An ESR and DFT study of hydration of the 2'-deoxyuridine-5-yl radical: a possible hydroxyl radical intermediate.
Ontology highlight
ABSTRACT:
SUBMITTER: Chomicz L
PROVIDER: S-EPMC4213299 | biostudies-literature | 2014 Dec
REPOSITORIES: biostudies-literature
Publications
An ESR and DFT study of hydration of the 2'-deoxyuridine-5-yl radical: a possible hydroxyl radical intermediate.
Chomicz Lidia L Petrovici Alex A Archbold Ian I Adhikary Amitava A Kumar Anil A Sevilla Michael D MD Rak Janusz J
Chemical communications (Cambridge, England) 20141201 93
The mechanism of radiation-induced frank strand break formation in irradiated 5-bromo-2'-deoxyuridine (BrdU)-labelled DNA is still unclear despite the proven radiosensitizing properties of BrdU. Combination of ESR spectroscopy and quantum chemical modelling points to a simple reaction between the uridine-5-yl radical and water molecules that produces the genotoxic hydroxyl radical. ...[more]
Similar Datasets
Project description:The reaction of hydroxyl radical (OH(•)) with DNA accounts for about half of radiation-induced DNA damage in living systems. Previous literature reports point out that the reaction of OH(•) with DNA proceeds mainly through the addition of OH(•) to the C═C bonds of the DNA bases. However, recently it has been reported that the principal reaction of OH(•) with dGuo (deoxyguanosine) is the direct hydrogen atom abstraction from its exocyclic amine group rather than addition of OH(•) to the C═C bonds. In the present work, these two reaction pathways of OH(•) attack on guanine (G) in the presence of water molecules (aqueous environment) are investigated using the density functional theory (DFT) B3LYP method with 6-31G* and 6-31++G** basis sets. The calculations show that the initial addition of the OH(•) at C(4)═C(5) double bond of guanine is barrier free and the adduct radical (G-OH(•)) has only a small activation barrier of ca. 1-6 kcal/mol leading to the formation of a metastable ion-pair intermediate (G(•+)---OH(-)). The formation of ion-pair is a result of the highly oxidizing nature of the OH(•) in aqueous media. The resulting ion-pair (G(•+)---OH(-)) deprotonates to form H(2)O and neutral G radicals favoring G(N(1)-H)(•) with an activation barrier of ca. 5 kcal/mol. The overall process from the G(C(4))-OH(•) (adduct) to G(N(1)-H)(•) and water is found to be exothermic in nature by more than 13 kcal/mol. (G-OH(•)), (G(•+)---OH(-)), and G(N(1)-H)(•) were further characterized by the CAM-B3LYP calculations of their UV-vis spectra and good agreement between theory and experiment is achieved. Our calculations for the direct hydrogen abstraction pathway from N(1) and N(2) sites of guanine by the OH(•) show that this is also a competitive route to produce G(N(2)-H)(•), G(N(1)-H)(•) and H(2)O.
| S-EPMC3240735 | biostudies-literature
Project description:This work reports ESR studies that identify the favored site of deprotonation of the guanine cation radical (G*+) in an aqueous medium at 77 K. Using ESR and UV-visible spectroscopy, one-electron oxidized guanine is investigated in frozen aqueous D2O solutions of 2'-deoxyguanosine (dGuo) at low temperatures at various pHs at which the guanine cation radical, G*+ (pH 3-5), singly deprotonated species, G(-H)* (pH 7-9), and doubly deprotonated species, G(-2H)*- (pH > 11), are found. C-8-deuteration of dGuo to give 8-D-dGuo removes the major proton hyperfine coupling at C-8. This isolates the anisotropic nitrogen couplings for each of the three species and aids our analyses. These anisotropic nitrogen couplings were assigned to specific nitrogen sites by use of 15N-substituted derivatives at N1, N2, and N3 atoms in dGuo. Both ESR and UV-visible spectra are reported for each of the species: G*+, G(-H)*, and G(-2H)*-. The experimental anisotropic ESR hyperfine couplings are compared to those obtained from DFT calculations for the various tautomers of G(-H)*. Using the B3LYP/6-31G(d) method, the geometries and energies of G*+ and its singly deprotonated state in its two tautomeric forms, G(N1-H)* and G(N2-H)*, were investigated. In a nonhydrated state, G(N2-H)* is found to be more stable than G(N1-H)*, but on hydration with seven water molecules G(N1-H)* is found to be more stable than G(N2-H)*. The theoretically calculated hyperfine coupling constants (HFCCs) of G*+, G(N1-H)*, and G(-2H)*- match the experimentally observed HFCCs best on hydration with seven or more waters. For G(-2H)*-, the hyperfine coupling constant (HFCC) at the exocyclic nitrogen atom (N2) is especially sensitive to the number of hydrating water molecules; good agreement with experiment is not obtained until nine or 10 waters of hydration are included.
