Reaction of hydrated electrons with guanine nucleosides: fast protonation on carbon of the electron adduct

Tracking Isomerizations of High-Energy Adenine Cation Radicals by UV-Vis Action Spectroscopy and Cyclic Ion Mobility Mass Spectrometry

We report experimental and computational studies of protonated adenine C-8 σ-radicals that are presumed yet elusive reactive intermediates of oxidative damage to nucleic acids. The radicals were generated in the gas phase by the collision-induced dissociation of C-8-Br and C-8-I bonds in protonated 8-bromo- and 8-iodoadenine as well as by 8-bromo- and 8-iodo-9-methyladenine. Protonation by electrospray of 8-bromo- and 8-iodoadenine was shown by cyclic-ion mobility mass spectrometry (c-IMS) to form the N-1-H, N-9-H and N-3-H, N-7-H protomers in 85:15 and 81:19 ratios, respectively, in accordance with the equilibrium populations of these protomers in water-solvated ions that were calculated by density functional theory (DFT). Protonation of 8-halogenated 9-methyladenines yielded single N-1-H protomers, which was consistent with their thermodynamic stability. The radicals produced from the 8-bromo and 8-iodo adenine cations were characterized by UV-vis photodissociation action spectroscopy (UVPD) and c-IMS. UVPD revealed the formation of C-8 σ-radicals along with N-3-H, N-7-H-adenine π-radicals that arose as secondary products by hydrogen atom migrations. The isomers were identified by matching their action spectra against the calculated vibronic absorption spectra. Deuterium isotope effects were found to slow the isomerization and increase the population of C-8 σ-radicals. The adenine cation radicals were separated by c-IMS and identified by their collision cross sections, which were measured relative to the canonical N-9-H adenine cation radical that was cogenerated in situ as an internal standard. Ab initio CCSD(T)/CBS calculations of isomer energies showed that the adenine C-8 σ-radicals were local energy minima with relative energies at 76-79 kJ mol^-1 above that of the canonical adenine cation radical. Rice-Ramsperger-Kassel-Marcus calculations of unimolecular rate constants for hydrogen and deuterium migrations resulting in exergonic isomerizations showed kinetic shifts of 10-17 kJ mol^-1, stabilizing the C-8 σ-radicals. C-8 σ-radicals derived from N-1-protonated 9-methyladenine were also thermodynamically unstable and readily isomerized upon formation.

The DNA Radical Code. Resolution of Identity in Dissociations of Trinucleotide Codon Cation Radicals in the Gas Phase

Sixty DNA trinucleotide cation radicals covering a large part of the genetic code alphabet were generated by electron transfer in the gas phase, and their chemistry was studied by collision-induced dissociation tandem mass spectrometry and theoretical calculations. The major dissociations involved loss of nucleobase molecules and radicals, backbone cleavage, and cross-ring fragmentations that depended on the nature and position of the nucleobases. Mass identity in dissociations of symmetrical trinucleotide cation radicals of the (XXX+2H)^+• and (XYX+2H)^+• type was resolved by specific ¹⁵N labeling. The specific features of trinucleotide cation radical dissociations involved the dominant formation of d₂⁺ ions, hydrogen atom migrations accompanying the formation of (w₂+H)^+•, (w₂+2H)⁺, and (d₂+2H)⁺ sequence ions, and cross-ring cleavages in the 3'- and 5'-deoxyribose moieties that depended on the nucleobase type and its position in the ion. Born-Oppenheimer molecular dynamics (BOMD) and density functional theory calculations were used to obtain structures and energies of several cation-radical protomers and conformers for (AAA+2H)^+•, (CCC+2H)^+•, (GGG+2H)^+•, (ACA+2H)^+•, and (CAA+2H)^+• that were representative of the different types of backbone dissociations. The ion electronic structure, protonation and radical sites, and hydrogen bonding were used to propose reaction mechanisms for the dissociations.

