Sugar radicals formed by photoexcitation of guanine cation radical in oligonucleotides

This work presents evidence that photoexcitation of guanine cation radical (G+*) in dGpdG and DNA-oligonucleotides TGT, TGGT, TGGGT, TTGTT, TTGGTT, TTGGTTGGTT, AGA, and AGGGA in frozen glassy aqueous solutions at low temperatures leads to hole transfer to the sugar phosphate backbone and results in high yields of deoxyribose radicals. In this series of oligonucleotides, we find that G+* on photoexcitation at 143 K leads to the formation of predominantly C5'* and C1'* with small amounts of C3'*. Photoconversion yields of G+* to sugar radicals in oligonucleotides decreased as the overall chain length increased. However, for high molecular weight dsDNA (salmon testes) in frozen aqueous solutions, substantial conversion of G+* to C1'* (only) sugar radical is still found (ca. 50%). Within the cohort of sugar radicals formed, we find a relative increase in the formation of C1'* with length of the oligonucleotide, along with decreases in C3'* and C5'*. For dsDNA in frozen solutions, only the formation of C1'* is found via photoexcitation of G+*, without a significant temperature dependence (77-180 K). Long wavelength visible light (>540 nm) is observed to be about as effective as light under 540 nm for photoconversion of G+* to sugar radicals for short oligonucleotides but gradually loses effectiveness with chain length. This wavelength dependence is attributed to base-to-base hole transfer for wavelengths >540 nm. Base-to-sugar hole transfer is suggested to dominate under 540 nm. These results may have implications for a number of investigations of hole transfer through DNA in which DNA holes are subjected to continuous visible illumination.     

One-electron oxidation of DNA oligomers that lack guanine: reaction and strand cleavage at remote thymines by long-distance radical cation hopping

The anthraquinone (AQ) photosensitized one-electron oxidation of DNA introduces a radical cation (electron "hole") that migrates through the duplex by hopping. The radical cation normally is trapped irreversibly by reaction at guanine. We constructed AQ-linked DNA oligomers composed exclusively of A/T base pairs. Their irradiation led to reaction and strand cleavage primarily at thymines. Long-distance radical cation hopping to distant thymines was demonstrated by the distance dependence of the process and by experiments with DNA oligomers that contain a single remote GG step. The reaction of the radical cation at thymine was shown to involve its 5-methyl group by the replacement of selected thymines with uracils. These findings show that the reactivity of radical cations in DNA cannot be explained simply by exclusive reliance on the relative oxidation potential of the nucleobases. Instead, the site of reaction is determined in accord with the Curtin-Hammett principle for reactive species in rapid equilibrium.     

Photochemistry of cation radicals in solution : photoinduced oxidation by the phenothiazine cation radical

Irradiation of phenothiazine cation radical, Ph^.+, with 1,1-diphenylethylene, DPE, causes its reduction to Ph and oxidation of DPE. Cyclodimeric products are formed from DPE^.+.     

Lifetimes and reaction pathways of guanine radical cations and neutral guanine radicals in an oligonucleotide in aqueous solutions

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.     

Formation of cation radicals from methylbenzenes on sulfated zirconia

The adsorption of methylbenzenes on sulfated zirconia has been studied by ESR. The catalyst is shown to possess acceptor sites capable to ionize methylbenzenes. The number of acceptor sites appeared to depend on the surface sulfur concentration. Oxygen is observed to strengthen the acceptor sites.     

Direct observation of guanine radical cation deprotonation in duplex DNA using pulse radiolysis

The dynamics of one-electron oxidation of guanine (G) base mononucleotide and that in DNA have been investigated by pulse radiolysis. The radical cation (G+*) of deoxyguanosine (dG), produced by oxidation with SO(4)-*, rapidly deprotonates to form the neutral G radical (G(-H)*) with a rate constant of 1.8 x 10(7) s(-1) at pH 7.0, as judged from transient spectroscopy. With experiments using different double-stranded oligonucleotides containing G, GG, and GGG sequences, the absorbance increases at 625 nm, characteristic of formation of the G(-H)*, were found to consist of two phases. The rate constants of the faster ( approximately 1.3 x 10(7) s(-1)) and slower phases ( approximately 3.0 x 10(6) s(-1)) were similar for the different oligonucleotides. On the other hand, in the oligonucleotide containing G located at the 5'- and 3'-terminal positions, only the faster phase was seen. These results suggest that the lifetime of the radical cation of the G:C base pair (GC+*), depending on its location in the DNA chain, is longer than that of free dG. In addition, the absorption spectral intermediates showed that hole transport to a specific G site within a 12-13mer double-stranded oligonucleotide is complete within 50 ns; that is, the rate of hole transport over 20 A is >10(7) s(-1).     

