Comment on "Proton Transfer of Guanine Radical Cations Studied by Time-Resolved Resonance Raman Spectroscopy Combined with Pulse Radiolysis".
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ABSTRACT:
SUBMITTER: Sevilla MD
PROVIDER: S-EPMC4866492 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:The mechanistic aspects of hydration of guanine radical cations, G(•+) in double- and single-stranded oligonucleotides were investigated by direct time-resolved spectroscopic monitoring methods. The G(•+) radical one-electron oxidation products were generated by SO4(•-) radical anions derived from the photolysis of S2O8(2-) anions by 308 nm laser pulses. In neutral aqueous solutions (pH 7.0), after the complete decay of SO4(•-) radicals (?5 ?s after the actinic laser flash) the transient absorbance of neutral guanine radicals, G(-H)(•) with maximum at 312 nm, is dominant. The kinetics of decay of G(-H)(•) radicals depend strongly on the DNA secondary structure. In double-stranded DNA, the G(-H)(•) decay is biphasic with one component decaying with a lifetime of ?2.2 ms and the other with a lifetime of ?0.18 s. By contrast, in single-stranded DNA the G(-H)(•) radicals decay monophasically with a ? 0.28 s lifetime. The ms decay component in double-stranded DNA is correlated with the enhancement of 8-oxo-7,8-dihydroguanine (8-oxoG) yields which are ?7 greater than in single-stranded DNA. In double-stranded DNA, it is proposed that the G(-H)(•) radicals retain radical cation character by sharing the N1-proton with the N3-site of C in the [G(•+):C] base pair. This [G(-H)(•):H(+)C ? G(•+):C] equilibrium allows for the hydration of G(•+) followed by formation of 8-oxoG. By contrast, in single-stranded DNA, deprotonation of G(•+) and the irreversible escape of the proton into the aqueous phase competes more effectively with the hydration mechanism, thus diminishing the yield of 8-oxoG, as observed experimentally.
| S-EPMC4004273 | biostudies-literature
Project description:The exposure of guanine in the oligonucleotide 5'-d(TCGCT) to one-electron oxidants leads initially to the formation of the guanine radical cation G(•+), its deptotonation product G(-H)(•), and, ultimately, various two- and four-electron oxidation products via pathways that depend on the oxidants and reaction conditions. We utilized single or successive multiple laser pulses (308 nm, 1 Hz rate) to generate the oxidants CO(3)(•-) and SO(4)(•-) (via the photolysis of S(2)O(8)(2-) in aqueous solutions in the presence and absence of bicarbonate, respectively) at concentrations/pulse that were ?20-fold lower than the concentration of 5'-d(TCGCT). Time-resolved absorption spectroscopy measurements following single-pulse excitation show that the G(•+) radical (pK(a) = 3.9) can be observed only at low pH and is hydrated within 3 ms at pH 2.5, thus forming the two-electron oxidation product 8-oxo-7,8-dihydroguanosine (8-oxoG). At neutral pH, and single pulse excitation, the principal reactive intermediate is G(-H)(•), which, at best, reacts only slowly with H(2)O and lives for ?70 ms in the absence of oxidants/other radicals to form base sequence-dependent intrastrand cross-links via the nucleophilic addition of N3-thymidine to C8-guanine (5'-G*CT* and 5'-T*CG*). Alternatively, G(-H)(•) can be oxidized further by reaction with CO(3)(•-), generating the two-electron oxidation products 8-oxoG (C8 addition) and 5-carboxamido-5-formamido-2-iminohydantoin (2Ih, by C5 addition). The four-electron oxidation products, guanidinohydantoin (Gh) and spiroiminodihydantoin (Sp), appear only after a second (or more) laser pulse. The levels of all products, except 8-oxoG, which remains at a low constant value, increase with the number of laser pulses.