Charge-Tagged Nucleosides in the Gas Phase: UV-Vis Action Spectroscopy and Structures of Cytidine Cations, Dications, and Cation Radicals

Cytidine ribonucleosides were furnished at O5' with fixed-charge 6-trimethylammoniumhexan-1-aminecarbonyl tags and studied by UV-vis photodissociation action spectroscopy in the gas phase to probe isolated nucleobase chromophores in their neutral, protonated, and hydrogen-adduct radical forms. The action spectrum of the doubly charged cytidine conjugate showed bands at 310 and 270 nm that were assigned to the N3- and O2-protonated cytosine tautomers formed by electrospray, respectively. In contrast, cytidine conjugates coordinated to dibenzo-18-crown-6-ether (DBCE) in a noncovalent complex were found to strongly favor protonation at N3, forming a single-ion tautomer. This allowed us to form cytidine N3-H radicals by electron transfer dissociation of the complex and study their action spectra. Cytidine radicals showed only very weak absorption in the visible region of the spectrum for dipole-disallowed transitions to the low (A and B) excited states. The main bands were observed at 360, 300, and 250 nm that were assigned with the help of theoretical vibronic spectra obtained by time-dependent density functional theory calculations of multiple (>300) radical vibrational configurations. Collision-induced dissociations of cytidine radicals proceeded by major cleavage of the N1-C1' glycosidic bond leading to loss of cytosine and competitive loss of N3-hydrogen atom. These dissociations were characterized by calculations of transition-state structures and energies using combined Born-Oppenheimer molecular dynamics and DFT calculations. Overall, cytidine radicals were found to be kinetically and thermodynamically more stable than previously reported analogous adenosine and guanosine radicals.

Reactivity of prehydrated electrons toward nucleobases and nucleotides in aqueous solution

DNA damage induced via dissociative attachment by low-energy electrons (0 to 20 eV) is well studied in both gas and condensed phases. However, the reactivity of ultrashort-lived prehydrated electrons ([Formula: see text]) with DNA components in a biologically relevant environment has not been fully explored to date. The electron transfer processes of [Formula: see text] to the DNA nucleobases G, A, C, and T and to nucleosides/nucleotides were investigated by using 7-ps electron pulse radiolysis coupled with pump-probe transient absorption spectroscopy in aqueous solutions. In contrast to previous results, obtained by using femtosecond laser pump-probe spectroscopy, we show that G and A cannot scavenge [Formula: see text] at concentrations of ≤50 mM. Observation of a substantial decrease of the initial yield of hydrated electrons ([Formula: see text]) and formation of nucleobase/nucleotide anion radicals at increasing nucleobase/nucleotide concentrations present direct evidence for the earliest step in reductive DNA damage by ionizing radiation. Our results show that [Formula: see text] is more reactive with pyrimidine than purine nucleobases/nucleotides with a reactivity order of T > C > A > G. In addition, analyses of transient signals show that the signal due to formation of the resulting anion radical directly correlates with the loss of the initial [Formula: see text] signal. Therefore, our results do not agree with the previously proposed dissociation of transient negative ions in nucleobase/nucleotide solutions within the timescale of these experiments. Moreover, in a molecularly crowded medium (for example, in the presence of 6 M phosphate), the scavenging efficiency of [Formula: see text] by G is significantly enhanced. This finding implies that reductive DNA damage by ionizing radiation depends on the microenvironment around [Formula: see text].

Multi-level Quantum Mechanics and Molecular Mechanics Study of Ring Opening Process of Guanine Damage by Hydroxyl Radical in Aqueous Solution

Combining multi-level quantum mechanics theories and molecular mechanics with an explicit water model, we investigated the ring opening process of guanine damage by hydroxyl radical in aqueous solution. The detailed, atomic-level ring-opening mechanism along the reaction pathway was revealed in aqueous solution at the CCSD(T)/MM levels of theory. The potentials of mean force in aqueous solution were calculated at both the DFT/MM and CCSD(T)/MM levels of the theory. Our study found that the aqueous solution has a significant effect on this reaction in solution. In particular, by comparing the geometries of the stationary points between in gas phase and in aqueous solution, we found that the aqueous solution has a tremendous impact on the torsion angles much more than on the bond lengths and bending angles. Our calculated free-energy barrier height 31.6 kcal/mol at the CCSD(T)/MM level of theory agrees well with the one obtained based on gas-phase reaction profile and free energies of solvation. In addition, the reaction path in gas phase was also mapped using multi-level quantum mechanics theories, which shows a reaction barrier at 19.2 kcal/mol at the CCSD(T) level of theory, agreeing very well with a recent ab initio calculation result at 20.8 kcal/mol.

Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics

Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.

Oxidatively induced DNA damage and its repair in cancer

Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.

