Astrochemically Relevant Radicals and Radical-Molecule Complexes: A New Insight from Matrix Isolation

The reactive open-shell species play a very important role in the radiation-induced molecular evolution occurring in the cold areas of space and presumably leading to the formation of biologically relevant molecules. This review presents an insight into the mechanism of such processes coming from matrix isolation studies with a main focus on the experimental and theoretical studies performed in the author's laboratory during the past decade. The radicals and radical cations produced from astrochemically relevant molecules were characterized by Fourier transform infrared (FTIR) and electron paramagnetic resonance (EPR) spectroscopy. Small organic radicals containing C, O, and N atoms are considered in view of their possible role in the formation of complex organic molecules (COMs) in space, and a comparison with earlier results is given. In addition, the radical-molecule complexes generated from isolated intermolecular complexes in matrices are discussed in connection with their model significance as the building blocks for COMs formed under the conditions of extremely restricted molecular mobility at cryogenic temperatures.

A method to implement inter-track interactions in Monte Carlo simulations with TOPAS-nBio and their influence on simulated radical yields following water radiolysis

OBJECTIVE

In FLASH radiotherapy (dose rates ≥ 40 Gy/s), a reduced normal tissue toxicity has been observed, while maintaining the same tumor control compared to conventional radiotherapy (dose rates ≤ 0.03 Gy/s). This protecting effect could not be fully explained yet. One assumption is that interactions between the chemicals of different primary ionizing particles, so-called inter-track interactions, trigger this outcome. In this work, we included inter-track interactions in Monte Carlo track structure simulations and investigated the yield of chemicals (G-value) produced by ionizing particles. 
Approach: For the simulations, we used the Monte Carlo toolkit TOPAS, in which inter-track interactions cannot be implemented without further effort. Thus, we developed a method enabling the simultaneous simulation of N original histories in one event allowing chemical species to interact with each other. To investigate the effect of inter-track interactions we analyzed the G-value of different chemicals using various radiation sources. We used electrons with an energy of 60 eV in different spatial arrangements as well as a 10 MeV and 100 MeV proton source. For electrons we set N between 1 and 60, for protons between 1 and 100.
Main results: In all simulations, the total G-value decreases with increasing N. In detail, the G-value for^●OH, H₃O and e_aqdecreases with increasing N, whereas the G-value of OH^-, H₂O₂and H₂increases slightly. The reason is that with increasing N, the concentration of chemical radicals increases allowing for more chemical reactions between the radicals resulting in a change of the dynamics of the chemical stage.
Signifcance: Inter-track interactions resulting in a variation of the yield of chemical species, may be a factor explaining the FLASH effect. To verify this hypothesis, further simulations are necessary in order to evaluate the impact of varying G-values on the yield of DNA damages.

MRI of radiation chemistry: First images and investigation of potential mechanisms

BACKGROUND

Paramagnetic species such as O2 and free radicals can enhance T1 and T2 relaxation times. If the change in relaxation time is sufficiently large, the contrast will be generated in magnetic resonance images. Since radiation is known to be capable of altering the concentration of O2 and free radicals during water radiolysis, it may be possible for radiation to induce MR signal change.

PURPOSE

We present the first reported instance of x-ray-induced MR signal changes in water phantoms and investigate potential paramagnetic relaxation enhancement mechanisms associated with radiation chemistry changes in oxygen and free radical concentrations.

METHODS

Images of water and 10 mM coumarin phantoms were acquired on a 0.35 T MR-linac before, during, and after a dose delivery of 80 Gy using an inversion-recovery dual-echo sequence with water nullified. Radiation chemistry simulations of these conditions were performed to calculate changes in oxygen and free radical concentrations. Published relaxivity values were then applied to calculate the resulting T1 change, and analytical MR signal equations were used to calculate the associated signal change.

