Time-resolved study of thymine dimer formation

The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (<1.4 x 10-3) or the triplet state reacts with unit efficiency in less than 200 ns to yield cyclobutane dimers.     

Analysis of fluoroquinolone-mediated photosensitization of 2'-deoxyguanosine, calf thymus and cellular DNA: determination of type-I, type-II and triplet-triplet energy transfer mechanism contribution

Fluoroquinolone (FQ) antibacterials are known to exhibit photosensitization properties leading to the formation of oxidative damage to DNA. In addition, photoexcited lomefloxacin (Lome) was recently shown to induce the formation of cyclobutane pyrimidine dimers via triplet-triplet energy transfer. The present study is aimed at gaining further insights into the photosensitization mechanisms of several FQ including enoxacin (Enox), Lome, norfloxacin (Norflo) and ofloxacin (Oflo). This was achieved by monitoring the formation of DNA base degradation products upon UVA-mediated photosensitization of 2'-deoxyguanosine, isolated and cellular DNA. Oflo and Norflo act mainly via a Type-II mechanism whereas Lome and, to a lesser extent, Enox behave more like Type-I photosensitizers. However, the extent of oxidative damage was found to be relatively low. In contrast, it was found that cyclobutane thymine dimers represent the major class of damage induced by Enox, Lome and Norflo within isolated and cellular DNA upon UVA irradiation. This striking observation confirms that FQ are able to promote efficient triplet energy transfer to DNA. The levels of photosensitized formation of strand breaks, alkali-labile sites and oxidative damage to cellular DNA, as measured by the comet assay, were confirmed to be rather low. Therefore, we propose that the phototoxic effects of FQ are mostly accounted for energy transfer mechanism rather than by Type-I or -II photosensitization processes.     

Contribution of Cytosine‐Containing Cyclobutane Dimers to DNA Damage Produced by Photosensitized Triplet–Triplet Energy Transfer

Mutagenic cyclobutane pyrimidine dimers (CPDs) can be induced in DNA through either direct excitation or photosensitized triplet–triplet energy transfer (TTET). In the latter pathway, thymines are expected to receive the excitation energy from the photosensitizer and react with adjacent pyrimidines. By using state‐of‐the art analytical tools, we provide herein additional information on the formation of cytosine‐containing CPDs. We thus determined the yield of all possible CPDs upon TTET in a series of natural DNAs with various base compositions. We show that the distribution of CPDs cannot be explained only by excitation of individual thymines. We propose that the mechanism for TTET involves at least dinucleotides as the minimal targets. The observation of the formation of cytosine–cytosine CPDs also suggests that additional pathways are involved in this photosensitized reaction.     

ULTRAVIOLET PHOTOCHEMISTRY OF THYMINE IN AQUEOUS SOLUTION

Abstract— We have investigated the ultraviolet photochemistry of thymine in aqueous solution. Four isomeric dimers are produced, and the yield of each has been measured as a function of thymine concentration, oxygen concentration, and temperature. At low thymine concentration, dimerization proceeds via the triplet state, while at high concentration it arises mainly from aggregates, probably from a singlet precursor. We have determined the ratios of rate constants for the triplet state mechanism and the quantum yield for dimerization from aggregates. The quantum yield for dimerization from the triplet state in thymine is smaller by a factor of about 10 than that in uracil, which in turn is smaller by another factor of 10 than that in orotic acid. It increases with the energy of the exciting radiation in a manner similar to the behaviour of uracil and orotic acid. On the other hand, dimer formation from aggregates is independent of photon energy. Dimerization from aggregates decreases with increasing temperature, while the total production of dimers from the triplet state is independent of temperature.     