| S-EPMC2526163 | biostudies-literature
Project description:In the antioxidant activity of quercetin (Q), stabilization of the energy in the quercetin radical (Q•) by delocalization of the unpaired electron (UE) in Q• is pivotal. The aim of this study is to further examine the delocalization of the UE in Q•, and to elucidate the importance of the functional groups of Q for the stabilization of the UE by combining experimentally obtained spin resonance spectroscopy (ESR) measurements with theoretical density functional theory (DFT) calculations. The ESR spectrum and DFT calculation of Q• and structurally related radicals both suggest that the UE of Q• is mostly delocalized in the B ring and partly on the AC ring. The negatively charged oxygen groups in the B ring (3' and 4') of Q• have an electron-donating effect that attract and stabilize the UE in the B ring. Radicals structurally related to Q• indicate that the negatively charged oxygen at 4' has more of an effect on concentrating the UE in ring B than the negatively charged oxygen at 3'. The DFT calculation showed that an OH group at the 3-position of the AC ring is essential for concentrating the radical on the C2-C3 double bond. All these effects help to explain how the high energy of the UE is captured and a stable Q• is generated, which is pivotal in the antioxidant activity of Q.
| S-EPMC7139295 | biostudies-literature
Project description:Cyclic voltammetry is a widely used and powerful tool for sensitively and selectively measuring hydrogen peroxide (H2O2). Herein, voltammetry was combined with electron paramagnetic resonance spectroscopy to identify and define the role of an oxygen-centered radical liberated during the oxidation of H2O2. The spin-trap reagents, 5,5-dimethyl-1-pyrroline N-oxide (DMPO) and 2-ethoxycarbonyl-2-methyl-3,4-dihydro-2H-pyrrole-1-oxide (EMPO), were employed. Spectra exhibit distinct hyperfine patterns that clearly identify the DMPO(•)-OH and EMPO(•)-OH adducts. Multiple linear regression analysis of voltammograms demonstrated that the hydroxyl radical is a principal contributor to the voltammetry of H2O2, as signal is attenuated when this species is trapped. These data incorporate a missing, fundamental element to our knowledge of the mechanisms that underlie H2O2 electrochemistry.
| S-EPMC6527099 | biostudies-literature
Project description:Non-reactive, comparative (2 × 1.2 ?s) molecular dynamics simulations were carried out to characterize the interactions between glutathione (GSH, host molecule) and hydroxyl radical (OH(•), guest molecule). From this analysis, two distinct steps were identified in the recognition process of hydroxyl radical by glutathione: catching and steering, based on the interactions between the host-guest molecules. Over 78% of all interactions are related to the catching mechanism via complex formation between anionic carboxyl groups and the OH radical, hence both terminal residues of GSH serve as recognition sites. The glycine residue has an additional role in the recognition of OH radical, namely the steering. The flexibility of the Gly residue enables the formation of further interactions of other parts of glutathione (e.g. thiol, ?- and ?-carbons) with the lone electron pair of the hydroxyl radical. Moreover, quantum chemical calculations were carried out on selected GSH/OH(•) complexes and on appropriate GSH conformers to describe the energy profile of the recognition process. The relative enthalpy and the free energy changes of the radical recognition of the strongest complexes varied from -42.4 to -27.8 kJ/mol and from -21.3 to 9.8 kJ/mol, respectively. These complexes, containing two or more intermolecular interactions, would be the starting configurations for the hydrogen atom migration to quench the hydroxyl radical via different reaction channels.
| S-EPMC3767814 | biostudies-literature
Project description:In this study, the acid-base properties of the adenine cation radical are investigated by means of experiment and theory. Adenine cation radical (A*(+)) is produced by one-electron oxidation of dAdo and of the stacked DNA-oligomer (dA)6 by Cl2*(-) in aqueous glass (7.5 M LiCl in H2O and in D2O) and investigated by ESR spectroscopy. Theoretical calculations and deuterium substitution at C8-H and N6-H in dAdo aid in our assignments of structure. We find the pKa value of A*(+) in this system to be ca. 8 at 150 K in seeming contradiction to the accepted value of < or = 1 at ambient temperature. However, upon thermal annealing to > or = 160 K, complete deprotonation of A*(+) occurs in dAdo in these glassy systems even at pH ca. 3. A*(+) found in (dA)6 at 150 K also deprotonates on thermal annealing. The stability of A*(+) at 150 K in these systems is attributed to charge delocalization between stacked bases. Theoretical calculations at various levels (DFT B3LYP/6-31G*, MPWB95, and HF-MP2) predict binding energies for the adenine stacked dimer cation radical of 12 to 16 kcal/mol. Further DFT B3LYP/6-31G* calculations predict that, in aqueous solution, monomeric A*(+) should deprotonate spontaneously (a predicted pKa of ca. -0.3 for A*(+)). However, the charge resonance stabilized dimer AA*(+) is predicted to result in a significant barrier to deprotonation and a calculated pKa of ca. 7 for the AA*(+) dimer which is 7 pH units higher than the monomer. These theoretical and experimental results suggest that A*(+) isolated in solution and A*(+) in adenine stacks have highly differing acid-base properties resulting from the stabilization induced by hole delocalization within adenine stacks.
