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.     

ROLE OF COMPLEX FORMATION IN THE PHOTOSENSITIZED DEGRADATION OF DNA INDUCED BY N'-FORMYLKYNURENINE

Abstract— N'-Formylkynurenine derivatives efficiently bind to DNA or polynucleotides. Homopolynucleotides and DNA display marked differences in the binding process. Association constants are derived which indicate that the oxidized indole ring is more strongly bound to DNA than the unoxidized one. Irradiation of such complexes with wavelengths greater than 320 nm induces pyrimidine dimer formation as well as DNA chain breaks. Complex formation is shown to play an important role in these photosensitized reactions.
The photodynamic action of N'-formylkynurenine on DNA constituents is negligible at neutral pH but guanine and xanthine derivatives are sensitizable at higher pH. Thymine dimer splitting can occur in aggregated frozen aqueous solutions of N'-formylkynurenine and thymine dimer but this photosensitized splitting is negligible in liquid solutions at room temperature.     

TRANSIENT INTERMEDIATES IN INTRAMOLECULARLY PHOTOSENSITIZED PYRIMIDINE DIMER SPLITTING BY INDOLE DERIVATIVES

Abstract— Intramolecularly photosensitized pyrimidine dimer splitting can serve as a model for some aspects of the monomerization of dimers in the enzyme-substrate complex composed of a photolyase and UV-damaged DNA. We studied compounds in which a pyrimidine dimer was covalently linked either to indole or to 5-methoxyindole. Laser flash photolysis studies revealed that the normally observed photoejection of electrons from the indole or the 5-methoxyindole to solvent was diminished by an order of magnitude for indoles with dimer attached (dimer-indole and dimer-methoxyindole). The fluorescence lifetime of dimer-indole in aqueous methanol was 0.85 ns, whereas that of the corresponding indole without attached dimer (tryptophol) was 9.7 ns. Similar results were obtained for the dimer-methoxyindole (0.53 ns) and 5-methoxytryptophol (4.6 ns). The quantum yield of dimer splitting for the dimer-methoxyindole (φ₂₈₇K7 = 0.08) was only slightly greater than the value found earlier for the dimer bearing the unsubstituted indole (4>_2K7= 0.04). Transient absorption spectroscopy also revealed lower yields of indole radical cations following laser flash photolysis of dimer-indole compared to the indole without attached dimer. Dimer-methoxyindole behaved similarly. These results are interpreted in terms of an enhanced rate of radiationless relaxation of the indole and methoxyindole excited singlet states in dimer-indoles. The possible quenching of the indole and methoxyindole excited states via electron abstraction by the covalently linked dimer is discussed.     

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.     

PHOTOCHEMICAL REACTION BETWEEN PROTEIN AND NUCLEIC ACIDS: PHOTOADDITION OF TRYPTOPHAN TO PYRIMIDINE BASES*1

Abstract— The photochemical interactions between tryptophan and nucleic acid bases were studied. When aqueous solutions of tryptophan were irradiated (Λ > 260 nm) at neutral pH in the presence of each of the nucleic acid bases, pyrimidine bases but not purine bases were altered. Air was found to decrease the rate of reaction. Two classes of photoproducts were isolated by thin layer and ion-exchange chromatography and partially characterized. One was the dihydro-pyrimidine forms of the base (see Reeve and Hopkins, 1979) and the other consisted of tryptophan-pyrimidine photoadducts. Four tryptophan-uracil and two tryptophan-thymine adducts each with a 1:1 molecular stochiometry were found. Spectroscopic measurements and a positive reaction with Ehrlich's reagent indicate that the indole nucleus remained intact, but that the pyrimidine base was reduced at the 5, 6 double bond. The absence of a positive ninhydrin reaction and the effect of pH on the quantum yield of the photoadduct formation indicated that the ionized a-amino acid group of tryptophan was involved in photoadduct formation. Indole derivatives lacking an a-amino group were also found to form photoadducts with pyrimidine bases. The experimental results are consistent with a reaction mechanism involving tryptophan excitation to the first excited singlet state as the initial event. Radical scavenging experiments indicate that tryptophan free radicals, formed by electron dissociation from the excited state, react with the ground state pyrimidine.     

