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.     

PHOTOCHEMISTRY OF URACIL. INTERSYSTEM CROSSING AND DIMERIZATION IN AQUEOUS SOLUTION

Abstract— Ultraviolet irradiation of ¹⁴C-uracil in aqueous solution results in the formation of hydrate and dimer photoproducts. The rate of dimerization increases with increasing uracil concentration, and decreases with increasing concentration of oxygen in solution. The kinetics are in agreement with a model previously proposed to account for the reactions, in which dimerization occurs by a reaction involving the triplet state of uracil, but hydration occurs from an excited singlet state. Oxygen reduces dimer formation by quenching the triplet. The quantum yield for intersystem crossing (ISC) to the triplet depends on the irradiation wavelength, increasing from 0.0014 at 280 nm to 0.016 at 230 nm. The ratio of rate constants for reaction of the triplet with oxygen and for dimerization is 1.1; the ratio of rate constants for triplet decay and for dimerization is 5.9 × 10^-5 M. The increase in ISC with photon energy suggests that ISC is favoured from excited vibrational levels. The quantum yield for hydration is about 0.002 at pH 4.5 for all wavelengths, but increases as the pH is decreased.     

DEPENDENCE OF INTERSYSTEM CROSSING ON EXCITATION ENERGY IN OROTIC ACID

Abstract— Photochemical dimerization in orotic acid in aqueous solution has been studied as a function of oxygen concentration, orotic acid concentration and the wavelength of irradiation under two pH conditions. One dimer was detected. Analysis of the data enabled us to obtain a minimum estimate of the efficiency of intersystem crossing, ø_ISC. from singlet to triplet levels. This efficiency increases by a factor of two with increasing energy of excitation over the wavelength range 240–302 nm, and by a similar factor between pH 3 and pH 1. The maximum value obtained was 0.15 for irradiation at 240 nm at pH 1. The relation between quantum yield and ø_ISC is discussed and possible mechanisms to explain this variation of ø_ISC with energy are proposed.     

ULTRAVIOLET-INDUCED REACTIONS OF THYMINE AND URACIL IN THE PRESENCE OF CYSTEINE

Abstract —Ultraviolet-radiation photolysis of thymine in the presence of cysteine gives rise to four isomeric dimers, dihydrothymine, and at least five cysteine addition products. Similar reactions occur for uracil but the products have not all been characterized in detail. The addition reactions arise from the triplet state of the pyrimidine. The initial step is production of a hydropyrimidine radical, which then reacts with cysteine to give the addition products. The triplet is quenched by cysteine with a rate constant of about 2 times 10⁸ M^-1 s^-1 for thymine and 2–9 times 10⁸ for uracil. The total yield of products gives a lower-limit estimate of the triplet yield and hence of the intersystem-crossing efficiency. These studies, combined with earlier determinations of dimer yields, show that 93% of the thymine triplets which interact with another thymine molecule are quenched without forming stable dimers. For uracil, the corresponding figure is 75%.     

THE IMPORTANCE OF COMPLEX FORMATION IN THE SENSITIZATION OF Eu(III) EMISSION BY OROTIC ACID

Abstract— Orotic acid (I) and 3-methylorotic acid (II) are the only orotic acid derivitives which efficiently sensitire emission from Eu(III) in D₂O solution. This emission is only weakly sensitized by I-methylorotic acid (III), 1,3-dimethylorotic acid (IV), the methyl and isopropyl esters of orotic acid (V) 6-acetyluracil (VI) and not sensitized at all by the bases uracil. thymine and their nucleosides. Substituent groups on either the carboxyl group or the N-l position of the ring thus prevent efficient energy transfer from the excited orotic acid to Eu(III). These structural requirements for efficient energy transfer are the same as the structural requirements for formation of a stable. bidentate. ground state complex between Eu(III) and orotic acid (VII) (Sarpotdar and Burr, 1978).
We, therefore, propose that sensitization of Eu(III) emission by orotic acid at pH 5 is an example of energy transfer within the bidentate complex of Eu(III) and orotic acid. We also propose that the complexed orotic acid is itself excited by eollisional energy transfer from free triplet excited orotic acid (since the concentration of complex measured to be present. 5–7%, is too low to account for the efficiency of the sensitization). We also propose that emission from the excited complexed Eu(III) can be either from the complexed ion or from free Eu(III)* resulting from dissociation of the complex during the lifetime of the excited ion.
The efficiency of Eu(III) sensitized emission is shown to depend on the concentrations of Eu(III). orotic acid and pH with relationships kinetically consistent with the above hypothesis.     