RESULTS

Compared to pre-irradiation reference images, water phantom images taken during and after irradiation showed little to no change, while coumarin phantom images showed a small signal loss in the irradiated region with a contrast-to-noise ratio (CNR) of 1.0-2.5. Radiation chemistry simulations found oxygen depletion of -11 µM in water and -31 µM in coumarin, resulting in a T1 lengthening of 24 ms and 68 ms respectively, and a simulated CNR of 1.0 and 2.8 respectively. This change was consistent with observations in both direction and magnitude. Steady-state superoxide, hydroxyl, hydroperoxyl, and hydrogen radical concentrations were found to contribute less than 1 ms of T1 change.

CONCLUSION

Observed radiation-induced MR signal changes were dominated by an oxygen depletion mechanism. Free radicals were concluded to play a minor secondary role under steady-state conditions. Future applications may include in vivo FLASH treatment verification but would require an MR sequence with a better signal-to-noise ratio and higher temporal resolution than the one used in this study.

Ionization and electron excitation of C60 in a carbon nanotube: A variable temperature/voltage transmission electron microscopic study

The destruction of specimen molecules by an electron beam (e-beam) is either beneficial, as in mass spectrometry capitalizing on ion formation, or deleterious, as in electron microscopy. In the latter application, the e-beam not only produces the specimen image, but also causes information loss upon prolonged irradiation. However, the atomistic mechanism of such loss has been unclear. Performing single-molecule kinetic analysis of C₆₀ dimerization in a carbon nanotube (CNT) under variable-temperature/voltage conditions, we identified three reactive species—that is, radical cation, singlet, and triplet excited states—reacting competitively as the voltage and the properties of the CNT were changed. The key enabler was in situ continuous recording of the whole reaction process, suggesting an upcoming new era of “cinematic chemistry.”

There is increasing attention to chemical applications of transmission electron microscopy, which is often plagued by radiation damage. The damage in organic matter predominantly occurs via radiolysis. Although radiolysis is highly important, previous studies on radiolysis have largely been descriptive and qualitative, lacking in such fundamental information as the product structure, the influence of the energy of the electrons, and the reaction kinetics. We need a chemically well-defined system to obtain such data and have chosen as a model a variable-temperature and variable-voltage (VT/VV) study of the [2 + 2] dimerization of a van der Waals dimer [60]fullerene (C₆₀) to C₁₂₀ in a carbon nanotube (CNT), as studied for several hundred individual reaction events at atomic resolution. We report here the identification of five reaction pathways that serve as mechanistic models of radiolysis damage. Two of them occur via a radical cation of the specimen generated by specimen ionization, and three involve singlet or triplet excited states of the specimen, as initiated by electron excitation of the CNT, followed by energy transfer to the specimen. The [2 + 2] product was identified by measuring the distance between the two C₆₀ moieties, and the mechanisms were distinguished by the pre-exponential factor and the Arrhenius activation energy—the standard protocol of chemical kinetic studies. The results illustrate the importance of VT/VV kinetic analysis in the studies of radiation damage and show that chemical ionization and electron excitation are inseparable, but different, mechanisms of radiation damage, which has so far been classified loosely under the single term “ionization.”

Mechanistic Advantages of Organotin Molecular EUV Photoresists

Extreme ultraviolet (EUV)-induced radiation exposure chemistry in organotin-oxo systems, represented by the archetypal [(R-Sn)₁₂O₁₄(OH)₆](A)₂ cage, has been investigated with density functional theory. Upholding existing experimental evidence of Sn-C cleavage-dominant chemistry, computations have revealed that either electron attachment or ionization can single-handedly trigger tin-carbon bond cleavage, partially explaining the current EUV sensitivity advantage of metal oxide systems. We have revealed that tin atoms at different parts of the molecule react differently to ionization and electron attachment and have identified such selectivity as a result of local coordination chemistry instead of the macro geometry of the molecule. An ionization-deprotonation pathway has also been identified to explain the observed evolution of an anion conjugate acid upon exposure and anion mass dependence in resist sensitivity.

