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1. Comment un électron induit un dommage oxydatif dans l’ADN

   Ma, Jun; Denisov, Sergey; Adhikary, Amitava A; Mostafavi, Mehran (January 2020, Les Actualités chimiques)

   null (Ed.)

   How can an electron induce oxidative damage in DNA DNA damage caused by the dissociative electron attachment (DEA) has been well-studied in the gas and solid phases. However, understanding of this process at the fundamental level in solution is still a challenge. The electrons, after losing their kinetic energy via ionization and excitation events, are thermalized and undergo a multistep hydration process with a time constant of ca. ≤ 1 ps, to becoming fully trapped as a hydrated or solvated electron (esol- or eaq-). Prior to the formation of esol-, the electron exists in its presolvated (or prehydrated) state (epre-) with no kinetic energy. We used picosecond pulse radiolysis to generate electrons in water or in liquid diethylene glycol (DEG) to observe the dynamics of capture of these electrons by DNA/RNA bases, nucleosides, and nucleotides. In diethylene glycol, we demonstrate that unlike esol- and epre-, eqf- effectively attaches itself to the RNA-nucleoside, ribothymidine, forming the excited state of the anion that undergoes the N1-C1 ́ glycosidic bond dissociation. Thanks to DEA, this process induced in fact by eqf- leads to an oxidation of the parent molecule similar to the hydroxyl radical (•OH), leading to the same glycosidic bond (N1-C1 ́) cleavage. 

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2. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules

   https://doi.org/10.1039/d1cp03884b  

   Zhou, Wenjing; Liu, Jianbo (November 2021, Physical Chemistry Chemical Physics)

   In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al. , Phys. Chem. Chem. Phys. , 2018, 20 , 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands ( i.e. , 9MG˙ + ·(H 2 O) 1–2 ) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙ + and are referred to as HA O6 and HA N7 , respectively. The primary products of HA O6 and HA N7 reactions, including [9MG + H O6 ] + /[9MG + H N7 ] + and ˙OH, react further to either form [8OH-9MG + H O6 ]˙ + and [8OH-9MG + H N7 ]˙ + via C8-hydroxylation or form radical cations of 6- enol -guanine (6- enol -G˙ + ) and 7H-guanine (7HG˙ + ) via S N 2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG + by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + H N7 ]˙ + has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy. 

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3. One-electron oxidation of ds(5′-GGG-3′) and ds(5′-G(8OG)G-3′) and the nature of hole distribution: a density functional theory (DFT) study

   https://doi.org/10.1039/c9cp06244k  

   Kumar, Anil; Adhikary, Amitava; Sevilla, Michael D.; Close, David M. (March 2020, Physical Chemistry Chemical Physics)

   null (Ed.)

   Of particular interest in radiation-induced charge transfer processes in DNA is the extent of hole localization immediately after ionization and subsequent relaxation. To address this, we considered double stranded oligomers containing guanine (G) and 8-oxoguanine (8OG), i.e. , ds(5′-GGG-3′) and ds(5′-G8OGG-3′) in B-DNA conformation. Using DFT, we calculated a variety of properties, viz. , vertical and adiabatic ionization potentials, spin density distributions in oxidized stacks, solvent and solute reorganization energies and one-electron oxidation potential ( E 0 ) in the aqueous phase. Calculations for the vertical state of the -GGG- cation radical showed that the spin was found mainly (67%) on the middle G. However, upon relaxation to the adiabatic -GGG- cation radical, the spin localized (96%) on the 5′-G, as observed in experiments. Hole localizations on the middle G and 3′-G were higher in energy by 0.5 kcal mol −1 and 0.4 kcal mol −1 , respectively, than that of 5′-G. In the -G8OGG- cation radical, the spin localized only on the 8OG in both vertical and adiabatic states. The calculated vertical ionization potentials of -GGG- and -G8OGG- stacks were found to be lower than that of the vertical ionization potential of a single G in DNA. The calculated E 0 values of -GGG- and -G8OGG- stacks are 1.15 and 0.90 V, respectively, which owing to stacking effects are substantially lower than the corresponding experimental E 0 values of their monomers (1.49 and 1.18 V, respectively). SOMO to HOMO level switching is observed in these oxidized stacks. Consequently, our calculations predict that local double oxidations in DNA will form triplet diradical states, which are especially significant for high LET radiations. 