KINETICS OF THE ULTRAVIOLET-INDUCED DIMERIZATION OF THYMINE IN FROZEN SOLUTIONS*

Abstract— It is known that thymine forms dimers when aqueous solutions are irradiated with ultraviolet light while in the frozen state, but does not form dimers when solutions are irradiated in the liquid state. The eutectic point of aqueous thymine solutions was found to be. —0.02°C. Since the irradiation of frozen solutions is always carried out at lower temperatures, the dimerization must be occurring in the solid state. Activation energies and quantum yields for dimer formation were determined by irradiating 1–mm layers of thymine solution at —5°C to — 707deg;C for various lengths of time. As expected, the activation energy was zero. After measuring the amount of radiation scattered by samples of ice, the extreme values for the quantum yield were found to be 0.73 and 4.08. The lower limit assumed that all the scattered light was absorbed by thymine; the upper limit assumed that none was absorbed. Since the theoretical maximum quantum yield is 2, the best estimate of the quantum yield is considered to be between 1 and 2.     

STUDIES ON THYMINE AND URACIL TRIPLET EXCITED STATE IN ACETONITRILE AND WATER

Abstract— Thymine and uracil triplet-triplet absorption spectra and triplet excited state lifetimes have been observed in acetonitrile and water by nanosecond laser flash spectroscopy. A study of triplet energy transfer from these pyrimidines to retino! has also allowed an estimation of the triplet extinction coefficient ε_TT of thymine and uracil. These ε_TT were then used to determine the triplet quantum yields Ø_T of both pyrimidines in acetonitrile and water.     

FORMATION OF CYCLOBUTANE THYMINE DIMERS PHOTOSENSITIZED BY PYRIDOPSORALENS: A TRIPLET-TRIPLET ENERGY TRANSFER MECHANISM

The 365 nm irradiation of thymine thin films in the presence of pyridopsoralens is shown to induce the formation of cyclobutane thymine dimers, in contrast to other compounds such as 8- and 5-methoxypsoralen. In order to elucidate the mechanism of such a photosensitized reaction, we have determined the energy of the lowest triplet state (T1) of these compounds, using phosphorescence spectroscopy and CNDO/S quantum chemistry calculations. The T1 energy values were found to be significantly higher for pyridopsoralens--up to 0.3 eV--than for 8- and 5-methoxypsoralen (approximately 2.8 eV), which are not able to photoinduce cyclobutane thymine dimers. The determination of the relative efficiency of cyclobutane thymine dimer formation was performed using chromatographic analysis. A good correlation was found between the energy of the T1 state of the psoralen derivatives and the related cyclobutane thymine dimer formation. Moreover, the photosensitized cyclobutane thymine dimer formation appeared to be temperature-dependent. Our results are consistent with a mechanism involving a triplet energy transfer from the pyridopsoralen to thymine.     

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.     

SINGLET AND TRIPLET ENERGY TRANSFER IN α-DIKETONE DERIVATIVES OF URACIL and THYMINE

Irradiation of 1-(3,4-dioxopentyl)uracil (UPD) and 1-(3.4-dioxopentyl)thymine (TPD) in acetonitrile solution at 25°C, at the wavelength (280 nm) where only the pyrimidine absorbs the light, sensitizes both fluorescence and phosphorescence of the diketone chromophore in the sidechain. From comparison of the intensity in the corrected excitation spectra with the absorption spectra in acetonitrile solution, it was estimated that the yield of singlet energy transfer in UPD was 0.17 and in TPD was 0.44. It was also observed that the ratio of phosphorescence to fluorescence was greater in the sensitized emission than in that from direct excitation of the diketone chromophore. The yield of triplet energy transfer thus measured corresponds to minimum values for the yields of intersystem crossing from singlet excited state to triplet excited state of 0.075 in the uracil chromophore of UPD and of 0.14 in the thymine chromophore of TPD. These are in agreement with other recent values for these quantities. The value of this type of system as an intramolecular triplet counter is discussed.     

THE INACTIVATION OF RIBONUCLEIC ACID FROM TOBACCO MOSAIC VIRUS BY ULTRAVIOLET RADIATION AT DIFFERENT WAVE-LENGTHS

Abstract— Although both thymine and uracil can form similar dimers, exposing RNA of tobacco mosaic virus lo ultraviolet radiation of different wavelengths did not reproduce any of the phenomena that implicate dimerization of thymine residues as a major cause of the inactivation of a bacterial transforming DNA. If uracil residues dimerize at all in the irradiated RNA, such dimerization either does not affect infectivity or is not photoreversible in the same way as dirnerization of thymine residues in DNA. Unlike inactivation of the transforming DNA, inactivation of the virus-RNA seems to be a function of the amount of absorbed radiation energy, irrespective of the wave-length within the range 285 to 230 mμ and irrespective of a change in the wave-length during irradiation.     