DNA damage modeled with Geant4-DNA: effects of plasmid DNA conformation and experimental conditions

The chemical stage of the Monte Carlo track-structure (MCTS) code Geant4-DNA was extended for its use in DNA strand break (SB) simulations and compared against published experimental data. Geant4-DNA simulations were performed using pUC19 plasmids (2686 base pairs) in a buffered solution of DMSO irradiated by⁶⁰Co or¹³⁷Csγ-rays. A comprehensive evaluation of SSB yields was performed considering DMSO, DNA concentration, dose and plasmid supercoiling. The latter was measured using the super helix density value used in a Brownian dynamics plasmid generation algorithm. The Geant4-DNA implementation of the independent reaction times method (IRT), developed to simulate the reaction kinetics of radiochemical species, allowed to score the fraction of supercoiled, relaxed and linearized plasmid fractions as a function of the absorbed dose. The percentage of the number of SB after •OH + DNA and H• + DNA reactions, referred as SSB efficiency, obtained using MCTS were 13.77% and 0.74% respectively. This is in reasonable agreement with published values of 12% and 0.8%. The SSB yields as a function of DMSO concentration, DNA concentration and super helix density recreated the expected published experimental behaviors within 5%, one standard deviation. The dose response of SSB and DSB yields agreed with published measurements within 5%, one standard deviation. We demonstrated that the developed extension of IRT in Geant4-DNA, facilitated the reproduction of experimental conditions. Furthermore, its calculations were strongly in agreement with experimental data. These two facts will facilitate the use of this extension in future radiobiological applications, aiding the study of DNA damage mechanisms with a high level of detail.

Fluorescent Labeling to Investigate Nanopatterning Processes in Extreme Ultraviolet Lithography

Extreme ultraviolet (EUV) lithography uses 13.5 nm light to reach the sub-20 nm resolution. However, the process of pattern formation induced by this high-energy light is not well-understood. In this work, we provide an inorganic EUV photoresist with fluorescence properties by introducing a carbazole derivative as a ligand, and we study its effect on the patterning process. Using the fluorescence properties, changes in the emission of the material after EUV exposure could be tracked by means of spectroscopy and microscopy. The resist sensitivity was substantially reduced by the incorporation of the carbazole benzoate ligands, which is attributed to hole trapping and steric hindrance. After EUV irradiation of the resist films, infrared, UV-visible absorption, and fluorescence spectroscopies showed that the carbazole units were still mostly intact, although their fluorescence intensity was lowered. Our work shows that fluorescent labeling can provide relevant mechanistic insights in the patterning process of resists, potentially with a molecular resolution.

TOPAS-nBio validation for simulating water radiolysis and DNA damage under low-LET irradiation

The chemical stage of the Monte Carlo track-structure simulation code Geant4-DNA has been revised and validated. The root-mean-square (RMS) empirical parameter that dictates the displacement of water molecules after an ionization and excitation event in Geant4-DNA has been shortened to better fit experimental data. The pre-defined dissociation channels and branching ratios were not modified, but the reaction rate coefficients for simulating the chemical stage of water radiolysis were updated. The evaluation of Geant4-DNA was accomplished with TOPAS-nBio. For that, we compared predicted time-dependentGvalues in pure liquid water for^·OH, e^-_aq, and H₂with published experimental data. For H₂O₂and H^·, simulation of added scavengers at different concentrations resulted in better agreement with measurements. In addition, DNA geometry information was integrated with chemistry simulation in TOPAS-nBio to realize reactions between radiolytic chemical species and DNA. This was used in the estimation of the yield of single-strand breaks (SSB) induced by¹³⁷Csγ-ray radiolysis of supercoiled pUC18 plasmids dissolved in aerated solutions containing DMSO. The efficiency of SSB induction by reaction between radiolytic species and DNA used in the simulation was chosen to provide the best agreement with published measurements. An RMS displacement of 1.24 nm provided agreement with measured data within experimental uncertainties for time-dependentGvalues and under the presence of scavengers. SSB efficiencies of 24% and 0.5% for^·OH and H^·, respectively, led to an overall agreement of TOPAS-nBio results within experimental uncertainties. The efficiencies obtained agreed with values obtained with published non-homogeneous kinetic model and step-by-step Monte Carlo simulations but disagreed by 12% with published direct measurements. Improvement of the spatial resolution of the DNA damage model might mitigate such disagreement. In conclusion, with these improvements, Geant4-DNA/TOPAS-nBio provides a fast, accurate, and user-friendly tool for simulating DNA damage under low linear energy transfer irradiation.