CHLORANIL-PHOTOSENSITIZED MONOMERIZATION OF DIMETHYLTHYMINE CYCLOBUTANE DIMERS and EFFECT OF MAGNESIUM PERCHLORATE

The photosensitized monomerization of the cyclobutane dimers of 1,3-dimethylthymine by p-chloranil was investigated by means of steady-state irradiation and laser-flash photolysis. Quantum yields for the monomerization are 0.34 for the cis,syn dimer, 0.39 for the trans,syn dimer, and much less than 10(-2) for the cis,anti isomer. Formation of the chloranil anion radical associated with quenching of triplet chloranil by the dimers demonstrates that electron transfer from dimers to triplet chloranil occurs to initiate the monomerization. Kinetic analysis suggested that the syn-dimer cation radicals undergo the ring cleavage at greater than or equal to 10(9) s-1 before escaping from the solvent cage, while the reactivity of the anti-dimer cation radical is very low. The different reactivities of the syn and anti dimer cation radicals are discussed in terms of through-bond coupling between the n orbitals of N(1) and N(1') involving the cyclobutane-ring sigma orbitals. In the cases of the syn-dimers, the sensitizer-dimer ion-radical pairs undergo the rapid geminate recombination that works as a major energy dissipating channel responsible for the lower-than-unity quantum yields. It has been found that the presence of Mg(ClO4)2 at 0.1 M enhances approximately 1.5 times either the monomerization of the syn dimers or the formation of the chloranil anion radical. A laser-flash photolysis study shows that Mg2+ forms a complex with either the triplet or the anion radical of chloranil. The net salt effects are attributed to the retardation of the rapid geminate recombination by the participation of Mg2+ in the sensitizer-dimer ion-radical pairs.     

A triplet mechanism for the formation of cyclobutane pyrimidine dimers in UV-irradiated DNA

The reaction pathways for the photochemical formation of cyclobutane thymine dimers in DNA are explored using hybrid density functional theory techniques. It is concluded that the thymine-thymine [2 + 2] cycloaddition displays favorable energy barriers and reaction energies in both the triplet and the singlet excited states. The stepwise cycloaddition in the triplet excited state involves the initial formation of a diradical followed by ring closure via singlet-triplet interaction. The triplet mechanism is thus completely different from the concerted singlet state cycloaddition processes. The key geometric features and electron spin densities are also discussed. Bulk solvation has a major effect by reducing the barriers and increasing the diradical stabilities. The present results provide a rationale for the faster cycloreaction observed in the singlet excited states than in the triplet excited states.     

Triplet excited fluoroquinolones as mediators for thymine cyclobutane dimer formation in DNA

A series of fluoroquinolones (FQs), including enoxacin (ENX), pefloxacin (PFX), norfloxacin (NFX), its N(4')-acetyl derivative (ANFX), ofloxacin (OFX), and rufloxacin (RFX) have been investigated to determine their potential as DNA photosensitizers via thymine cyclobutane dimer (T<>T) formation in DNA. At fluoroquinolone concentrations and light doses insufficient to produce direct single strand breaks, ENX, PFX, and NFX were able to produce T<>T dimers in DNA, revealed by enzymatic treatment with T4 endonuclease V. By contrast, ANFX, OFX, and RFX were inefficient in this assay. The absolute values of the triplet energies of ENX, PFX, NFX, ANFX, OFX, and RFX were estimated by means of laser flash photolysis, using flurbiprofen, 4-biphenylcarboxylic acid, and naproxen as energy acceptors. They were found to be 273, 269, 269, 265, 262, and 253 kJ/mol, respectively. Other triplet excited state properties of the FQs, including quantum yields and lifetimes, were also studied. All the results indicate that the threshold ET value required for a given compound to become a potential DNA photosensitizer via T<>T formation is in the range defined by the triplet energies of NFX and ANFX (265-269 kJ/mol). This provides the basis for an alert rule: any chemical (drugs, cosmetics, pesticides, etc.) with higher ET has to be considered with regard to its potential photogenotoxicity.     

PHOTOSENSITIZED SPLITTING OF PYRIMIDINE DIMERS IN DNA BY INDOLE DERIVATIVES AND TRYPTOPHAN-CONTAINING PEPTIDES

Abstract —Indole derivatives, such as serotonin or the oligopeptide Lys-Trp-Lys, are able to photosensitize the splitting of thymine dimers in DNA. These indole derivatives have to be bound to DNA in order to efficiently photosensitize the splitting reaction. Serotonin may also induce the photosensitized formation of thymine-containing dimers in native DNA. In this case, an equilibrium is reached when 5 per cent of the total thymines are dimerized. In both cases (splitting and dimer formation), the formation of electron donor-acceptor complexes between either dimers or two adjacent thymine monomers, and excited indole rings, could be an intermediate step in the reactions. Thymine-dimer splitting would then result from an electron transfer reaction involving the indole ring as the electron donor. These results are discussed with respect to the mechanism of action of the photoreactivating enzyme.     