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.     

THYMINE HYDRATE FORMED BY ULTRAVIOLET AND GAMMA IRRADIATION OF AQUEOUS SOLUTIONS

Abstract— Evidence is presented for the formation of a thymine hydrate upon ultraviolet (UV) or gamma irradiation of aqueous solutions. The UV quantum efficiency exhibits a dependence on pH similar to that shown for uracil hydration, but the yield is three orders of magnitude smaller than for uracil. Hydration is not affected by wavelength, oxygen, or concentration of thymine. The reversal rate of the photohydrate to thymine is similar to the reversal rates of both isomers of the thymine hydrate formed by γ radiolysis, and depends on pH in the same way as the rate for the uracil photohydrate. The photohydrate of thymine is chromatographically identical to the cis isomer of 6-hydroxy-5, 6-dihydrothymine.     

THE MECHANISM OF PHOTOCHEMICAL ADDITION OF CYSTEINE TO URACIL AND FORMATION OF DIHYDROURACIL

Abstract— A proposed mechanism for the photochemical addition of L -cysteine to uracil with the concurrent formation of dihydrouracil is shown to proceed through the triplet excited state of uracil which can abstract hydrogen atoms from cysteine to form dihydrouracil. This triplet state is the same one as that leading to photodimerization. The thiyl radicals generated add to ground state uracil molecules. The data permit a re-evaluation of the quantum yield for intersystem crossing of uracil in water which shows dimerization in aqueous solution to have a maximum efficiency of 56 per cent. The formation of the cross-adduct and dihydrouracil may be sensitized but the efficiency of the reaction is related to the ability of the sensitizer to be photoreduced and not to its triplet energy.     

TRANSIENTS OF URACIL and THYMINE DERIVATIVES and THE QUANTUM YIELDS OF ELECTRON EJECTION and INTERSYSTEM CROSSING UPON 20 ns PHOTOLYSIS AT 248 nm

Transients of uracil and a series of 17 correlated pyrimidines, e.g. methylated bases, nucleosides, nucleotides, and polyuridylic acid [poly(U)] were studied after 248 nm excitation by 20 ns laser pulses. The transient absorption spectra in aqueous solution at room temperature reveal the triplet state and the hydrated electron (e-aq), while the corresponding radical cation could not be observed at pH 6-7. Fast loss of the chromophore in the 260-290 nm range within 0.1 microsecond was observed in aqueous solution in some cases [e.g. poly(U), 5'-UMP, uridine, uracil] and in others (thymine, thymidine) virtually not. This photobleaching is assigned to formation of the photohydrate. The concentration of e-aq shows a quadratic dependence on the laser pulse intensity (IL) in the range (0.2-2) x 10(7) W cm-2 and the quantum yield of electron ejection (phi c-) thus depends linearly on IL. This behaviour, suggesting that the photoionization involves a two-step absorption process, was found for poly(U) and all pyrimidine monomers examined. At a constant IL value of 2 x 10(7) W cm-2, phi c- ranges from 3 x 10(-3) for 1,3-dimethylthymine to 4 x 10(-2) for poly(U). The triplet state shows a much larger transient absorbance (delta A, typically in a broad range, e.g. 290-500 nm) than that of the neutral radical resulting from the radical cation. The triplet state in organic solvents (acetonitrile and ethanol) shows generally a significantly larger delta A value than in aqueous solution. The estimated quantum yields of intersystem crossing at room temperature are compared with those of phosphorescence at -196 degrees C.     

Structure and dynamics of poly(T) single-strand DNA: implications toward CPD formation

The formation of cyclobutane pyrimidine dimers between adjacent thymines by UV radiation is thought to be the first event in a cascade leading to skin cancer. Recent studies showed that thymine dimers are fully formed within 1 ps of UV irradiation, suggesting that the conformation at the moment of excitation is the determining factor in whether a given base pair dimerizes. MD simulations on the 50 ns time scale are used to study the populations of reactive conformers that exist at any given time in T18 single-strand DNA. Trajectory analysis shows that only a small percentage of the conformations fulfill distance and dihedral requirements for thymine dimerization, in line with the experimentally observed quantum yield of 3%. Plots of the pairwise interactions in the structures predict hot spots of DNA damage where dimerization in the ssT18 is predicted to be most favored. The importance of hairpin formation by intra-strand base pairing for distinguishing reactive and unreactive base pairs is discussed in detail. The data presented thus explain the structural origin of the results from the ultrafast studies of thymine dimer formation.     