Excited State Photoreaction between the Indole Side Chain of Tryptophan and Halocompounds Generates New Fluorophores and Unique Modifications

Photoreaction of indole containing compounds with chloroform and other trichlorocompounds generates products with redshifted fluorescence. In proteins, this reaction can be used for the fluorescent detection of proteins. Little characterization of products generated through the photochemical reaction of indoles with halocompounds has been done, yet is fundamental for the development of other fluorophores, protein labeling agents, and bioactive indole derivatives. Here, we have characterized which isomers form in the photoreaction between tryptophan and chloroform using ¹H‐NMR of tryptophan and methylated derivatives to reveal that the two major products that are formed result from modification at the 4‐ and 6‐carbon positions of the indole ring. Reaction at position 6 generates 6‐formyl tryptophan and the reaction at position 4 generates an imine because the formyl derivative that is initially formed reacts further with the tryptophan amine group. The spectroscopic properties and product molecular weights of photoproducts formed from photoreaction of tryptophan with other trihalo and monohalocompounds are also determined. The indole ring of tryptophan can be modified with various additions from halocompounds, including the addition of labels to the indole ring via methylene groups. This opens possibilities for generating novel tryptophan based fluorophores and protein labeling strategies using this photochemistry.     

PHOTOSENSITIZATION OF PYRIMIDINE DIMER SPLITTING BY A COVALENTLY BOUND INDOLE

Abstract— Photosensitized pyrimidine dimer splitting characterizes the enzymatic process of DNA repair by the DNA photolyases. Possible pathways for the enzymatic reaction include photoinduced electron transfer to or from the dimer. To study the mechanistic photochemistry of splitting by a sensitizer representative of excited state electron donors, a compound in which an indole is covalently linked to a pyrimidine dimer has been synthesized. This compound allowed the quantitative measurement of the quantum efficiency of dimer splitting to be made without uncertainties resulting from lack of extensive preassociation of the unlinked dimer and sensitizer free in solution. Irradiation of the compound with light at wavelengths absorbed only by the indolyl group (approximately 280 nm) resulted in splitting of the attached dimer. The quantum yield of splitting of the linked system dissolved in N₂0-saturated aqueous solution was found to be 0.04 ± 0.01. The fluorescence typical of indoles was almost totally quenched by the attached dimer. A splitting mechanism in which an electron is efficiently transferred intramolecularly from photoexcited indole to ground state dimer has been formulated. The surprisingly low quantum yield of splitting has been attributed to inefficient splitting of the resulting dimer radical anion. Insights gained from this study have important mechanistic implications for the analogous reaction effected by the DNA photolyases.     

SOLVENT DEPENDENCE OF PYRIMIDINE DIMER SPLITTING IN A COVALENTLY LINKED DIMER-INDOLE SYSTEM

Cyclobutadipyrimidines (pyrimidine dimers) undergo splitting that is photosensitized by indole derivatives. We have prepared a compound in which a two-carbon linker connects a dimer to an indolyl group. Indolyl fluorescence quenching indicated that the two portions of the molecule interact in the excited state. Intramolecular photosensitization of dimer splitting was remarkably solvent dependent, ranging from phi spl = 0.06 in water to a high value of phi spl = 0.41 in the least polar solvent mixture examined, 1,4-dioxane-isopentane(5 : 95). A derivative with a 5-methoxy substituent on the indolyl ring behaved similarly. These results have been interpreted in terms of electron transfer from the excited indolyl group to the dimer, which would produce a charge-separated species. The dimer anion within such a species could split or undergo back electron transfer. The possibility that back electron transfer is in the Marcus inverted region can be used to rationalize the observed solvent dependence of splitting. In the inverted region, the high driving force of a charge recombination exceeds the reorganization energy of the solvent, which is less for solvents of low polarity than those of high polarity. If this theory is applicable to the hypothetical charge-separated species, a slower back electron transfer, and consequently higher splitting efficiencies, would be expected in solvents of lower polarity. Photolyases may have evolved in which a low polarity active site retards back transfer of an electron and thereby contributes to the efficiency of the enzymatic dimer splitting.     

DETECTION OF PYRIMIDINE DIMERS AND MONOADDUCTSINDUCED BY 7-METHYLPYRIDO(3,4-c) PSORALEN AND UVA IN CHINESE HAMSTER V79 CELLS BY ENZYMATIC CLEAVAGE AND HIGH-PRESSURE LIQUID CHROMATOGRAPHY

Abstract The photochemotherapeutically active psoralen derivative 7-methylpyrido(3,4-c) psoralen (MePyPs) has been recently shown to be able to photoinduce monoadducts of the C₄-cycloaddition type as well as pyrimidine dimers in DNA in vitro . In the present study, we report on the induction of these two types of photolesions in mammalian cells in culture. The MePyPs photocycloadducts were quantified in V79 Chinese hamster cells after treatment with MePyPs plus UVA following enzymatic hydrolysis of the DNA by DNase I, S1 nuclease and acidic phosphatase treatments. Concomitantly induced pyrimidine dimers were determined by two methods, high-pressure liquid chromatography and alkaline gel electrophoresis after dimer-specific endonucleolytic cleavage. The results show that, in Chinese hamster cells treated with MePyPs plus UVA, the yield of pyrimidine dimers is approximately 5-10% that of MePyPs-DNA photocycloadducts. Because psoralen monoadditions to DNA alone are generally not considered as being very phototoxic, a synergistic interaction of monoadditions with pyrimidine dimers may be expected to occur in order to explain the high photobiological effectiveness of this psoralen derivative.     

