Tag Archives: DNA damage

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

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by Renata Kaczmarek, Samuel Ward, Dipra Debnath,Taisiya Jacobs, Alexander D. Stark, Dariusz Korczyński, Anil Kumar, Michael D. Sevilla, Sergey A. Denisov, Viacheslav Shcherbakov, Pascal Pernot, Mehran Mostafavi, Roman Dembinski, Amitava Adhikary

Chem. Eur. J. 2020, 26, 9495-9505; https://doi.org/10.1002/chem.202000247

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.

Ultrafast Processes Occurring in Radiolysis of Highly Concentrated Solutions of Nucleosides/Tides

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by Jun Ma, Sergey A. Denisov, Amitava Adhikary  and Mehran Mostafavi 

Int. J. Mol. Sci. 2019, 20, 4963; https://doi.org/10.3390/ijms20194963

Among the radicals (hydroxyl radical (•OH), hydrogen atom (H•), and solvated electron (esol−)) that are generated via water radiolysis, •OH has been shown to be the main transient species responsible for radiation damage to DNA via the indirect effect. Reactions of these radicals with DNA-model systems (bases, nucleosides, nucleotides, polynucleotides of defined sequences, single stranded (ss) and double stranded (ds) highly polymeric DNA, nucleohistones) were extensively investigated. The timescale of the reactions of these radicals with DNA-models range from nanoseconds (ns) to microseconds (µs) at ambient temperature and are controlled by diffusion or activation. However, those studies carried out in dilute solutions that model radiation damage to DNA via indirect action do not turn out to be valid in dense biological medium, where solute and water molecules are in close contact (e.g., in cellular environment). In that case, the initial species formed from water radiolysis are two radicals that are ultrashort-lived and charged: the water cation radical (H2O•+) and prethermalized electron. These species are captured by target biomolecules (e.g., DNA, proteins, etc.) in competition with their inherent pathways of proton transfer and relaxation occurring in less than 1 picosecond. In addition, the direct-type effects of radiation, i.e., ionization of macromolecule plus excitations proximate to ionizations, become important. The holes (i.e., unpaired spin or cation radical sites) created by ionization undergo fast spin transfer across DNA subunits. The exploration of the above-mentioned ultrafast processes is crucial to elucidate our understanding of the mechanisms that are involved in causing DNA damage via direct-type effects of radiation. Only recently, investigations of these ultrafast processes have been attempted by studying concentrated solutions of nucleosides/tides under ambient conditions. Recent advancements of laser-driven picosecond electron accelerators have provided an opportunity to address some long-term puzzling questions in the context of direct-type and indirect effects of DNA damage. In this review, we have presented key findings that are important to elucidate mechanisms of complex processes including excess electron-mediated bond breakage and hole transfer, occurring at the single nucleoside/tide level

Observation of dissociative quasi-free electron attachment to nucleoside via excited anion radical in solution

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by Jun Ma, Anil Kumar, Yusa Muroya, Shinichi Yamashita, Tsuneaki Sakurai, Sergey A. Denisov, Michael D. Sevilla, Amitava Adhikary, Shu Seki and Mehran Mostafavi 

Nature Communications 2019, 10; https://doi.org/10.1038/s41467-018-08005-z

Damage to DNA via dissociative electron attachment has been well-studied in both the gas and condensed phases; however, understanding this process in bulk solution at a fundamental level is still a challenge. Here, we use a picosecond pulse of a high energy electron beam to generate electrons in liquid diethylene glycol and observe the electron attachment dynamics to ribothymidine at different stages of electron relaxation. Our transient spectroscopic results reveal that the quasi-free electron with energy near the conduction band effectively attaches to ribothymidine leading to a new absorbing species that is characterized in the UV-visible region. This species exhibits a nearly concentration-independent decay with a time constant of ~350 ps. From time-resolved studies under different conditions, combined with data analysis and theoretical calculations, we assign this intermediate to an excited anion radical that undergoes N1-C1′ glycosidic bond dissociation rather than relaxation to its ground state.

Ultrafast Electron Attachment and Hole Transfer Following Ionizing Radiation of Aqueous Uridine Monophosphate

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by Jun Ma, Sergey A. Denisov, Jean-Louis Marignier, Pascal Pernot, Amitava Adhikary, Shu Seki and Mehran Mostafavi

J. Phys. Chem. Lett. 2018, 9, 5105–5109; https://doi.org/10.1021/acs.jpclett.8b02170

The primary localization process of radiation-induced charges (holes (cation radical sites) and excess electrons) remains poorly understood, even at the level of monomeric DNA/RNA models, in particular, in an aqueous environment. We report the first spectroscopic study of charge transfer occurring in radiolysis of aqueous uridine 5′-monophosphate (UMP) solutions and its components: uridine, uracil, ribose, and phosphate. Our results show that prehydrated electrons effectively attach to the base site of UMP; the holes in UMP formed by either direct ionization or reaction of UMP with the radiation-mediated water cation radical (H2O•+) facilely localize on the ribose site, despite the fact that a part of them were initially created on either the phosphate or uracil. The nature of phosphate-to-sugar hole transfer is characterized as a barrierless intramolecular electron transfer with a time constant of 2.5 ns, while the base-to-sugar hole transfer occurs much faster, within a 5 ps electron pulse.