PHOTOPHYSICAL PROPERTIES OF NUCLEIC ACID COMPONENTS—1. THE PYRIMIDINES: THYMINE, URACIL, N, N-DIMETHYL DERIVATIVES AND THYMIDINE

Abstract— Low-temperature (and some room temperature) absorption and emission, fluorescence and phosphorescence, data including quantum yields and lifetimes have been obtained from the title pyrimidine bases as a function of the nature of the solvent environment. Modest vibrational resolution has been observed for the first time in the absorption spectra, particularly for thymine and uracil. The excitation spectra also show structure. The quantum yields of fluorescence (φ_F) and phosphorescence are independent of the excitation wavelength. Thymine, thymidine and uracil have profoundly different photophysical properties in polar-aprotic vs polar-protic solvents. The N, N-dimethyl substitution of thymine and uracil produces photophysical changes comparable to the solvent change for the unsubsti-tuted bases. The species involved in the emission processes is the keto (lactam) form. It is probable that ^1,3(n,π*) state(s) has(have) changed order relative to a lowest ¹(π,π*) state as a consequence of both the solvent change and N, N-dimethyl substitution. The lowest triplet state is assigned as ³(n π*). We propose that an important factor contributing to the previously reported excitation wavelength dependence of φ_F and φ_T1 (φ_isc) for nucleic-acid components is the equilibrium coexistence of H-bonded and non-H-bonded forms each having different photophysical properties. Consideration is given of the impact of the significantly different photophysical properties of nucleic-acid bases as a function of the nature of the solvent upon the photochemical properties.     

2+2] Photocycloaddition reaction dynamics of triplet pyrimidines

Taking the 266 nm excited pyrimidine (uracil or thymine) with cyclopentene as model reaction systems, we have examined the photoproduct formation dynamics from the [2 + 2] photocycloaddition reactions of triplet pyrimidines in solution and provided mechanistic insights into this important DNA photodamage reaction. By combining two compliment methods of nanosecond time-resolved transient IR and UV-vis laser flash-photolysis spectroscopy, the photoproduct formation dynamics as well as the triplet quenching kinetics are measured. Characteristic IR absorption bands due to photoproduct formation have been observed and product quantum yields are determined to be ～0.91% for uracil and ～0.41% for thymine. Compared to the measured large quenching rate constants of triplet uracil (1.5 × 10(9) M(-1)s(-1)) or thymine (0.6 × 10(9) M(-1)s(-1)) by cyclopentene, the inefficiency in formation of photoproducts indicates competitive physical quenching processes may exist on the route leading to photoproducts, resulting in very small product yields eventually. Such an energy wasting process is found to be resulted from T(1)/S(0) surface crossings by the hybrid density functional calculations, which compliments the experiments and reveals the reaction mechanism.     

Depopulation of Highly Excited Singlet States of DNA Model Compounds: Quantum Yields of 193 and 245 nm Photoproducts of Pyrimidine Monomers and Dinucleoside Monophosphates

Abstract— Formation of uracil and orotic acid photodimers, uridine and 5'-UMP photohydrates, TpT photodimers and (6-4)photoproducts, dCpT photohydrates and (6-4)photo-products and UpU, CpC and CpU photohydrates were studied in neutral deoxygenated aqueous solution at room temperature upon irradiation at either 193 or 254 nm. The photoproducts were identified and quantified and the contribution from photoionization to substrate decomposition, using λ_irr= 193 nm, was separated. The ratio of the quantum yields of respective stable products,η=φ¹⁹³/φ²⁵⁴ is indicative of the yield of internal conversion from the second to the first excited singlet state, S₂→ S₁. For the observed photodimers η decreases from 0.94 for uracil to 0.7 for TpT and further to 0.55 for orotic acid. For the (6-4)photoproducts of TpT and dCpT T| = 0.5-0.8 and for the photohydrates in the cases of UpU, CpC, CpU and dCpT TJ ranges from 0.55 to 1.     

ALTERATIONS IN DNA IRRADIATED WITH ULTRAVIOLET RADIATION—I. THE FORMATION PROCESS OF CYCLOBUTYLPYRIMIDINE DIMERS: CROSS SECTIONS, ACTION SPECTRA and QUANTUM YIELDS

Abstract— We have determined the dimerization and monomerization cross sections of the Thy < > Thy (cyclobutyl dimer of thymine and thymine) and the Cyt < > Thy (cyclobutyl dimer of cytosine and thymine) dimers in Escherichia coti [³H]-DNA ([³H]-thymine labeled DNA) at five wavelengths in the range 240–300 nm. It may be concluded from the dimerization action spectra for the two dimers that the excitation of Thy (thymine) is mainly responsible for the photochemical dimerization reaction in both cases. The calculated quantum yields of dimerization and monomerization are also presented in this paper and several questions, raised by the results obtained at 300 nm, are discussed.