Oxidation of purine nucleotides by Triplet 3,3',4,4'-benzophenone tetracarboxylic acid in aqueous solution: pH-dependence

The photo-oxidation of purine nucleotides adenosine-5′-monophosphate (AMP) and guanosine-5′-monophosphate (GMP) by 3,3′,4,4′-benzophenone tetracarboxylic acid (TCBP) has been investigated in aqueous solutions using nanosecond laser flash photolysis (LFP) and time-resolved chemically induced dynamic nuclear polarization (CIDNP). The pH dependences of quenching rate constants and of geminate polarization are measured within a wide range of pH values. As a result, the chemical reactivity of reacting species in different protonation states is determined. In acidic solution (pH < 4.9), the quenching rate constant is close to the diffusion-controlled limit: k_q = 1.3 × 10⁹ M^–1 s^–1 (GMP), and k_q = 1.2 × 10⁹ M^–1 s^–1 (AMP), whereas in neutral and basic solutions it is significantly lower: k_q = 2.6 × 10⁸ M^–1 s^–1 (GMP, 4.9 < pH < 9.4), k_q = 3.5 × 10⁷ M^–1 s^–1 (GMP, pH > 9.4), k_q = 1.0 × 10⁸ M^–1 s^–1 (AMP, pH > 6.5). Surprisingly, the strong influence of the protonation state of the phosphoric group on the oxidation of adenosine-5′-monophosphate is revealed: the deprotonation of the AMP phosphoric group (6.5) decreases the quenching rate constant from 5.0 × 10⁸ M^–1 s^–1 (4.9 < pH < 6.5) to 1.0 × 10⁸ M^–1 s^–1 (pH > 6.5).

Mechanisms of free radical-induced damage to DNA

Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates. Hydrated electron and H atom also add to the heterocyclic bases. These reactions lead to adduct radicals, further reactions of which yield numerous products. These include DNA base and sugar products, single- and double-strand breaks, 8,5'-cyclopurine-2'-deoxynucleosides, tandem lesions, clustered sites and DNA-protein cross-links. Reaction conditions and the presence or absence of oxygen profoundly affect the types and yields of the products. There is mounting evidence for an important role of free radical-induced DNA damage in the etiology of numerous diseases including cancer. Further understanding of mechanisms of free radical-induced DNA damage, and cellular repair and biological consequences of DNA damage products will be of outmost importance for disease prevention and treatment.

Hydroxyl radical (OH•) reaction with guanine in an aqueous environment: a DFT study

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.

Theoretical investigations on the formation of nitrobenzanthrone-DNA adducts

3-Nitrobenzanthrone (3-NBA) is a potent mutagen and suspected human carcinogen identified in diesel exhaust. The thermochemical formation cascades were calculated for six 3-NBA-derived DNA adducts employing its arylnitrenium ion as precursor using density functional theory (DFT). Clear exothermic pathways were found for four adducts, i.e., 2-(2'-deoxyadenosin-N(6)-yl)-3-aminobenzanthrone, 2-(2'-deoxyguanosin-N(2)-yl)-3-aminobenzanthrone, N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone and 2-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone. All four have been observed to be formed in cell-free experimental systems. The formation of N-(2'-deoxyadenosin-8-yl)-3-aminobenzanthrone is predicted to be not thermochemically viable explaining its absence in either in vitro or in vivo model systems. However, 2-(2'-deoxyadenosin-8-yl)-3-aminobenzanthrone, can be formed, albeit not as a major product, and is a viable candidate for an unknown adenine adduct observed experimentally. 2-nitrobenzanthrone (2-NBA), an isomer of 3-NBA, was also included in the calculations; it has a higher abundance in ambient air than 3-NBA, but a much lower genotoxic potency. Similar thermochemical profiles were obtained for the calculated 2-NBA-derived DNA adducts. This leads to the conclusion that enzymatic activation as well as the stability of its arylnitrenium ion are important determinants of 2-NBA genotoxicity.