| S-EPMC3303975 | biostudies-literature
Project description:Organic phosphates and phosphonates are present in a number of cellular components that can be damaged by exposure to ionizing radiation. This work reports femtosecond time-resolved mass spectrometry (FTRMS) studies of three organic phosphonate radical cations that model the DNA sugar-phosphate backbone: dimethyl methylphosphonate (DMMP), diethyl methylphosphonate (DEMP), and diisopropyl methylphosphonate (DIMP). Upon ionization, each molecular radical cation exhibits unique oscillatory dynamics in its ion yields resulting from coherent vibrational excitation. DMMP has particularly well-resolved 45 fs ( 732 ± 28 cm - 1 ) oscillations with a weak feature at 610⁻650 cm - 1 , while DIMP exhibits bimodal oscillations with a period of ∼55 fs and two frequency features at 554 ± 28 and 670⁻720 cm - 1 . In contrast, the oscillations in DEMP decay too rapidly for effective resolution. The low- and high-frequency oscillations in DMMP and DIMP are assigned to coherent excitation of the symmetric O⁻P⁻O bend and P⁻C stretch, respectively. The observation of the same ionization-induced coherently excited vibrations in related molecules suggests a possible common excitation pathway in ionized organophosphorus compounds of biological relevance, while the distinct oscillatory dynamics in each molecule points to the potential use of FTRMS to distinguish among fragment ions produced by related molecules.
| S-EPMC6384684 | biostudies-literature
Project description:This work presents evidence that photo-excitation of guanine radical cations results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. In dsDNA at low temperatures, formation of C1'* is observed from photo-excitation of G*+ in the 310-480 nm range with no C1'* formation observed > or =520 nm. Illumination of guanine radical cations in 2'dG, 3'-dGMP and 5'-dGMP in aqueous LiCl glasses at 143 K is found to result in remarkably high yields (approximately 85-95%) of sugar radicals, namely C1'*, C3'* and C5'*. The amount of each of the sugar radicals formed varies dramatically with compound structure and temperature of illumination. Radical assignments were confirmed using selective deuteration at C5' or C3' in 2'-dG and at C8 in all the guanine nucleosides/tides. Studies of the effect of temperature, pH, and wavelength of excitation provide important information about the mechanism of formation of these sugar radicals. Time-dependent density functional theory calculations verify that specific excited states in G*+ show considerable hole delocalization into the sugar structure, in accord with our proposed mechanism of action, namely deprotonation from the sugar moiety of the excited molecular radical cation.
| S-EPMC1243799 | biostudies-literature
Project description:The solvation of ions changes the physical, chemical and thermodynamic properties of water, and the microscopic origin of this behaviour is believed to be ion-induced perturbation of water's hydrogen-bonding network. Here we provide microscopic insights into this process by monitoring the dissipation of energy in salt solutions using time-resolved terahertz-Raman spectroscopy. We resonantly drive the low-frequency rotational dynamics of water molecules using intense terahertz pulses and probe the Raman response of their intermolecular translational motions. We find that the intermolecular rotational-to-translational energy transfer is enhanced by highly charged cations and is drastically reduced by highly charged anions, scaling with the ion surface charge density and ion concentration. Our molecular dynamics simulations reveal that the water-water hydrogen-bond strength between the first and second solvation shells of cations increases, while it decreases around anions. The opposite effects of cations and anions on the intermolecular interactions of water resemble the effects of ions on the stabilization and denaturation of proteins.
| S-EPMC9417992 | biostudies-literature
Project description:One-electron oxidation of two series of diaryldichalcogenides (C6F5E)2 (13a-c) and (2,6-Mes2C6H3E)2 (16a-c) was studied (E = S, Se, Te). The reaction of 13a and 13b with AsF5 and SbF5 gave rise to the formation of thermally unstable radical cations [(C6F5S)2]˙+ (14a) and [(C6F5Se)2]˙+ (14b) that were isolated as [Sb2F11]- and [As2F11]- salts, respectively. The reaction of 13c with AsF5 afforded only the product of a Te-C bond cleavage, namely the previously known dication [Te4]2+ that was isolated as [AsF6]- salt. The reaction of (2,6-Mes2C6H3E)2 (16a-c) with [NO][SbF6] provided the corresponding radical cations [(2,6-Mes2C6H3E)2]˙+ (17a-c; E = S, Se, Te) in the form of thermally stable [SbF6]- salts in nearly quantitative yields. The electronic and structural properties of these radical cations were probed by X-ray diffraction analysis, EPR spectroscopy, and density functional theory calculations and other methods.