STRUCTURE-REACTIVITY RELATIONSHIPS IN REDOX-PHOTOSENSITIZED SPLITTING OF PYRIMIDINE DIMERS AND UNUSUAL ENHANCING EFFECT OF MOLECULAR OXYGEN *

Abstract Redox photosensitization using the phenanthrene-p-dicyanobenzene pair in acetonitrile has been applied to the respective four isomeric dimers of N.N′-dimethylthymine (DMT) and N,N′-dimethyluracil (DMU) as well as to several related cyclobutane compounds. The head-to-head (syn) dimers of both DMT and DMU can undergo photosensitized splitting in the following order of efficiency: cis, syn dimer of DMT > cis, syn dimer of DMU > trans, syn dimer of DMT. On the other hand, the head-to-tail (anti) dimers are totally unreactive and have higher oxidation potentials than the corresponding syn dimers. It is suggested that the key mechanistic pathway is the formation of π complexes between the dimers and the photo-generated cation radical of phenanthrene by way of which splitting of the cyclobutane ring catalytically occurs without the formation of the discrete cation radical of the dimers. Structure-reactivity relationships are interpreted in terms of through-bond interactions between the n orbitals of N(l) and N(l′) involving the C(6)-C(6′) bond, as well as in terms of steric repulsion. It was found that aeration of solution greatly enhances the quantum yields of photosensitized splitting; the limiting quantum yield for splitting of the cis, syn dimer of DMT is 100.     

Photosensitized Thymine Dimerization via Delocalized Triplet Excited States

A new mechanism of photosensitized formation of thymine (Thy) dimers is proposed, which involves generation of a delocalized triplet excited state as the key step. This is supported by chemical evidence obtained by combining one benzophenone and two Thy units with different degrees of freedom, whereby the photoreactivity is switched from a clean Paternò–Büchi reaction to a fully chemo‐, regio‐, and stereoselective [2+2] cycloaddition.     

ULTRAVIOLET LIGHT IRRADIATION OF DEFINED-SEQUENCE DNA UNDER CONDITIONS OF CHEMICAL PHOTOSENSITIZATION

Abstract— The formation of cyclobutane pyrimidine dimers and UV light-induced (6-4) products was examined under conditions of triplet state photosensitization. DNA fragments of defined sequence were irradiated with 313 nm light in the presence of either acetone qr silver ion. UV irradiation in the presence of both silver ion and acetone enhanced the formation of TT cyclobutane dimers, yet no (6-4) photoproducts were formed at appreciable levels. When photoproduct formation was also measured in pyrimidine dinucleotides, only cyclobutane dimers were formed when the dinucleotides were exposed to 313 nm light in the presence of photosensitizer. The relative distribution of each type of cyclobutane dimer formed was compared for DNA fragments that were irradiated with 254, 313, or 313 nm UV light in the presence of acetone. The dimer distribution for DNA irradiated with 254 and 313 nm UV light were very similar, whereas the distribution for DNA irradiated with 313 nm light in the presence of acetone favored TT dimers. Alkaline labile lesions at guanine sites were also seen when DNA was irradiated with 313 nm light in the presence of acetone.     

SIMULTANEOUS ESTABLISHMENT OF MONOCLONAL ANTIBODIES SPECIFIC FOR EITHER CYCLOBUTANE PYRIMIDINE DIMER OR (6-4)PHOTOPRODUCT FROM THE SAME MOUSE IMMUNIZED WITH ULTRAVIOLET-IRRADIATED DNA

Six new monoclonal antibodies (TDM-2, TDM-3, 64M-2, 64M-3, 64M-4 and 64M-5) specific for ultraviolet (UV) induced DNA damage have been established. In the antibody characterization experiments, two TDM antibodies were found to show a dose-dependent binding to UV-irradiated DNA (UV-DNA), decrease of binding to UV-DNA after cyclobutane pyrimidine dimer photoreactivation, binding to DNA containing cyclobutane thymine dimers, and unchanged binding to UV-DNA after photoisomerization of (6-4)photoproducts to Dewar photoproducts. These results indicated that the epitope of TDM monoclonal antibodies was the cyclobutane pyrimidine dimer in DNA. On the other hand, four 64M antibodies were found to show a dose-dependent binding to UV-DNA, unchanged binding to UV-DNA after cyclobutane pyrimidine dimer photoreactivation, undetectable binding to DNA containing thymine dimers, and decrease of binding to UV-DNA after photoisomerization of (6-4)photoproducts. These results indicated that the epitope of 64M antibodies was the (6-4)photoproduct in DNA. This is the first report of the simultaneous establishment of monoclonal antibodies against the two different types of photolesions from the same mouse. By using these monoclonal antibodies, we have succeeded in measuring both cyclobutane pyrimidine dimers and (6-4)photoproducts in the DNA from human primary cells irradiated with physiological UV doses.     