Synthesis and Properties of Targeted Radioisotope Carriers Based on Poly(Acrylic Acid) Nanogels

Radiation crosslinking was employed to obtain nanocarriers based on poly(acrylic acid)—PAA—for targeted delivery of radioactive isotopes. These nanocarriers are internally crosslinked hydrophilic macromolecules—nanogels—bearing carboxylic groups to facilitate functionalization. PAA nanogels were conjugated with an engineered bombesin-derivative—oligopeptide combined with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetate chelating moiety, aimed to provide selective radioligand transport. 4-(4,6-Dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium (DMTMM) toluene-4-sulfonate was used as the coupling agent. After tests on a model amine—p-toluidine—both commercial and home-synthesized DOTA-bombesin were successfully coupled to the nanogels and the obtained products were characterized. The radiolabeling efficiency of nanocarriers with ¹⁷⁷Lu, was chromatographically tested. The results provide a proof of concept for the synthesis of radiation-synthesized nanogel-based radioisotope nanocarriers for theranostic applications.

Revealing Reactions between the Electron Beam and Nanoparticle Capping Ligands with Correlative Fluorescence and Liquid-Phase Electron Microscopy

Liquid-phase transmission electron microscopy (LP-TEM) enables real-time imaging of nanoparticle self-assembly, formation, and etching with single nanometer resolution. Despite the importance of organic nanoparticle capping ligands in these processes, the effect of electron beam irradiation on surface-bound and soluble capping ligands during LP-TEM imaging has not been investigated. Here, we use correlative LP-TEM and fluorescence microscopy (FM) to demonstrate that polymeric nanoparticle ligands undergo competing crosslinking and chain scission reactions that nonmonotonically modify ligand coverage over time. Branched polyethylenimine (BPEI)-coated silver nanoparticles were imaged with dose-controlled LP-TEM followed by labeling their primary amine groups with fluorophores to visualize the local thickness of adsorbed capping ligands. FM images showed that free ligands crosslinked in the LP-TEM image area over imaging times of tens of seconds, enhancing local capping ligand coverage on nanoparticles and silicon nitride membranes. Nanoparticle surface ligands underwent chain scission over irradiation times of minutes to tens of minutes, which depleted surface ligands from the nanoparticle and silicon nitride surface. Conversely, solutions of only soluble capping ligand underwent successive crosslinking reactions with no chain scission, suggesting that nanoparticles enhanced the chain scission reactions by acting as radiolysis hotspots. The addition of a hydroxyl radical scavenger, tert-butanol, eliminated chain scission reactions and slowed the progression of crosslinking reactions. These experiments have important implications for performing controlled and reproducible LP-TEM nanoparticle imaging as they demonstrate that the electron beam can significantly alter ligand coverage on nanoparticles in a nonintuitive manner. They emphasize the need to understand and control the electron beam radiation chemistry of a given sample to avoid significant perturbations to the nanoparticle capping ligand chemistry, which are invisible in electron micrographs.

First-Principles Simulations of Biological Molecules Subjected to Ionizing Radiation

Ionizing rays cause damage to genomes, proteins, and signaling pathways that normally regulate cell activity, with harmful consequences such as accelerated aging, tumors, and cancers but also with beneficial effects in the context of radiotherapies. While the great pace of research in the twentieth century led to the identification of the molecular mechanisms for chemical lesions on the building blocks of biomacromolecules, the last two decades have brought renewed questions, for example, regarding the formation of clustered damage or the rich chemistry involving the secondary electrons produced by radiolysis. Radiation chemistry is now meeting attosecond science, providing extraordinary opportunities to unravel the very first stages of biological matter radiolysis. This review provides an overview of the recent progress made in this direction, focusing mainly on the atto- to femto- to picosecond timescales. We review promising applications of time-dependent density functional theory in this context.