Influence of DNA structure on the reactivity of the guanine radical cation

Oxidative damage of DNA via radical cation formation is a common cause of mutagenesis, cancer and of the physiological changes associated with aging. By using state-of-the-art ab initio molecular dynamics simulations, we study the mechanism that guides the first steps of this process. In the mechanism proposed here, guanine, which among the bases has the lowest oxidation potential, and the phosphate backbone play a crucial role. We found that the rate limiting step is the water protolysis. We illuminate the role of the local environment in considerably lowering the barrier. Of particular relevance in this respect is the role of the phosphate backbone.     

The guanine cation radical: investigation of deprotonation states by ESR and DFT

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.     

Polyaryl anion radicals via alkali metal reduction of arylurea oligomers

A series of N-methylated polyarylurea oligomers have been reduced with potassium metal in HMPA. These reductions result in the transient formation of arylurea anion radicals, which undergo reductive elimination of the urea linkages. The aryl moieties appear in the products as the anion radicals of oligoaryl systems. The reaction is intramolecular, and the sequencing in the polyaryl anion radical remains the same as in the polyarylureas due to the urea-enforced pi-pi stacking interactions.     

Density functional theory study of the beta-carotene radical cation and deprotonated radicals

The beta-carotene radical cation and deprotonated neutral radicals were studied at the density functional theory (DFT) level using different density functionals and basis sets: B3LYP/3-21G, SVWN5/6-31G*, BPW91/DGDZVP2, and B3LYP/6-31G**. The geometries, total energies, spin distributions, and isotropic and anisotropic hyperfine coupling constants of these species were calculated. Deprotonation of the methyl group at the double bond of the cyclohexene ring of the carotenoid radical cation at 5 or 5' produces the most stable neutral radical because of retention of the pi-conjugated system while less stable deprotonation at 9 or 9' and 13 or 13' of the chain methyl groups causes significant distortion of the conjugation. The predicted methyl hyperfine coupling constants of 13-16 MHz of the neutral radicals are in good agreement with the previous electron nuclear double resonance (ENDOR) spectrum of photolyzed beta-carotene on a solid support. DFT calculations on the beta-carotene radical cation in a polar water environment showed that the polar environment does not cause significant changes in the proton hyperfine constants from those in the isolated gas-phase molecule. DFT calculated methyl proton hyperfine coupling constants of less than 7.2 MHz are in agreement with those reported for the radical cation in photosystem II (PS II) and those found in the absence of UV light for the radical cation on a silica alumina matrix.     

Reaction of thianthrene cation radical with grignard reagents : Evidence for electron transfer and trapping of alkyl radicals by the thianthrene cation radical

Reactions are reported between RMgCl and thianthrene cation radical perchlorate (Th^.+ClO^-₄) suspended in ether and tetrahydrofuran (THF). In ether solution reactions R = Bu, s-Bu, t-Bu, 5-hexenyl, and cyclopentylmethyl. Major products were the alkane, the alkene R(-H) in some cases, and, in the cases of R = Bu, 5-hexenyl, and cyclopentylmethyl, the 5-alkylthianthrenium perchlorate (ThR⁺ClO^-₄). When 5-hexenylMgCl was used a mixture of 5-(5-hexenyl)- and 5-(cyclopentylmethyl)thianthrenium per-chlorates in the ratio of approximately 2 was obtained. Since the ratio of 5-hexenyl/cyclopentylmethyl in the Grignard reagent was 10.4, it is concluded that the C₆ sulfonium ions were formed by radical trapping by Th^.+ after single electron transfer from Grignard to cation radical had occurred, thus allowing for cyclization of 5-hexenyl radical. Formation of ThBu⁺ClO^-₄ is attributed to the trapping of butyl radical by Th^·+, while formation of RH and R(-H) is in all cases also attributed to alkyl radical reactions. Reactions in THF(R = Me, i-Pr, Bu, s-Bu, t-Bu, Ph) led almost exclusively to RH and Th. Polymerization of THF was also initiated and took place slowly giving rise to low molecular weight poly(THF). By using THF-d₈, as solvent for reaction between BuMgCl and Th^.+, it was possible to find Bu groups (¹H-NMR) in the poly(THF-d₈). Polymerization of THF is attributed, in some cases (R = Me, Bu), to alkyl-cation transfer from ThR⁺ to THF. In other cases initiation of polymerization by R⁺ and THF(-H)⁺ is considered.     

Cation radicals. XXVIII. Isolation and some reactions of dibenzodioxin cation radical perchlorate

Preparation and isolation of dibenzodioxin cation radical perchlorate ( 2 ) by oxidation of dibenzodioxin in ethyl acetate-lithium perchlorate at a platinum anode has been achieved. Reasonably pure 2 in amounts of 150–200 mg. were obtained reliably and reproducibly. Reaction of 2 with both nitrite and nitrate ions gave 2-nitrodibenzodioxin ( 3 ). Reaction of 2 with pyridine gave N-(2-dibenzodioxinyl)pyridinium perchlorate ( 4 ). Reaction with water gave, as anticipated, the stoichiometric amount of dibenzodioxin. Reaction with ammonia, propylamine, t-butylamine, and cyanide ion also gave dibenzodioxin with no evidence that nucleophilic substitution had occurred. It is believed that the formation of 3 and 4 represent the first examples of nucleophilic substitution into dibenzodioxin via its cation radical.     

