refractory with time and most patients with serious cancers die of drug resistance. Recently, we have discovered a unique dissociative electron-transfer mechanism of action of cisplatin, the first and most widely used platinum-based anticancer drug. Here, we show that the combination of cisplatin with an exemplary biological electron donor, N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD), may overcome the resistance of cancer cells to cisplatin. Our steady-state absorption and fluorescence spectroscopic measurements confirm the effective dissociative electron-transfer reaction between TMPD and cisplatin. More significantly, we found that the combination of 100 μM TMPD with cisplatin enhances double-strand breaks of plasmid DNA by a factor of approximately 3.5 and dramatically reduces the viability of cisplatin-sensitive human cervical (HeLa) cancer cells and highly cisplatin-resistant human ovarian (NIH:OVCAR-3) and lung (A549) cancer cells. Furthermore, this combination enhances apoptosis and DNA fragmentation by factors of 2-5 compared with cisplatin alone. These results demonstrate that this combination treatment not only results in a strong synergetic effect, but also makes resistant cancer cells sensitive to cisplatin. Because cisplatin is the cornerstone agent for the treatment of a variety of human cancers (including testicular, ovarian, cervical, bladder, head/neck, and lung cancers), our results show both the potential to improve platinum-based chemotherapy of various human cancers and the promise of femtomedicine as an emerging frontier in advancing cancer therapy.

Electron-induced elimination of the bromide anion from brominated nucleobases. A computational study

The enhancement of radiodamage to DNA labeled with halonucleobases is attributed to the reactive radical produced from a halonucleobase by the attachment of an electron. We examined at the B3LYP/6-31++G** level electron capture by four brominated nucleobases (BrNBs): 8-bromo-9-methyladenine, 8-bromo-9-methylguanine, 5-bromo-1-methylcytosine, and 5-bromo-1-methyluracil followed by the release of the bromide anion and a nucleobase radical. We demonstrate that neutral BrNBs in both gas and aqueous phases are better electron acceptors than unsubstituted NBs and that resulting anion radicals, BrNBs(•-), can easily transform into the product complex of the bromide anion and the nucleobase radical ([Br(-)···NB(•)]). The overall thermodynamic stimulus for the process starting with the neutral BrNB and ending with the isolated bromide anion and the NB(•) radical is similar in the case of all four BrNBs studied, which suggests their comparable radiosensitizing capabilities.

Electron stimulated desorption of anions from native and brominated single stranded oligonucleotide trimers

We measured the low energy electron stimulated desorption (ESD) of anions from thin films of native (TXT) and bromine monosubstituted (TBrXT) oligonucleotide trimers deposited on a gold surface (T = thymidine, X = T, deoxycytidine (C), deoxyadenosine (A) or deoxyguanosine (G), Br = bromine). The desorption of H(-), CH(3)(-)/NH(-), O(-)/NH(2)(-), OH(-), CN(-), and Br(-) was induced by 0 to 20 eV electrons. Dissociative electron attachment, below 12 eV, and dipolar dissociation, above 12 eV, are responsible for the formation of these anions. The comparison of the results obtained for the native and brominated trimers suggests that the main pathways of TBrXT degradation correspond to the release of the hydride and bromide anions. Significantly, the presence of bromine in oligonucleotide trimers blocks the electron-induced degradation of nuclobases as evidenced by a dramatic decrease in CN(-) desorption. An increase in the yields of OH(-) is also observed. The debromination yield of particular oligonucleotides diminishes in the following order: BrdU > BrdA > BrdG > BrdC. Based on these results, 5-bromo-2(')-deoxyuridine appears to be the best radiosensitizer among the studied bromonucleosides.

Formation mechanism and structure of a guanine-uracil DNA intrastrand cross-link

The formation and structure of the 5'-G[8-5]U-3' intrastrand cross-link are studied using density functional theory and molecular dynamics simulations due to the potential role of this lesion in the activity of 5-halouracils in antitumor therapies. Upon UV irradiation of 5-halouracil-containing DNA, a guanine radical cation reacts with the uracil radical to form the cross-link, which involves phosphorescence or an intersystem crossing and a rate-determining step of bond formation. Following ionizing radiation, guanine and the uracil radical react, with a rate-limiting step involving hydrogen atom removal. Although cross-link formation from UV radiation is favored, comparison of calculated reaction thermokinetics with that for related experimentally observed purine-pyrimidine cross-links suggests this lesion is also likely to form from ionizing radiation. For the first time, the structure of 5'-G[8-5]U-3' within DNA is identified by molecular dynamics simulations. Furthermore, three conformations of cross-linked DNA are revealed, which differ in the configuration of the complementary bases. Distortions, such as unwinding, are localized to the cross-linked dinucleotide and complementary nucleotides, with minimal changes to the flanking bases. Global changes to the helix, such as bending and groove alterations, parallel cisplatin-induced distortions, which indicate 5'-G[8-5]U-3', may contribute to the cytotoxicity of halouracils in tumor cell DNA using similar mechanisms.