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4. UV-Vis Photodissociation Action Spectroscopy Reveals Cytosine-Guanine Hydrogen Transfer in DNA Tetranucleotide Cation Radicals upon One-Electron Transfer

   https://doi.org/10.1021/acd.jpcb.0c01693  

   Huang, Shu R.; Liu, Y.; Turecek, Frantisek (April 2020, The journal of physical chemistry)

   ABSTRACT: We report the generation and spectroscopic study of hydrogen-rich DNA tetranucleotide cation radicals (GATC+2H)+• and (AGTC+2H)+•. The radicals were generated in the gas phase by one-electron reduction of the respective dications (GATC +2H)2+ and (AGTC+2H)2+ and characterized by collision-induced dissociation and photodissociation tandem mass spectrometry and UV−vis photodissociation action spectroscopy. Among several absorption bands observed for (GATC+2H)+•, the bands at 340 and 450 nm were assigned to radical chromophores. Timedependent density functional theory calculations including vibronic transitions in the visible region of the spectrum were used to provide theoretical absorption spectra of several low-energy tetranucleotide tautomers having cytosine-, adenine-, and thymine- based radical chromophores that did not match the experimental spectrum. Instead, the calculations indicated the formation of a new isomer with the 7,8-H-dihydroguanine cation radical moiety. The isomerization involved hydrogen migration from the cytosine N-3−H radical to the C-8 position in N-7-protonated guanine that was calculated to be 87 kJ mol−1 exothermic and had a low-energy transition state. Although the hydrogen migration was facilitated by the spatial proximity of the guanine and cytosine bases in the low-energy (GATC+2H)+• intermediate formed by electron transfer, the reaction was calculated to have a large negative activation entropy. Rice−Ramsperger−Kassel−Marcus (RRKM) and transition state theory kinetic analysis indicated that the isomerization occurred rapidly in hot cation radicals produced by electron transfer with the population-weighed rate constant of k = 8.9 × 103 s−1. The isomerization was calculated to be too slow to proceed on the experimental time scale in thermal cation radicals at 310 K. 

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5. Identification of the vibrational marker of tyrosine cation radical using ultrafast transient infrared spectroscopy of flavoprotein systems

   https://doi.org/10.1007/s43630-021-00024-y  

   Pirisi, Katalin; Nag, Lipsa; Fekete, Zsuzsanna; Iuliano, James N.; Tolentino Collado, Jinnette; Clark, Ian P.; Pécsi, Ildikó; Sournia, Pierre; Liebl, Ursula; Greetham, Gregory M.; et al (March 2021, Photochemical & Photobiological Sciences)

   null (Ed.)

   Abstract Tryptophan and tyrosine radical intermediates play crucial roles in many biological charge transfer processes. Particularly in flavoprotein photochemistry, short-lived reaction intermediates can be studied by the complementary techniques of ultrafast visible and infrared spectroscopy. The spectral properties of tryptophan radical are well established, and the formation of neutral tyrosine radicals has been observed in many biological processes. However, only recently, the formation of a cation tyrosine radical was observed by transient visible spectroscopy in a few systems. Here, we assigned the infrared vibrational markers of the cationic and neutral tyrosine radical at 1483 and 1502 cm −1 (in deuterated buffer), respectively, in a variant of the bacterial methyl transferase TrmFO, and in the native glucose oxidase. In addition, we studied a mutant of AppABLUF blue-light sensor domain from Rhodobacter sphaeroides in which only a direct formation of the neutral radical was observed. Our studies highlight the exquisite sensitivity of transient infrared spectroscopy to low concentrations of specific radicals. 

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