On the hydrogen loss from protonated nucleobases after electronic excitation or collisional electron capture

In this work, we have subjected protonated nucleobases MH(+) (M = guanine, adenine, thymine, uracil and cytosine) to a range of experiments that involve high-energy (50 keV) collision induced dissociation and electron capture induced dissociation. In the latter case, both neutralisation reionisation and charge reversal were done. For the collision induced dissociation experiments, the ions interacted with O(2). In neutral reionisation, caesium atoms were used as the target gas and the protonated nucleobases captured electrons to give neutrals. These were reionised to cations a microsecond later in collisions with O(2). In choosing Cs as the target gas, we have assured that the first electron transfer process is favourable (by about 0.1-0.8 eV depending on the base). In the case of protonated adenine, charge reversal experiments (two Cs collisions) were also carried out, with the results corroborating those from the neutralisation reionisation experiments. We find that while collisional excitation of protonated nucleobases in O(2) may lead to hydrogen loss with limited probabilities, this channel becomes dominant for electron capture events. Indeed, when sampling reionised neutrals on a microsecond timescale, we see that the ratio between MH(+) and M(+) is 0.2-0.4 when one electron is captured from Cs. There are differences in these ratios between the bases but no obvious correlation with recombination energies was found.

The energetics of rearrangement and water elimination reactions in the radiolysis of the DNA bases in aqueous solution (eaq- and *OH attack): DFT calculations

DFT calculations on the relative stability of various nucleobase radicals induced by e(aq)(-) and (*)OH have been carried out for assessing the energetics of rearrangements and water elimination reactions, taking the solvent effect of water into account. Uracil and thymine radical anions are protonated fast at O2 and O4, whereby the O2-protonated anions are higher in energy (50 kJ mol(-1), equivalent to a 9-unit lower pK(a)). The experimentally observed pK(a)=7 is thus that of the O4-protonated species. Thermodynamically favored protonation occurs slowly at C6 (driving force, thymine: 49 kJ mol(-1), uracil: 29 kJ mol(-1)). The cytosine radical anion is rapidly protonated by water at N3. Final protonation at C6 is disfavored here. The kinetically favored pyrimidine C5 (*)OH adducts rearrange into the thermodynamically favored C6 (*)OH adducts (driving force, thymine: 42 kJ mol(-1)). Very similar in energy is a water elimination that leads to the Ura-5-methyl radical. Purine (*)OH adducts at C4 and C5 (plus C2 in guanine) eliminate water in exothermic reactions, while water elimination from the C8 (*)OH adducts is endothermic. The latter open the ring en route to the FAPY products, an H transfer from the C8(*)OH to N9 being the most likely process.

Chemical radiation studies of 8-bromo-2'-deoxyinosine and 8-bromoinosine in aqueous solutions

The reactions of hydrated electrons (e(aq) (-)) with 8-bromo-2'-deoxyinosine (8) and 8-bromoinosine (12) have been investigated by radiolytic methods coupled with product studies and have been addressed computationally by means of BB1K-HMDFT calculations. Pulse radiolysis revealed that one-electron reductive cleavage of the C--Br bond gives the C8 radical 9 or 13 followed by a fast radical translocation to the sugar moiety. Selective generation of a C5' radical occurs in the 2'-deoxyribo derivative, whereas in the ribo analogue the reaction is partitioned between the C5' and C2' positions with similar rates. Both C5' radicals undergo cyclizations, 10-->11 and 14-->15, with rate constants of 1.4 x 10(5) and of 1.3 x 10(4) s(-1), respectively. The redox properties of radicals 10 and 11 have also been investigated. A synthetically useful photoreaction has also been developed as a one-pot procedure that allows the conversion of 8 to 5',8-cyclo-2'-deoxyinosine in a high yield and a diastereoisomeric ratio (5'R)/(5'S) of 4:1. The present results are compared with data previously obtained for 8-bromoadenine and 8-bromoguanine nucleosides. Theory suggests that the behavior of 8-bromopurine derivatives with respect to solvated electrons can be attributed to differences in the energy gap between the pi*- and sigma*-radical anions.

Hydrogen loss from nucleobase nitrogens upon electron attachment to isolated DNA and RNA nucleotide anions

Electron transfer to isolated nucleotide monoanions in collisions with Na vapor induces hydrogen loss from nitrogen of the transient nucleobase anion. The cross section for this process is linearly correlated with the number of N-H hydrogens and is highest for guanine. The process is much faster than microseconds since only dehydrogenated dianions survived for mass spectrometric detection. The lifetime of the adenosine 5(')-monophospate dianions was measured to be 0.2 ms in an electrostatic ion storage ring but also a longer-lived component with a lifetime of at least 10 ms was identified. Implications of dissociation along the N-H coordinate for a nucleotide in DNA are briefly discussed in terms of Watson-Crick base pairs.

Excess electron transfer in G-quadruplex

The excess electron transfer in a G-quadruplex is successfully probed by using the reaction of hydrated electrons with quadruplex complex of pentamers and the 8-bromoguanine moieties as the detection system.