INHIBITION OF TRANSIENT GENE EXPRESSION IN CHINESE, HAMSTER OVARY CELLS BY TRIPLET-SENSITIZED UV-B IRRADIATION OF TRANSFECTED DNA

The biological effectiveness of thymine-thymine cyclobutane dimers specifically induced by photosensitized ultraviolet-B irradiation was analyzed by host-cell reactivation of triplet-sensitized, UV-B irradiated plasmid pRSV beta gal DNA transfected into normal and repair-deficient Chinese hamster ovary cells. For comparison, pRSV beta gal DNA was also UV-C irradiated and transfected into the same cell lines. Ultraviolet endonuclease-sensitive site induction was determined after UV-C irradiation or acetophenone-sensitized UV-B irradiation of plasmid pRSV beta gal DNA. These data were used to calculate the number of cyclobutane pyrimidine dimers required to inactivate expression of the lacZ reporter gene in each irradiation condition. Transfection with UV-C-irradiated plasmid DNA resulted in a significantly greater reduction of reporter gene expression than did transfection with acetophenone-sensitized UV-B-irradiated pRSV beta gal DNA at equivalent induction of enzyme-sensitive sites. Since only a fraction of the inhibition could be accounted for by noncyclobutane dimer photoproducts, these results suggest that cytosine-containing pyrimidine cyclobutane dimers may be more effective than thymine-thymine dimers in inhibiting transient gene expression as measured in such host-cell reactivation experiments in mammalian cells.     

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.     

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.     

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.     

SINGLET ENERGY TRANSFER BETWEEN AROMATIC AMINO ACIDS AND NUCLEIC ACID BASES. THEORETICAL CALCULATIONS

Abstract— Critical Forster distances for excitation energy transfer at the singlet level between the tyrosyl or tryptophyl residues of proteins and nucleic acid bases have been calculated. Efficient singlet energy transfer can be expected from tyrosine to nucleic acid bases both at room temperature (10 0 < 17 A) and at low temperature (20 < R₀ < 23 Å). At low temperature nucleic acid bases should be able to transfer their singlet excitation energy to the indole ring of tryptophan with a reasonable probability (9 < R₀ < 15 A).     

PHOTO-CIDNP DETECTION OF PYRIMIDINE DIMER RADICAL CATIONS IN ANTHRAQUINONESULFONATE- SENSITIZED SPLITTING

Anthraquinone-2-sulfonate (AQS) photosensitizes pyrimidine dimer splitting. Electron abstraction from the dimer is thought to induce dimer splitting, but direct evidence for the existence and intermediacy of dimer radical cations has been lacking. By employing photochemically induced dynamic nuclear polarization, we have found emission signals in the NMR spectra of dimers upon photolysis of dimers in the presence of anthraquinone-2-sulfonate. The two dimers employed were cis, syn-thymine dimer in which the N(1)-positions were linked by a three-carbon bridge and the N(3), N(3')-dimethyl derivative of that compound. The anthraquinone-2-sulfonate sensitized photochemically induced dynamic nuclear polarization spectrum of the methylated derivative exhibited an emission signal from the dimer-C(6) hydrogens. This result implied the existence of a dimer radical cation (mD+.) formed by electron abstraction by excited anthraquinone-2-sulfonate and nuclear spin sorting within a solvent caged radical ion pair [mD+. AQS-.]. Product pyrimidine photochemically induced dynamic nuclear polarization signals were also seen [enhanced absorption by C(6)-hydrogens and emission by C(5)-methyl groups]. Nuclear spin polarization in the product resulted from spin sorting in one or more of its precursors, including mD+. The results support the conclusion that dimer radical cations not only exist but are intermediates in the photosensitized splitting of pyrimidine dimers by anthraquinonesulfonate.     