Role of the guanine N1 imino proton in the migration and reaction of radical cations in DNA oligomers

Oxidation of a guanine nucleobase to its radical cation in DNA oligomers causes an increase in the acidity of the N1 imino proton that may lead to its spontaneous transfer to N3 of the paired cytosine. This proton transfer is suspected of playing an important role in long-distance radical cation hopping in DNA and the decisive product-determining role in the reaction of the radical cation with H2O or O2. We prepared and investigated DNA oligomers in which certain deoxycytidines are replaced by 5-fluoro-2'-deoxycytidines (F5dC). The pKa of F5C was determined to be 1.7 units below that of dC, which causes proton transfer from the guanine radical cation to be thermodynamically unfavorable. Photoinitiated one-electron oxidation of the DNA by UV irradiation of a covalently attached anthraquinone derivative introduces a radical cation that hops throughout the oligomer and is trapped selectively at GG steps. The introduction of F5dC does not affect the efficiency of charge hopping, but it significantly reduces the amount of reaction at the GG sites, as revealed by subsequent reaction with formamidopyrimidine glycosylase. These findings suggest that transfer of the guanine radical cation N1 proton to cytosine does not play a significant role in long-range charge transfer, but this process does influence the reactions with H2O and/or O2.     

Optically active free radicals: circular dichroism of vitamin E acetate radical cation

The circular dichroism properties of the vitamin E acetate and its radical cation were observed and analyzed.     

Electron transfer in DNA from guanine and 8-oxoguanine to a radical cation of the carbohydrate backbone

Photolysis of a 4'-pivaloyl-substituted nucleotide in single- and double-stranded DNA (1) generated an enol ether radical cation 4 that was reduced to enol ether 17 by electron transfer from the nearest guanoside (G). Variation of the nucleotide sequence demonstrated a strong distance dependence of this electron-transfer rate with beta = 1.0 +/- 0.1 A(-1). When 8-oxoguanosine (G(oxo)) was used as the electron donor, the rate of the electron transfer increased by a factor of 4 but the distance dependence of the transfer remained unchanged within experimental error. In single strands, the number of intervening A, T, and C nucleotides had a much smaller effect; the rate remained nearly constant for two, three, or four intervening nucleotides. This is explained by the flexibility of the single-stranded oligonucleotides.     

Evolution of spins in ultrastable triplet radical pair formed by magnesium phthalocyanine cation and verdazyl radicals

Quenching of the triplet state of magnesium tetra-4-tert-butylphthalocyanine by verdazylium cations, and also quenching of the methoxy and nitro derivatives, have been investigated by pulse photolysis in propylene carbonate at room temperature. The quenching process is related to transfer of an electron from the excited pigment to the cation and the formation of an unusually stable, energy-intensive triplet radical pair that includes a stable cation radical of the phthalocyanine and a free verdazyl radical. The lifetime of the radical pair (10^–3 sec) depends on the nature of the substituents in the verdazyl and is determined by the rate of triplet-singlet evolution of spins in the pair. The reaction mechanism is examined critically in this article, as well as the possible structure of the pair.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 28, No. 2, pp. 148–152, March–April, 1992.     

Synthesis of heteroarenes using cascade radical cyclisation via iminyl radicals

Cascade radical cyclisation involving homolytic aromatic substitution has been used to synthesise new tetracycles. Treatment of vinyl iodide radical precursors with Me(3)Sn. radicals (from hexamethylditin) yielded intermediate vinyl radicals which undergo 5-exo cyclisation onto suitably placed nitrile groups to yield intermediate iminyl radicals. The iminyl radicals undergo aromatic homolytic substitution via 6-endo cyclisation (or 5-exo cyclisation followed by neophyl rearrangement) with loss of hydrogen (H.) in a H-abstraction step. We propose that this abstraction was facilitated by tert-butoxyl (t-BuO.) radicals from di-tert-butyl peroxide or methyl radicals, generated from breakdown of trimethylstannyl radicals (Me(3)Sn.). The biologically active alkaloids mappicine and luotonin A were synthesised using the new methodology. A novel radical conversion of nitriles to primary amides is proposed.     

Formation of intramolecular poly(4-hydroxystyrene) dimer radical cation

Poly(4-hydroxystyrene) (PHS) has been used in lithography as a backbone polymer and is also a promising material for extreme-ultraviolet or electron beam lithography. The dynamics of PHS radical cations generated upon exposure to electron beam were investigated. The transient absorption of PHS was observed in the near-infrared region in p-dioxane solutions by pulse radiolysis. Charge resonance (CR) bands that represent pi-pi interaction between the two chromophores of the intramolecular PHS dimer radical cation were observed, whereas p-cresol shows no distinct CR band. Although the radical cations of phenol derivatives are known to be easily deprotonated, it was found that the dimer radical cation formation leads to less deprotonation by its charge resonance stabilization.