PHOTOCHEMICAL REACTIONS OF AROMATIC KETONES WITH NUCLEIC ACIDS AND THEIR COMPONENTS I—. PURINE AND PYRIMIDINE BASES AND NUCLEOSIDES*.

Abstract— The photochemical reactions of benzophenone and acetophenone with purine and pyrimidine derivatives in aqueous solutions have been investigated by flash photolysis and steady-state experiments. Upon excitation of these two ketones in aqueous solutions, two transient species are observed: molecules in their triplet state and ketyl radicals. The triplet state lifetimes are 65 μsec for benzophenone and 125 μsec for acetophenone. The ketyl radicals disappear by a second order reaction, controlled by diffusion. In the presence of pyrimidine derivatives, the triplet state is quenched and the ketyl radical concentration is decreased without any change in its kinetics of disappearance. Ketone molecules in their triplet state react with purine derivatives leading to an increase in the yield of ketyl radicals due to H-atom abstraction from the purines. Steady-state experiments show that benzophenone and acetophenone irradiated in aqueous solution at wavelengths longer than 290 nm undergo photochemical reactions. The rate of these photochemical reactions is increased in the presence of pyrimidine derivatives and even more in the presence of purine derivatives. Following energy transfer from the triplet state of benzophenone to diketopyrimidines, cyclobutane dimers are formed. The energy transfer rate decreases in the order orotic acid > thymine > uracil. Benzophenone molecules in their triplet state can also react chemically with pyrimidine derivatives to give addition photoproducts. All these results are discussed with respect to photosensitized reactions in nucleic acids involving ketones as sensitizers.     

Elucidation of the Dexter‐Type Energy Transfer in DNA by Thymine–Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides

C‐nucleosides of 4‐methylbenzophenone, 4‐methoxybenzophenone, and 2′‐methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A‐T base pairs was observed that agrees with a Dexter‐type triplet–triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.     

Ring opening of the cyclobutane in a thymine dimer radical anion

The reactions of hydrated electrons (e(aq) (-)) with thymine dimer 2 and thymidine have been investigated by radiolytic methods coupled with product studies, and addressed computationally by means of BB1K-HMDFT calculations. Pulse radiolysis revealed that one-electron reduction of the thymine dimer 2 affords the radical anion of thymidine (5) with t(1/2)<35 ns. Indeed, the theoretical study suggests that radical anion 3, in which the spin density and charge distribution are located in both thymine rings, undergoes a fast partially ionic splitting of the cyclobutane with a half-life of a few ps. This model fits with the in vivo observation of thymine dimer repair in DNA by photolyase. gamma-Radiolysis of thymine dimer 2 demonstrates that the one-electron reduction and the subsequent cleavage of the cyclobutane ring does not proceed by means of a radical chain mechanism, that is, in this model reaction the T(-)* is unable to transfer an electron to the thymine dimer 2.     

Do Photolyases Need To Provide Considerable Activation Energy for the Splitting of Cyclobutane Pyrimidine Dimer Radical Anions?

cis-syn Cyclobutane pyrimidine dimers, major UV-induced DNA lesions, are efficiently repaired by DNA photolyases. The key step of the repair reaction is a light-driven electron transfer from the FADH(-) cofactor to the dimer; the resulting radical anion splits spontaneously. Whether the splitting reaction requires considerable activation energy is still under dispute. Recent reports show that the splitting reaction of a dimer radical anion has a significant activation barrier (0.45 eV), and so photolyases have to provide considerable energy. However, these results contradict observations that cis-syn dimer radical anions split into monomers at -196 degrees C, and that the full process of DNA photoreactivation was fast (1.5-2 ns). To investigate the activation energies of dimer radical anions, three model compounds 1-3 were prepared. These include a covalently linked cyclobutane thymine dimer and a tryptophan residue (1) or a flavin unit (3), and the covalently linked uracil dimer and tryptophan (2). Their properties of photosensitised splitting of the dimer units by tryptophan or flavin unit were investigated over a large temperature range, -196 to 70 degrees C. The activation energies were obtained from the temperature dependency of splitting reactions for 1 and 2, 1.9 kJ mol(-1) and 0.9 kJ mol(-1) for the thymine and uracil dimer radical anions, respectively. These values are much lower than that obtained for E. coli photolyase (0.45 eV), and are surmountable at -196 degrees C. The activation energies provide support for previous observations that repair efficiencies for uracil dimers are higher than thymine dimers, both in enzymatic and model systems. The mechanisms of highly efficient enzymatic DNA repair are discussed.     

