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The photophysical and photochemical behavior of a series of hairpin-forming DNA conjugates possessing a 5'-tethered pyrenecarboxamide chromophore and one or two bromouracil bases has been investigated. Quenching of the pyrene fluorescence and transient absorption spectra characteristic of the pyrene cation radical are observed only when bromouracil is located at the first or second base pair position nearest to the point of pyrene attachment. These observations are consistent with an intercalated structure for these conjugates in which pyrene is adjacent to the second base pair. Selective quenching of singlet pyrene by bromouracil but not by thymine is consistent with the free energy for charge separation estimated using Weller's equation. Low quantum yields for loss of bromide when bromouracil is not adjacent to pyrene are attributed to inefficient charge separation via either a multistep electron transport or a single-step superexchange mechanism. Quantum yields are only weakly dependent upon the distance between pyrene and bromouracil, as expected for a multistep electron transport mechanism. Loss of bromide from conjugates possessing two bromouracils occurs sequentially. For adjacent bromouracils, competitive loss of bromide from both bromouracils is observed, whereas for nonadjacent bromouracils loss of bromide from the proximal bromouracil occurs prior to any loss from the distal bromouracil, consistent with a slower rate constant for electron transport vs loss of bromide.

Oxidative damage to guanine bases initiated by photolysis of the water-soluble radical generator 2,2'-azobis(2-amidinopropane) dihydrochloride (AAPH) has been investigated by laser kinetic spectroscopy. In the neutral oxygenated aqueous solutions, 355 nm laser flash photolysis of AAPH generates a whole spectrum of free radicals including 2-amidinoprop-2-peroxyl (ROO(*)), 2-amidinoprop-2-oxyl (RO(*)), and superoxide (O(2)(*-)) radicals. These oxyl radicals with negligible absorption in a near UV-visible range were monitored in the reactions leading to the products with characteristic absorption spectra. This approach reveals that RO(*) radicals induce fast one-electron oxidation of 2'-deoxyguanosine (dG) to form guanine neutral radicals, dG(-H)(*). In contrast, ROO(*) radicals do not react at observable rates with dG. The O(2)(*-) radicals were detected using a classical test reaction with tetranitromethane to form nitroform. The major pathway for formation of the end-products of guanine oxidation is the combination of the G(-H)(*) and O(2)(*-) radicals to form 2,5-diamino-4H-imidazolone (Iz). This mechanism was confirmed by analysis of the end-products produced by oxidation of two substrates: (1) the guanosine derivative 2',3',5'-tri-O-acetylguanosine (tri-O-Ac-G) and (2) the 5'-d(CCATCGCTACC) sequence. The major products isolated by HPLC and identified by mass spectrometry methods were the tri-O-Ac-Iz and 5'-d(CCATC[Iz]CTACC products.

The mechanistic aspects of the methylation of guanine in DNA initiated by methyl radicals that are derived from the metabolic oxidation of some chemical carcinogens remain poorly understood. In this work, we investigated the kinetics and the formation of methylated guanine products by two methods: (i) the combination of *CH3 radicals and guanine neutral radicals, G(-H)*, and (ii) the direct addition of *CH3 radicals to guanine bases. The simultaneous generation of *CH3 and dG(-H)* radicals was triggered by the competitive one-electron oxidation of dimethyl sulfoxide (DMSO) and 2'-deoxyguanosine (dG) by photochemically generated sulfate radicals in deoxygenated aqueous buffer solutions (pH 7.5). The photolysis of methylcob(III)alamin to form *CH3 radicals was used to investigate the direct addition of these radicals to guanine bases. The major end products of the radical combination reactions are the 8-methyl-dG and N2-methyl-dG products formed in a ratio of 1:0.7. In contrast, the methylation of dG by *CH3 radicals generates mostly the 8-methyl-dG adduct and only minor quantities of N2-methyl-dG (1:0.13 ratio). The methylation of the self-complementary 5'-d(AACGCGAATTCGCGTT) duplexes was achieved by the selective oxidation of the guanines with carbonate radical anions in the presence of DMSO as the precursor of *CH3 radicals. The methyl-G lesions formed were excised by the enzymatic digestion and identified by LC-MS/MS methods using uniformly 15N-labeled 8-methyl-dG and N2-methyl-dG adducts as internal standards. The ratios of 8-methyl-G/N2-methyl-G lesions derived from the combination of methyl radicals with G(-H)* radicals positioned in double-stranded DNA or that with the free nucleoside dG(-H)* radicals were found to be similar. Utilizing the photochemical method and dipropyl or dibutyl sulfoxides as sources of alkyl radicals, the corresponding 8-alkyl-dG and N2-alkyl-dG adducts were also generated in ratios similar to those obtained with DMSO.

The excited-state behavior of synthetic DNA dumbbells possessing stilbenedicarboxamide (Sa) linkers separated by short A-tracts or alternating A-T base-pair sequences has been investigated by means of fluorescence and transient absorption spectroscopy. Electronic excitation of the Sa chromophores results in conversion of a locally excited state to a charge-separated state in which one Sa is reduced and the other is oxidized. This symmetry-breaking process occurs exclusively via a multistep mechanism-hole injection followed by hole transport and hole trapping-even at short distances. Rate constants for charge separation are strongly distance-dependent at short distances but become less so at longer distances. Disruption of the A-tract by inversion of a single A-T base pair results in a pronounced decrease in both the rate constant and efficiency of charge separation. Hole trapping by Sa is highly reversible, resulting in rapid charge recombination that occurs via the reverse of the charge separation process: hole detrapping, hole transport, and charge return to regenerate the locally excited Sa singlet state. These results differ in several significant respects from those previously reported for guanine or stilbenediether as hole traps. Neither charge separation nor charge recombination occur via a single-step superexchange mechanism, and hole trapping is slower and detrapping faster when Sa serves as the electron donor. Both the occurrence of symmetry breaking and reversible hole trapping by a shallow trap in a DNA-based system are without precedent.

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.

Aqueous photochemistry of diazen-1-ium-1,2,2-triolate (Angeli's anion) and (Z)-1[N-(3-aminopropyl)-N-(3-aminopropyl)amino]diazen-1-ium-1,2-diolate (DPTA NONOate) has been investigated by laser kinetic spectroscopy. In neutral aqueous solutions, 266 nm photolysis of these diazeniumdiolates generates a unique spectrum of primary products including the ground-state triplet (3NO-) and singlet (1HNO) nitroxyl species and nitric oxide (NO*). Formation of these spectrophotometrically invisible products is revealed and quantitatively assayed by analyzing a complex set of their cross-reactions leading to the formation of colored intermediates, the N2O2*- radical and N3O3- anion. The experimental design employed takes advantage of the extremely slow spin-forbidden protic equilibration between 3NO- and 1HNO and the vast difference in their reactivity toward NO*. To account for the kinetic data, a novel combination reaction, 3NO-+1HNO, is introduced, and its rate constant of 6.6x10(9) M-1 s-1 is measured by competition with the reduction of methyl viologen by 3NO-. The latter reaction occurring with 2.1x10(9) M-1 s-1 rate constant and leading to the stable, colored methyl viologen radical cation is useful for detection of 3NO-. The distributions of the primary photolysis products (Angeli's anion: 22% 3NO-, 58% 1HNO, and 20% NO*; DPTA NONOate: 3% 3NO-, 12% 1HNO, and 85% NO*) show that neither diazeniumdiolate is a highly selective photochemical generator of nitroxyl species or nitric oxide, although the selectivity of DPTA NONOate for NO* generation is clearly greater.