Micro- to Nanoscale Bio-Hybrid Hydrogels Engineered by Ionizing Radiation

Bio-hybrid hydrogels consist of a water-swollen hydrophilic polymer network encapsulating or conjugating single biomolecules, or larger and more complex biological constructs like whole cells. By modulating at least one dimension of the hydrogel system at the micro- or nanoscale, the activity of the biological component can be extremely upgraded with clear advantages for the development of therapeutic or diagnostic micro- and nano-devices. Gamma or e-beam irradiation of polymers allow a good control of the chemistry at the micro-/nanoscale with minimal recourse to toxic reactants and solvents. Another potential advantage is to obtain simultaneous sterilization when the absorbed doses are within the sterilization dose range. This short review will highlight opportunities and challenges of the radiation technologies to produce bio-hybrid nanogels as delivery devices of therapeutic biomolecules to the target cells, tissues, and organs, and to create hydrogel patterns at the nano-length and micro-length scales on surfaces.

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S- )=S was calculated to be slightly lower than that of guanine in 5'-dGMP. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S- . 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S- . 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S- . 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.

Meeting report on ICRR2019, the 16th International Congress on Radiation Research

The 16th International Congress of Radiation Research (ICRR2019) was held in Manchester, UK, in August 2019. The Congress, which is held every four years, covered a wide spectrum of topics relevant for all aspects of radiation research including basic mechanisms, translational research, radiotherapy and health effects, and ecology. Here, we provide a report of the plenary and keynote talks presented at the meeting.

Validation and investigation of reactive species yields of Geant4-DNA chemistry models

PURPOSE

Indirect biological damage due to reactive species produced in water radiolysis reactions is responsible for the majority of biological effect for low linear energy transfer (LET) radiation. Modeling water radiolysis and the subsequent interactions of reactive species, as well as track structures, is essential to model radiobiology on the microscale. Recently, chemistry models have been developed for Geant4-DNA to be used in combination with the comprehensive existing physics models. In the current work, the first detailed, independent, in silico validation of all species yields with published experimental observations and comparison with other radiobiological simulations is presented. Additionally, the effect of LET of protons and heavier ions on reactive species yield in the model was examined, as well as the completeness of the chemical reactions following the radiolysis within the time after physical interactions simulated in the model.

METHODS

Yields over time of reactive species were simulated for water radiolysis by incident electrons, protons, alpha particles, and ions with various LETs using Geant4 and RITRACKS simulation tools. Water dissociation and recombination was simulated using Geant4 to determine the completeness of chemical reactions at the end of the simulation. Yield validation was performed by comparing yields simulated using Geant4 with experimental observations and other simulations. Validation was performed for all species for low LET radiation and the solvated electron and hydroxyl radical for high LET ions.

RESULTS

It was found that the Geant4-DNA chemistry yields were generally in good agreement with experimental observations and other simulations. However, the Geant4-DNA yields for the hydroxyl radical and hydrogen peroxide at the end of the chemistry stage were found to be respectively considerably higher and lower than the experimentally observed yields. Increasing the LET of incident hadrons increased the yield of secondary species and decreased the yield of primary species. The effect of LET on the yield of the hydroxyl radical at 100 ns simulated with Geant4 was in good agreement with experimental measurements. Additionally, by the end of the simulation only 40% of dissociated water molecules had been recombined and the rate of recombination was slowing.

CONCLUSIONS

The yields simulated using Geant4 are within reasonable agreement with experimental observations. Higher LET radiation corresponds with increased yields of secondary species and decreased yields of primary species. These trends combined with the LET having similar effects on the 100 ns hydroxyl radical yield for Geant4 and experimental measurements indicate that Geant4 accurately models the effect of LET on radiolysis yields. The limited recombination within the modeled chemistry stage and the slowing rate of recombination at the end of the stage indicate potential long-range indirect biological damage.

Effects of irradiation conditions on the radiation sensitivity of microorganisms in the presence of OH-radical scavengers

PURPOSE

The purpose of the paper was to investigate the protective effect of some scavengers of OH radicals (hydroxyl radicals) on the radiation sensitivity of bacteria (in some cases also yeast) under normoxic (in air) or hypoxic (suboxic) conditions and to compare the obtained results with those published earlier for the yeast, all in a wide interval of irradiation conditions. Another aim was to investigate a possible impact of the reaction order of the reaction between the scavengers and the OH radicals on the protection of the cells.