| S-EPMC5588450 | biostudies-literature
Project description:Hydroxyl radical footprinting is a valuable technique for studying protein structure, but care must be taken to ensure that the protein does not unfold during the labeling process due to oxidative damage. Footprinting methods based on submicrosecond laser photolysis of peroxide that complete the labeling process faster than the protein can unfold have been recently described; however, the mere presence of large amounts of hydrogen peroxide can also cause uncontrolled oxidation and minor conformational changes. We have developed a novel method for submicrosecond hydroxyl radical protein footprinting using a pulsed electron beam from a 2 MeV Van de Graaff electron accelerator to generate a high concentration of hydroxyl radicals by radiolysis of water. The amount of oxidation can be controlled by buffer composition, pulsewidth, dose, and dissolved nitrous oxide gas in the sample. Our results with ubiquitin and beta-lactoglobulin A demonstrate that one submicrosecond electron beam pulse produces extensive protein surface modifications. Highly reactive residues that are buried within the protein structure are not oxidized, indicating that the protein retains its folded structure during the labeling process. Time-resolved spectroscopy indicates that the major part of protein oxidation is complete in a time scale shorter than that of large scale protein motions.
| S-EPMC2733211 | biostudies-literature
Project description:Single-electron oxidation of neutral boryl-linked tetraaminoethylene derivatives 4 led to the formation of radical cations 4?+ , which have been isolated and fully characterized. X-ray diffraction analysis, EPR spectroscopy, and computational studies revealed that the unpaired electron is delocalized over the B2N4C2 skeleton and the spin density mainly resides on the carbon and boron atoms.
| S-EPMC5674142 | biostudies-literature
Project description:The divinyldiarsene radical cations [{(NHC)C(Ph)}As]2 (GaCl4 ) (NHC=IPr: C{(NDipp)CH}2 3; SIPr: C{(NDipp)CH2 }2 4; Dipp=2,6-iPr2 C6 H3 ) and dications [{(NHC)C(Ph)}As]2 (GaCl4 )2 (NHC=IPr 5; SIPr 6) are readily accessible as crystalline solids on sequential one-electron oxidation of the corresponding divinyldiarsenes [{(NHC)C(Ph)}As]2 (NHC=IPr 1; SIPr 2) with GaCl3 . Compounds 3-6 have been characterized by X-ray diffraction, cyclic voltammetry, EPR/NMR spectroscopy, and UV/vis absorption spectroscopy as well as DFT calculations. The sequential removal of one electron from the HOMO, that is mainly the As-As ?-bond, of 1 and 2 leads to successive elongation of the As=As bond and contraction of the C-As bonds from 1/2?3/4?5/6. The UV/vis spectrum of 3 and 4 each exhibits a strong absorption in the visible region associated with SOMO-related transitions. The EPR spectrum of 3 and 4 each shows a broadened septet owing to coupling of the unpaired electron with two 75 As (I=3/2) nuclei.
| S-EPMC6899687 | biostudies-literature
Project description:Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotides with noncontiguous guanines G and grouped as contiguous GG and GGG sequences were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd:YAG laser pulses, the DNA-bound BPT molecules were photoionized to BPT*+ radicals by a consecutive two-photon ionization mechanism. The BPT*+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron-transfer reactions, and the rate constants of these reactions follow the trend 5'-..GGG.. > 5'-..GG.. > 5'-..G... In the case of CO3*- radicals, the oxidation of guanine occurs by intermolecular collision pathways, and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO3*- radicals, as well as by BPT*+, are base sequence context-dependent and are greater than those in isolated guanines at the 5'-G in 5'-...GG... sequences, and the first two 5'- guanines in the 5'-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkali-labile guanine products. In the case of the intermolecular one-electron oxidant CO3*-, the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA-bound oxidant BPT*+, the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.
| S-EPMC3713794 | biostudies-literature