Developing a computational model that accurately reproduces the structural features of a dinucleoside monophosphate unit within B-DNA

The ability of a dinucleoside monophosphate to mimic the conformation of B-DNA was tested using a combination of different phosphate models (anionic, neutral, counterion), environments (gas, water), and density functionals (B3LYP, MPWB1K, M06-2X) with the 6-31G(d,p) basis set. Three sequences (5'-GX(Py)-3', where X(Py) = T, U or (Br)U) were considered, which vary in the (natural or modified) 3' pyrimidine nucleobase (X(Py)). These bases were selected due to their presence in natural DNA, structural similarity to T and/or applications in radical-initiated anti-tumour therapies. The accuracy of each of the 54 model, method and sequence combinations was judged based on the ability to reproduce key structural features of natural B-DNA, including the stacked base-base orientation and important backbone torsion angles. B3LYP yields distorted or tilted relative base-base orientations, while many computational challenges were encountered for MPWB1K. Despite wide use in computational studies of DNA, the neutral (protonated) phosphate model could not consistently predict a stacked arrangement for all sequences. In contrast, stacked base-base arrangements were obtained for all sequences with M06-2X in conjunction with both the anionic and (sodium) counterion phosphate models. However, comparison of calculated and experimental backbone conformations reveals the charge-neutralized counterion phosphate model best mimics B-DNA. Structures optimized with implicit solvent (water) are comparable to gas-phase structures, which suggests similar results should be obtained in an environment of intermediate polarity. We recommend the use of either gas-phase or water M06-2X optimizations with the counterion phosphate model to study the structure and/or reactivity of natural or modified DNA with a dinucleoside monophosphate.

Direct observation of ultrafast-electron-transfer reactions unravels high effectiveness of reductive DNA damage

Both water and electron-transfer reactions play important roles in chemistry, physics, biology, and the environment. Oxidative DNA damage is a well-known mechanism, whereas the relative role of reductive DNA damage is unknown. The prehydrated electron (e(pre)-), a novel species of electrons in water, is a fascinating species due to its fundamental importance in chemistry, biology, and the environment. e(pre)- is an ideal agent to observe reductive DNA damage. Here, we report both the first in situ femtosecond time-resolved laser spectroscopy measurements of ultrafast-electron-transfer (UET) reactions of e(pre)- with various scavengers (KNO(3), isopropanol, and dimethyl sulfoxide) and the first gel electrophoresis measurements of DNA strand breaks induced by e(pre)- and OH(•) radicals co-produced by two-UV-photon photolysis of water. We strikingly found that the yield of reductive DNA strand breaks induced by each e(pre)- is twice the yield of oxidative DNA strand breaks induced by each OH(•) radical. Our results not only unravel the long-standing mystery about the relative role of radicals in inducing DNA damage under ionizing radiation, but also challenge the conventional notion that oxidative damage is the main pathway for DNA damage. The results also show the potential of femtomedicine as a new transdisciplinary frontier and the broad significance of UET reactions of e(pre)- in many processes in chemistry, physics, biology, and the environment.

Photoelectron spectroscopic studies of 5-halouracil anions

The parent negative ions of 5-chlorouracil, UCl(-) and 5-fluorouracil, UF(-) have been studied using anion photoelectron spectroscopy in order to investigate the electrophilic properties of their corresponding neutral halouracils. The vertical detachment energies (VDE) of these anions and the adiabatic electron affinities (EA) of their neutral molecular counterparts are reported. These results are in good agreement with the results of previously published theoretical calculations. The VDE values for both UCl(-) and UF(-) and the EA values for their neutral molecular counterparts are much greater than the corresponding values for both anionic and neutral forms of canonical uracil and thymine. These results are consistent with the observation that DNA is more sensitive to radiation damage when thymine is replaced by halouracil. While we also attempted to prepare the parent anion of 5-bromouracil, UBr(-), we did not observe it, the mass spectrum exhibiting only Br(-) fragments, i.e., 5-bromouracil apparently underwent dissociative electron attachment. This observation is consistent with a previous assessment, suggesting that 5-bromouracil is the best radio-sensitizer among these three halo-nucleobases.

Unexpected photoproduct generated via the acetone-sensitized photolysis of 5-bromo-2'-deoxyuridine in a water/isopropanol solution: experimental and computational studies

The acetone-sensitized photolysis of 5-bromo-2'-deoxyuridine (5-BrdU) in a water/isopropanol solution with 300 nm photons leads to the formation of 2'-deoxyuridine (dU) and a comparable amount of another photoproduct that has not been reported in the literature so far. The negative and positive mass spectra recorded for this species indicate that they originate from the molecular mass of 286 Da, which corresponds to an adduct of 2'-deoxyuridine and 2-propanol. Quantum chemical calculations carried out at the DFT and TDDFT levels reveal both the structure and the UV spectrum of that adduct. The latter computational characteristic matches well the experimental UV spectrum of the new photoproduct. Our findings indicate that the acetone-sensitized photolysis of 5-BrdU is more complicated than has hitherto been assumed. Nevertheless, since electron transfer is one of the pathways responsible for 5-BrdU decay, acetone-sensitized photolysis of the halogen derivatives of nucleobases could be a convenient tool for studying their radiosensitivity in aqueous solutions.

Bond breaks of nucleotides by dissociative electron transfer of nonequilibrium prehydrated electrons: a new molecular mechanism for reductive DNA damage

DNA damage is a central mechanism in the pathogenesis and treatment of human diseases, notably cancer. Little is known about reductive DNA damage in causing genetic mutations during oncogenesis and killing cancer cells during radiotherapy. The prehydrated electron (e(-)(pre)) has the highest yield among all the radicals generated in cells during ionizing radiation and has subpicosecond lifetimes (10(-13) s) and energies below 0 eV, but its role in DNA damage is unknown. In this work, our real-time measurements by femtosecond time-resolved laser spectroscopy have revealed that while adenine and cytosine can effectively trap an e(-)(pre) to form stable anions, thymidine and especially guanine are highly susceptible to dissociative electron transfer of e(-)(pre), leading to bond dissociation in DNA. Our finding demonstrates a dissociative electron transfer pathway for reductive DNA damage that might be related to various diseases such as cancer and stroke. Moreover, this finding challenges the conventional notion that damage to the genome is mainly induced by the oxidizing OH* radical and might eventually lead to improved radiotherapy of cancer and radioprotection of humans.

Site-specific covalent attachment of DNA to proteins using a photoactivatable Tus-Ter complex

Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.