PHOTOCHEMICAL AND FREE RADICAL INITIATED REACTIONS OF1,3-DIMETHYLTHYMINE WITH ISOPROPANOL

Abstract— A photochemically induced reaction of 1 ,3-dimethylthymine (DMT) with isopropanol leads to the formation of four alcohol adducts. The products have been identified as the cis and trans isomers of 5 ,6-dihydro-1,3-dimethyll-6-(2-hydroxy-2-propyl) thymine (I and II), 2.4-diaza-8-hydroxy-2.4,6.8-tetramethylbicyclo[4.2.0]octan-1,3-dione (III), and 5 ,6-dihydro-1,3-dimethyl-6-(2-oxo-l-propyl)-thymine (IV). An acetone photosensitized reaction of DMT with isopropanol gives the same products in a similar relative yield distribution. In both of these reactions, cyclobutane dimers of DMT are produced as well. Free radical reactions of 2-hydroxyisopropyl radicals with DMT, initiated by decomposition of di- t -butyl peroxide, leads to formation of only one of the cis and trans isomers described above. along with 1 ,3-dimethyl-5-(2-hydroxy-2-methyl-1-propyl)uracil (V).     

Photochemical reactions of aromatic ketones with nucleic acids and their components. 3. Chain breakage and thymine dimerization in benzophenone photosensitized DNA

Abstract— Excitation of benzophenone in the presence of calf thymus and E. coli DNA leads to photosensitized damages to the macromolecule. Two main reactions are observed: thymine dimerization and chain break formation. Benzophenone photosensitized chain breaks are also observed in polyadenylic acid. The melting temperature of DNA decreases with the duration of irradiation. Under our experimental conditions, the ratio of the yields of dimers and single-chain breaks produced in DNA is about 1. Photosensitized damage to deoxyribose residues leading to chain breakage is shown to be similar to that produced by X or γ ray irradiation. The oxygen effect upon chain break production is studied and discussed in relation with its effect upon intermediate species. Thymine dimers are formed following energy transfer from benzophenone in its triplet state. In previous flash-photolysis studies we showed that benzophenone in its triplet state reacts with water molecules to give ketyl and OH radicals. Ketyl radicals are not involved in reactions with DNA. It is proposed that OH radicals produced in the above reaction are responsible for the production of single-chain breaks by attack on the deoxyribose residues.     

Triplet-Induced Lesion Formation at CpT and TpC Sites in DNA

UV irradiation induces DNA lesions particularly at dipyrimidine sites. Using time-resolved UV pump (250 nm) and mid-IR probe spectroscopy the triplet pathway of cyclobutane pyrimidine dimer (CPD) formation within TpC and CpT sequences was studied. The triplet state is initially localized at the thymine base but decays with 30 ns under formation of a biradical state extending over both bases of the dipyrimidine. Subsequently this state either decays back to the electronic ground state on the 100 ns time scale or forms a cyclobutane pyrimidine dimer lesion (CPD). Stationary IR spectroscopy and triplet sensitization via 2′-methoxyacetophenone (2-M) in the UVA range shows that the lesions are formed with an efficiency of approximately 1.5 %. Deamination converts the cytosine moiety of the CPD lesions on the time scale of 10 hours into uracil which gives CPD(UpT) and CPD(TpU) lesions in which the coding potential of the initial cytosine base is vanished.     

酶蛋白直接修复嘧啶二聚体机理的模型研究

去辅基的DNA光解酶在280 nm光辐照下, 能高效修复底物嘧啶二聚体(Φ＝0.56). 为了模拟酶蛋白的这一修复过程, 合成了色氨酸(Trp)和/或酪氨酸(Tyr)与胸腺嘧啶二聚体(D)共价连接的化合物, 作为酶-底物复合物的模型, 研究了它们在295 nm光照射下氨基酸残基光敏化二聚体裂解的性质, 测定了二聚体裂解量子产率(Φ), 获得一些新的结果并对其进行了分析.