MATERIALS AND METHODS

In order to study the protective effect of OH scavengers we used various concentrations of methanol and potassium formate (in some cases also ethanol) in isotonic salt solutions. These solutions containing living bacteria (Escherichia coli) or yeast (Saccharomyces cerevisiae) were irradiated with ⁶⁰Co radiation using various doses and dose rates. Irradiation was performed in air, in some cases under the hypoxic conditions. The number of surviving cells was determined prior to and after irradiation in suspension with and without scavengers. The surviving fractions after irradiation with and without scavenger were evaluated.

RESULTS

The surviving fraction of bacterial cells increases linearly with increasing concentration of both scavengers. The fraction of surviving cells does not increase with increasing concentration of the scavengers under suboxic conditions. The protective effect Ϭ increases linearly with increasing scavenging efficiency and this dependence is much sharper under normoxic conditions than under suboxic ones. The specific protection k is much higher for the methanol than for the potassium formate.

CONCLUSIONS

The basic characteristics of the impact of scavengers of OH radicals on radiation sensitivity of both bacteria and yeast are the same in a wide interval of doses and dose rates. The specific protection effect is much higher under the normoxic conditions. This protective effect is inversely proportional to the rate constant of the reaction between the scavenger and the OH radicals. It seems to be obvious that the presence of oxygen during irradiation is a necessary condition for the protective action of the scavengers which may be partially controlled by some transport processes and may be connected with the radiation sensitivity of the cells. On the other hand, the change of the reaction order of the reaction of the scavenger with the OH radicals has turned out to be unimportant.

Ultrafast Chemistry of Water Radical Cation, H₂O•+, in Aqueous Solutions

Oxidation reactions by radicals constitute a very important class of chemical reactions in solution. Radiation Chemistry methods allow producing, in a controlled way, very reactive oxidizing radicals, such as OH^•, CO₃^•–, NO₃^•, SO₄^•–, and N₃^•. Although the radical cation of water, H₂O^•+, with a very short lifetime (shorter than 1 ps) is the precursor of these radicals in aqueous solutions, its chemistry is usually known to be limited to the reaction of proton transfer by forming OH^• radical. Herein, we stress situations where H₂O^•+ undergoes electron transfer reaction in competition with proton transfer.

Genuine binding energy of the hydrated electron

The unknown influence of inelastic and elastic scattering of slow electrons in water has made it difficult to clarify the role of the solvated electron in radiation chemistry and biology. We combine accurate scattering simulations with experimental photoemission spectroscopy of the hydrated electron in a liquid water microjet, with the aim of resolving ambiguities regarding the influence of electron scattering on binding energy spectra, photoelectron angular distributions, and probing depths. The scattering parameters used in the simulations are retrieved from independent photoemission experiments of water droplets. For the ground-state hydrated electron, we report genuine values devoid of scattering contributions for the vertical binding energy and the anisotropy parameter of 3.7 ± 0.1 eV and 0.6 ± 0.2, respectively. Our probing depths suggest that even vacuum ultraviolet probing is not particularly surface-selective. Our work demonstrates the importance of quantitative scattering simulations for a detailed analysis of key properties of the hydrated electron.

OH cleavage from tyrosine: debunking a myth

During macromolecular X-ray crystallography experiments, protein crystals held at 100 K have been widely reported to exhibit reproducible bond scission events at doses on the order of several MGy. With the objective to mitigate the impact of radiation damage events on valid structure determination, it is essential to correctly understand the radiation chemistry mechanisms at play. OH-cleavage from tyrosine residues is regularly cited as amongst the most available damage pathways in protein crystals at 100 K, despite a lack of widespread reports of this phenomenon in protein crystal radiation damage studies. Furthermore, no clear mechanism for phenolic C-O bond cleavage in tyrosine has been reported, with the tyrosyl radical known to be relatively robust and long-lived in both aqueous solutions and the solid state. Here, the initial findings of Tyr -OH group damage in a myrosinase protein crystal have been reviewed. Consistent with that study, at increasing doses, clear electron density loss was detectable local to Tyr -OH groups. A systematic investigation performed on a range of protein crystal damage series deposited in the Protein Data Bank has established that Tyr -OH electron density loss is not generally a dominant damage pathway in protein crystals at 100 K. Full Tyr aromatic ring displacement is here proposed to account for instances of observable Tyr -OH electron density loss, with the original myrosinase data shown to be consistent with such a damage model. Systematic analysis of the effects of other environmental factors, including solvent accessibility and proximity to disulfide bonds or hydrogen bond interactions, is also presented. Residues in known active sites showed enhanced sensitivity to radiation-induced disordering, as has previously been reported.