| S-EPMC4590776 | biostudies-literature
Project description:In this work, we have synthesized 5-thiocyanato-2'-deoxyuridine (SCNdU) along with the C6-deuterated nucleobase 5-thiocyanatouracil (6-D-SCNU) and studied their reactions with radiation-produced electrons. ESR spectra in ?-irradiated nitrogen-saturated frozen homogeneous solutions (7.5 M LiCl in H2O or D2O) of these compounds show that electron-induced S-CN bond cleavage occurs to form a thiyl radical (dU-5-S? or 6-D-U-5-S?) and CN(-)via the initial ?-anion radical (SCNdU?(-)) intermediate in which the excess electron is on the uracil base. HPLC and LC-MS/MS studies of ?-irradiated N2-saturated aqueous solutions of SCNdU in the presence of sodium formate as a OH-radical scavenger at ambient temperature show the formation of the dU-5S-5S-dU dimer in preference to dU by about 10 to 1 ratio. This shows that both possible routes of electron-induced bond cleavage (dUC5-SCN and S-CN) in SCNdU?(-) and dU-5-S? formation are preferred for the production of the ?-type uracilyl radical (dU?) by 10 fold. DFT/M06-2x/6-31++G(d,p) calculations employing the polarizable continuum model (PCM) for aqueous solutions show that dU-5-S? and CN(-) formation was thermodynamically favored by over 15 kcal mol(-1) (?G) compared to dU? and SCN(-) production. The activation barriers for C5-S and S-CN bond cleavage in SCNdU?(-) amount to 8.7 and 4.0 kcal mol(-1), respectively, favoring dU-5-S? and CN(-) formation. These results support the experimental observation of S-CN bond cleavage by electron addition to SCNdU that results in the formation of dU-5-S? and the subsequent dU-5S-5S-dU dimer. This establishes SCNdU as a potential radiosensitizer that could cause intra- and inter-strand crosslinking as well as DNA-protein crosslinking via S-S dimer formation.
| S-EPMC4481187 | biostudies-literature
Project description:Hydroxyl radical protein footprinting (HRPF) by fast photochemical oxidation of proteins (FPOP) is a powerful benchtop tool used to probe protein structure, interactions, and conformational changes in solution. However, the reproducibility of all HRPF techniques is limited by the ability to deliver a defined concentration of hydroxyl radicals to the protein. This ability is impacted by both the amount of radical generated and the presence of radical scavengers in solution. In order to compare HRPF data from sample to sample, a hydroxyl radical dosimeter is needed that can measure the effective concentration of radical that is delivered to the protein, after accounting for both differences in hydroxyl radical generation and nonanalyte radical consumption. Here, we test three radical dosimeters (Alexa Fluor 488, terepthalic acid, and adenine) for their ability to quantitatively measure the effective radical dose under the high radical concentration conditions of FPOP. Adenine has a quantitative relationship between UV spectrophotometric response, effective hydroxyl radical dose delivered, and peptide and protein oxidation levels over the range of radical concentrations typically encountered in FPOP. The simplicity of an adenine-based dosimeter allows for convenient and flexible incorporation into FPOP applications, and the ability to accurately measure the delivered radical dose will enable reproducible and reliable FPOP across a variety of platforms and applications.
| S-EPMC4631671 | biostudies-literature
Project description:There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1~7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ~0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ~2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration.
| S-EPMC3695931 | biostudies-literature
Project description:A DFT study of U(VI) hydroxy complexes was performed with special attention paid to the [(UO2)3(OH)5(H2O)4-7]+ and [(UO2)4(OH)7(H2O)5-8]+ species. It was established that the ionicity of the U=O bond increased when moving from [(UO2)(H2O)5]2+, [(UO2)2(OH)(H2O)8]3+, [(UO2)2(OH)2(H2O)6]2+, [(UO2)3(OH)5(H2O)4-6]+ to [(UO2)4(OH)7(H2O)5-8]+ species. In both [(UO2)3(OH)5(H2O)4-6]+ and [(UO2)4(OH)7(H2O)5-8]+ complexes, the U=O bond was observed to have a range of different lengths which depended on the composition of the first coordination sphere of UO22+. The cyclic structures of trimeric complexes were somewhat more stable than their linear structures, which was probably due to the steric effect.
| S-EPMC5533873 | biostudies-other