Faster Dissociation: Measured Rates and Computed Effects on Barriers in Aryl Halide Radical Anions

Carbon-halogen bond dissociation rates for a series of aryl halide radical anions (ArX-: X = Cl, Br) in NMP were measured at room temperature by pulse radiolysis with 10-11 s time resolution. To obtain accurate dissociation rates, care was taken to measure and correct for competing decay channels. The observed rates correlated well with activation energies computed in the gas phase by density functional (DFT) calculations. The rates did not correlate well with electron affinities or dissociation energies obtained by the same computational methods, although such correlations are reported in the literature and are expected on the basis of simple models. The calculations also found that the transition state structures had bent carbon-halogen bonds. Bending enables large reductions of the activation energies by an electronic effect involving mixing of phi* and sigma* states. This bending-induced mixing is computed to increase the dissociation rates by a few orders of magnitude and is thus essential to understanding these reactions.

Photochemical and photophysical studies of guanine derivatives: intermediates contributing to its photodestruction mechanism in aqueous solution and the participation of the electron adduct

The low-intensity steady-state (254 nm), microsecond flash and nanosecond (266 nm) laser photolysis of some guanine (Gua) derivatives in aqueous solution were studied. A photodestruction yield between 10(-3) and 10(-2) at a base concentration of 75 microM was determined for 254 nm irradiation at room temperature using high-performance liquid chromatography. This yield decreases with increasing purine concentration. For a similar concentration of the purine bases (2 +/- 1) x 10(-5) M, the yield increases as follows: Gua approximately 9-ethylguanine < deoxyguanosine approximately guanosine (Guo) < guanosine 5'-monophosphate. At concentrations higher than 2 x 10(-4) M the Gua derivatives' photodestruction yield seems to converge to a limiting value of the order of 10(-4). This behavior is explained in terms of self-quenching and aggregation effects which deactivate the excited states of the bases. The yields of electron photoejection have been determined in the nanosecond laser photolysis (0.083) and in the low-intensity steady-state (5.8 x 10(-3)) for Guo. Competition experiments using electron scavengers suggest that the electron adducts of the bases are one of the principal species participating in the photodestruction mechanism of these monomeric Gua. Close to 75% of the total destruction yield has contributions from initial reactions of the photojected electron at neutral pH. The quantum yield of photodestruction of Guo increases when the pH is increased as follows: 4.7 x 10(-3) (pH 1.1), 6.5 x 10(-3) (pH 2.9), 7.7 x 10(-3) (pH 7.5) and 8.1 x 10(-3) (pH 11.9). This dependence on pH and the electron scavenger experiments provide further evidence for the radical anion or its protonated form as one of the principal species involved in the photodestruction of the bases at the different pH. Under oxygen saturated conditions a 22% increase in the destruction yield is observed for Guo. However, for the dinucleotides adenylyl (3'-->5')-guanosine and thymidylyl (3'-->5')2'-deoxyguanosine, the participation of the electron is 41 and 36%, respectively, suggesting that going into a more DNA or RNA-like structure, the participation of the electron adducts species in the photodamage of DNA and RNA decreases. A mechanism of photodestruction for the Gua derivatives is proposed which takes into account these findings.

Photochemistry of DNA and related biomolecules: quantum yields and consequences of photoionization

The reactions of nucleic acids and constituents, which can be induced by laser UV irradiation, are described. Emphasis is placed on the quantum yields of various stable photoproducts of DNA and model compounds upon irradiation at 193, 248, 254 or 266 nm. In particular, those quantum yields and processes are discussed which involve photoionization as the initial step and occur in aqueous solution under well defined conditions, e.g. type of atmosphere. The efficiencies of some photoproducts, with respect to photoionization using irradiation at 193 or 248 nm, are presented. Radical cations of nucleobases are important sources of damage of biological substrates since they can cause lesions other than dimers and adducts, e.g. strand breakage, abasic sites, crosslinks or inactivation of plasmid and chromosomal DNA. While competing photoreactions, such as hydration, dimerization or adduct formation, diminish the selectivity of the photoionization method, a combination with model studies on pyrimidine- and purine-containing constituents of DNA has brought about an enhanced insight into the reaction mechanisms. The knowledge concerning the lethal events in plasmid and cellular DNA has been greatly improved by correlation with the chemical effects obtained by gamma-radiolysis, vacuum-UV (< 190 nm) and low-intensity irradiation at 254 nm.