Oxygen additions in serial femtosecond crystallographic protein structures

In principle, serial femtosecond crystallography (SFX) could yield data sets that are completely free of the effects caused by slow, radiation-induced chemical reactions, for example, oxygen additions, responsible for radiation damage. However, experimental evidence is presented here that SFX data sets obtained by techniques that expose different parts of the same specimen to single pulses of radiation do not have this property, even if the specimen in question is frozen. The diffraction image of each such crystal obtained with the first pulse of radiation is certain to represent the structure of a protein that has not been modified chemically, but all of the images obtained subsequently from the same crystal will represent structures that have been modified to a lesser or greater extent by oxygen additions because of the rapid diffusion of oxygenic free radicals through the specimen. The higher the level of oxygen additions a crystal suffers during data collection, the poorer the statistical quality of data set obtained from it will, and the higher the free R-factors of the resulting structural model.

X-ray radiation-induced addition of oxygen atoms to protein residues

The additions of oxygen and peroxide to residues that result when proteins are exposed to the free radicals produced using the Fenton reaction or X-rays have been studied for over a century. Nevertheless little is known about the impact these modifications have on protein crystal structures. Here evidence is presented that both kinds of modifications occur in protein crystals on a significant scale during the collection of X-ray diffraction data. For example, at least 538 of the 5,351 residues of protein molecules in the crystal used to obtain the structure for photosystem II described by the PDB accession number 3ARC became oxygenated during data collection.

The contribution of thermally labile sugar lesions to DNA double-strand break formation in cells grown in the presence of BrdU

PURPOSE

Radiosensitization by bromodeoxyuridine (BrdU) is commonly attributed to an increase in the yield of double-strand breaks (DSB) in the DNA and an associated decrease in the reparability of these lesions. Radiation chemistry provides a mechanism for the increased yield of DSB through the generation, after bromine loss, of a highly reactive uracilyl radical that attacks the sugar moiety of the nucleotide to produce a single-strand break (SSB). The effects underpinning DSB repair inhibition remain, in contrast, incompletely characterized. A possible source of reduced reparability is a change in the nature or complexity of the DSB in BrdU-substituted DNA. Recent studies show that DSB-complexity or DSB-nature may also be affected by the presence within the cluster of thermally labile sugar lesions (TLSL) that break the DNA backbone only if they chemically evolve to SSB, a process thought to occur within the first hour post-irradiation. Since BrdU radiosensitization might be associated with increased yields and reduced reparability of DSB, we investigated whether BrdU underpins these effects by shifting the balance in the generation of TLSL.

METHODS AND MATERIALS

We employed asymmetric-field-inversion gel electrophoresis (AFIGE), a pulsed-field gel electrophoresis (PFGE) method to quantitate DSB in a battery of five cells lines grown in the presence of different concentrations of BrdU. We measured specifically the yields of promptly forming DSB (prDSB) using low temperature lysis protocols, and the yields of total DSB (tDSB = prDSB + tlDSB; tlDSB form after evolution to SSB of TLSL) using high temperature lysis protocols.

RESULTS

We report that incorporation of BrdU generates similar increases in the formation of tlDSB and prDSB, but variations are noted among the different cell lines tested.

CONCLUSIONS

The similar increase in the yields of tlDSB and prDSB in BrdU substituted DNA showed that shifts in the yields of these forms of lesions could not be invoked to explain BrdU radiosensitization.