DNA光复活作用机理的研究进展*

"环丁烷型嘧啶二聚体(Pyr< > Pyr) 是太阳光中紫外线造成DNA 损伤的主要光化学产物。DNA 光复活酶(或称光解酶) 能够利用可见光裂解二聚体的环丁烷环而修复DNA。本文对DNA 光复活过程中的光解酶对Pyr< > Pyr 的识别和光催化Pyr< > Pyr 裂解反应进行了综述, 介绍了DNA 光解酶的结构、DNA 的主要UV 光化学产物。较详尽地评述了国际上在光解酶催化二聚体裂解的途径以及模型研究方面的最新进展, 并预测了该领域的发展前景。     

Convenient synthesis of chiral tryptophan derivatives using Negishi cross-coupling

A facile synthetic procedure for chiral tryptophan derivatives using Negishi cross-coupling reaction of serine-derived iodoalanine with 3-haloindole is described. The best result was obtained when the reaction of N-tosyl-3-bromoindole with N-Cbz-iodoalanine methyl ester was carried out by the combination of Pd₂(dba)₃ and sterically hindered ferrocenyl ligand Q-PHOS. This reaction condition not only gave the desired tryptophan derivative as high as 76% yield, but also suppressed the formation of undesired products, the dehalogenated indole and the homodimer of indole, which were difficult to separate. This reaction was extended to the synthesis of various tryptophan derivatives having substituents on the benzene ring. The characteristic of this reaction is the practical biomimetic synthesis of chiral tryptophan derivatives in one-step.     

THERMAL REQUIREMENTS OF PHOTOSENSITIZED PYRIMIDINE DIMER SPLITTING

Abstract— A cis, syn -pyrimidine dimer (derived from thymine and orotate) covalently linked to 5-methoxyindole has been studied as a mechanistic model of photosensitized pyrimidine dimer splitting. In this dimer-indole, photoinitiated electron transfer to the dimer causes splitting in a manner that parallels the mechanism by which the DNA photolyases are thought to act. Dissolved in EPA (diethyl ether-isopentane-ethyl alcohol, 5: 5: 1, by vol) at room temperature, the dimer-indole exhibited indole fluorescence quenching and underwent splitting upon irradiation at 300 nm. In an EPA glass at 77 K, however, no splitting was detectable. To distinguish the effects of temperature and immobilization, photolysis experiments were performed on PMM [poly(methyl methacrylate)] films containing dimer-indole. In PMM at room temperature, dimer-indole underwent splitting when irradiated at 300 nm, which indicated that immobilization per se was not responsible for the failure of dimer-indole to split at low temperature. Furthermore, no splitting was observed when dimer-indole was irradiated in PMM at 77 K. These results imply that a step following photoinitiated, intramolecular electron transfer from indole to dimer has an insurmountable activation barrier at 77 K. The mechanistic implications for the photolyases are considered.     

STUDIES ON THE PHOTO DEGRADATION OF TRYPTOPHAN

Abstract— The photodegradation of tryptophan in aqueous solution increases steadily with decrease in wavelength over the U.V. range 370–230 mμ, but the action spectrum does not parallel the absorption spectrum over these wavelengths. Thus appreciable decomposition occurs at wavelengths greater than 300 mp, even though at the concentrations tested the indole ring does not absorb energy in this region, and a photosensitive auto-oxidation mechanism is suggested to account for this.
The quantum efficiency for the destruction tryptophan at 265 mμ is 0 01 at pH 4 , 5 and 7 , but increases to 0.02 at pH 12. For the acetyl, ester and amide derivatives it is 0.03 in neutral solution.
The yellowing of tryptophan solutions during irradiation is accompanied by the appearance of an absorption maximum at about 305 mμ in the differential absorption spectrum. The increase in optical density at this wavelength bears a direct relationship to the decrease in optical density at 280 mμ: the degree of yellowing is related to the degree of destruction of tryptophan. It is less pronounced in neutral solution than at higher or lower pH values.
The yellowing of N-substituted tryptophan derivatives at 265 mμ is appreciably less than that of tryptophan, whereas derivatives with a free amino group are indistinguishable from the unsubstituted amino acid in this respect.     

PHOTO-OXIDATION OF N'-FORMYLKYNURENINE AND TRYPTOPHAN PEPTIDES BY SUNLIGHT OR SIMULATED SUNLIGHT

Abstract— N'-Formylkynurenine, a photochemical breakdown product of tryptophan in proteins, was exposed to sunlight or simulated sunlight at neutral pH. N-Formylanthranilic acid and 4-hydroxyquinoline were identified in the reaction products. Neither has been previously described as a photo-oxidation product of tryptophan-containing compounds. They were not found after photo-oxidation of glycyltryptophan or tryptophylglycine, although the indole ring was broken in both compounds.