Addition of e-aq and H atoms to hypoxanthine and inosine and the reactions of alpha-hydroxyalkyl radicals with purines. A pulse radiolysis and product analysis study

The reactions of hydrated electrons e-aq with hypoxanthine and inosine were followed using pulse radiolysis methods. In a neutral solution the electron adduct of inosine is immediately protonated at the heteroatoms of the purine ring by water (k >> 2.5 x 10(6)s-1) to give In(N,O-H).. These N,O-protonated intermediates have a single absorption maximum at 300 nm. In basic solution the protonation of the electron adduct of inosine by water leads to other intermediate products with an absorption maximum at 350 nm. These intermediates are believed to be the C-protonated electron adducts of inosine (In(N,O-H).). In (N,O-H). and In(C-H). differ strongly in their ability to reduce p-nitroacetophenone (PNAP). In(N,O-H). are strong reductants and reduce PNAP quantitatively to PNAP.-. Based on the pH dependence of PNAP.- yields, two types of tautomers of In(C-H). could be distinguished. One of the tautomers can reduce PNAP, albeit with slower rate than In(N,O-H)., the other tautomer has no reducing properties. The latter is the one with the higher pKa and therefore thermodynamically more stable. The absorption spectrum of the intermediates produced in the reaction of e-aq with hypoxanthine at neutral pH is very similar to that of In(N,O-H). with a maximum at 300 nm. However, no build-up at 350 nm was observed in basic solution as in the case of the electron adduct of inosine. The reaction of H atoms with inosine produces in basic solution intermediate radicals with the same absorption spectrum as the C-protonated electron adducts of inosine. It is suggested that both the reactions of e-aq and H. with inosine in basic solution produce the same radical, namely the H-adduct of inosine (In(C-H)) with the highest pKa. alpha-Hydroxyalkyl radicals were found to react very slowly with purine bases and nucleosides in neutral to basic solutions. In acidic solution their reactivity increases and a number of rate constants were determined by pulse radiolysis measurements at pH 0.4. The intermediates from the reaction of 2-hydroxy-2-propyl radicals with inosine could be observed pulse spectrometrically in neutral and in basic solutions. In basic solution this reaction leads to intermediates with the same absorption maximum at 350 nm as that of the H-adduct of inosine. Furthermore, the yield of acetone was found to increase strongly in basic pH.(ABSTRACT TRUNCATED AT 400 WORDS)

Electron migration in oligonucleotides upon gamma-irradiation in solution

Electron migration in irradiated solutions of DNA was investigated using 5-bromouracil synthetically incorporated into oligonucleotides of defined base composition as a molecular indicator of electron interactions. Solvated electrons interact quantitatively with 5-bromouracil, leading to a highly reactive 5-yl radical which can abstract an adjacent hydrogen atom to yield uracil. Yields of uracil, or loss of 5-bromouracil, from irradiated oligonucleotide samples were measured using gas chromatography-mass spectrometric analysis of their trimethylsilylated acid hydrolysates. To examine the effects of base composition and DNA conformation on electron migration, a set of oligonucleotides containing 5-bromouracil at selected positions with three base (guanine, cytosine, thymine or adenine) spacers (e.g. [BrU(GGG)3]3) were irradiated in their single- or double-stranded form following annealing with appropriate complementary sequences. Differences in uracil yields suggested that electron migration occurred to different extents in oligonucleotides containing different base sequences. In irradiated single-stranded oligonucleotides, the yield of uracil decreased in the order A > T > > C approximately G. However, in irradiated double-stranded oligonucleotides, the yield of uracil decreased in the order G > C approximately T > A. These differences were attributed to proton-transfer reactions facilitated by base pairing in double-stranded oligonucleotides. The distance over which the electron would migrate was then determined using a series of oligonucleotides containing 5-bromouracil at selected positions with guanine spacers (i.e. [BrU(G)n]3 (n = 3, 5, 7, 9). Oligonucleotides were irradiated in their double-stranded form following annealing with the appropriate complementary sequences. Analysis of the loss of 5-bromouracil revealed that electron migration occurred efficiently over c. 3-4 guanine bases assuming that migration could occur as efficiently in either direction along the DNA molecule. These data can be compared with studies reporting more extensive migration for electrons generated by direct ionization of DNA.