Quantitative study of contrast enhancement in soft X-ray micrographs of insect eyes by tissue selective mass loss

Quantitative studies of soft X-ray induced radiation damage in zone-plate-based X-ray microspectroscopy have so far concentrated on investigations of homogeneous specimens. However, more complex materials can show unexpected radiation-induced behaviour. Here a quantitative radiochemical analysis of biological tissue from Xantophan morganii praedicta eyes is presented. Contrast enhancement due to tissue selective mass loss leading to a significant improvement of imaging quality is reported. Since conventional quantitative analysis of the absorbed dose cannot conclusively explain the experimental observations on photon-energy-dependent radiation damage, a significant contribution of photo- and secondary electrons to soft matter damage for photon energies above the investigated absorption edge is proposed.

Radical Ions of Cycloparaphenylenes: Size Dependence Contrary to the Neutral Molecules

Cycloparaphenylenes (CPPs) have attracted wide attention because of their interesting properties owing to distorted and strained aromatic systems and radially oriented p orbitals. For application of CPPs, information on their charged states (radical cation and radical anion) is essential. Here, we measured absorption spectra of the radical cations and the radical anions of CPPs with various ring sizes over a wide spectral region by means of radiation chemical methods. The peak position of the near-IR bands for both the radical cation and the radical anion shifted to lower energies with an increase in the ring size. This trend is contrary to what is observed for transitions between the HOMO and LUMO of the neutral CPP. The observed spectra of the CPP radical ions were reasonably assigned based on time-dependent density functional theory. These results indicate that the next HOMO and the next LUMO levels are important in the electronic transitions of radical ions.

Water Calorimetry: A Correction to the Heat Defect Calculations

In a recent publication, we used a reaction model (model III) to calculate the heat defect for the irradiation of aqueous solutions with ionizing radiation at 21 °C. Subsequent work has revealed that the literature value used for one of the rate constants in the model was incorrect. A revised model (model IIIR) incorporates the correct rate constant for 21 °C. Versions of models III and IIIR were created for irradiations at 4 °C. For our current water calorimetry protocol, the values of the heat defect for H2/O2-water (water saturated with a flow of 43 % H2 and 57 % O2, by volume) at 21 °C predicted by model III and model IIIR are similar but the value for 4 °C predicted by III is 30 % smaller than the value predicted by IIIR. Model IIIR predicts that the values of the heat defect at 21 °C and 4 °C lie within the range -0.023±0.002, in agreement with the values obtained from our water calorimetry measurements done using pure water and H2-saturated water at 21 °C and 4 °C. The yields of hydrogen peroxide in H2/O2-water at 21 °C and 4 °C were measured and agree with the predictions of model IIIR. Our water calorimetry measurements made with pure water and H2-saturated water are now of sufficient quality that they can be used to determine the heat defect for H2/O2-water better than can be done by simulations. However, consistency between the three systems continues to be an excellent check on water purity which is crucial, especially for the pure water system.

An Absorbed Dose Water Calorimeter: Theory, Design, and Performance

Two calibrated thermistors sandwiched between two insulative polyethylene films were immersed in a 30 cm cube of water having a low thermal diffusivity. The product of the specific heat of water and temperature rise gave the combined effect of the local absorbed dose and any heat defect at a position along a temperature profile produced by cobalt-60 irradiation. The dose rate was near 18 mGy/s and exposure times were 3 min. The standard deviation for a daily set of measurements was about 0.6 percent. Calculations showed that conductive heat transfer produced a negligible effect at the position of measurement along the beam axis. Tests showed the absence of convection. Temperature drifts before irradiation were quickly controlled by changing the power dissipated in the water between two immersed electrodes. Reproducible measurements were obtained in distilled water supplies that had a wide range of impurities. Measurements, after saturating the water with nitrogen or oxygen, showed no difference. A difference of 0.6 percent would have been easily detectable. Tests with several chemicals added to water showed some unexpected results and changes in the measured absorbed dose rate versus accumulated dose. The measured absorbed dose rate in distilled water under the conditions described was 3.5 percent higher than that determined from measurements with a graphite calorimeter.