PHOTO-CIDNP STUDY OF PYRIMIDINE DIMER SPLITTING II: REACTIONS INVOLVING PYRIMIDINE RADICAL ANION INTERMEDIATES

A series of photo-CIDNP (chemically induced dynamic nuclear polarization) experiments were performed on pyrimidine monomers and dimers, using the electron-donor Nα-acetyltryptophan (AcTrp) as a photosensitizer. The CIDNP spectra give evidence for the existence of both the dimer radical anion, which is formed by electron transfer from the excited AcTrp* to the dimer, and its dissociation product, the monomer radical anion. The AcTrp spectra are completely different from those obtained with an oxidizing sensitizer like anthraquinone-2-sulfonate, because of different unpaired electron spin density distributions in pyrimidine radical anion and cation. In the spectra of the anti (1,3-dimethyluracil) dimers, polarization is detected that originates from a spin-sorting process in the dimer radical pair, pointing to a relatively long lifetime of the dimer radical anions involved. Although the dimer radical anions of the 1,1′-trimethylene-bridged pyrimidines may have a relatively long lifetime as well, their protons have only very weak hyperfine interaction, which explains why no polarization originating from the dimer radical pair is detected. In the spectra of the bridged pyrimidines, polarized dimer protons are observed as a result of spin sorting in the monomer radical pair, from which it follows that the dissociation of dimer radical anion into monomer radical anion is reversible. A study of CIDNP intensities as a function of pH shows that a pH between 3 and 4 is optimal for observing monomer polarization that originates from spin-sorting in the monomer radical pair. At higher pH the geminate recombination polarization is partly cancelled by escape polarization arising in the same product.     

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.     

DETECTION OF RADICAL ION INTERMEDIATES IN FLAVIN-PHOTOSENSITIZED PYRIMIDINE DIMER SPLITTING

Photosensitized splitting of cis-syn- and trans-syn-l,3-dimethyluracil dimers by 2′,3′,4′,5′-tetraacetylri-boflavin in acetonitrile containing a trace of perchloric acid was studied by laser flash photolysis. Protonation of the flavin prior to excitation resulted in excited singlet and triplet states that abstracted an electron from the dimers and yielded the protonated flavin radical (F1H₂′⁺), which was detected by absorption spectroscopy. Electron abstraction by the excited singlet state predominated over abstraction by the triplet state. Approximately one-third to one-half of the excited states quenched by the trans-syn dimer yielded F1H₂⁺, the balance presumably undergoing back electron transfer within the geminate radical ion pair generated by the initial electron transfer. A covalently linked dimer-flavin exhibited very inefficient flavin radical ion formation, consistent with the known low efficiency of dimer splitting in this system. These results constitute the first identification of a flavin radical ion intermediate in photosensitized pyrimidine dimer splitting.     

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.     

FORMATION OF 5-HYDROXYMETHYLCYTOSINE-CONTAINING PYRIMIDINE DIMERS IN UV-IRRADIATED BACTERIOPHAGE T4 DNA

Cyclobutyl pyrimidine dimers composed of 5-hydroxymethylcytosine and thymine (5HMC>T dimer for a mutant of T4 ( denV ) that is unable to excise pyrimidine dimers from its DNA. The ability of 5HMC to form dimers suggests that other modified pyrimidines such as 5-methylcytosine can participate in dimer formation, particularly at the UV wavelengths in sunlight likely to be responsible for the induction of skin cancer.     

Model Studies of DNA Photorepair: Enthalpy of Cleavage of a Pyrimidine Dimer Measured by Photothermal Beam Deflection Calorimetry

Abstract— The enzyme DNA photolyase mediates the repair of pyrimidine dimers. This repair step, a net retro [²+2] reaction, proceeds through either the cation or anion radical of the pyrimidine dimer. In order to understand how electron transfer makes the repair process possible, its energetics have been examined by photothermal beam deflection calorimetry, fluorescence quenching and quantum yield studies. The enthalpy for the cleavage reaction of cis-syn 1,3-dimethylthymine dimer itself was found to be -19 kcal/mol. In addition, from the redox potentials, the enthalpies for the cleavage reactions of the dimer cation radical and the anion radical were determined to be -19 kcal/mol and -28 kcal/mol, respectively.     

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.     

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.     

REMOVAL OF THYMINE-CONTAINING PYRIMIDINE DIMERS FROM UV LIGHT-IRRADIATED DNA BY S1 ENDONUCLEASE

Abstract— S₁ endonuclease was shown to remove thymine-containing pyrimidine dimers from UV-irradiated human DNA, although efficient removal could be demonstated only by using long digestion times, relatively high enzyme concentrations, and irradiation sufficient to yield dimer substitutions in DNA of 1 per 1W300 (dimers/base pair). Neutral and alkaline sucrose gradient analysis of strand break induction by S, of UV-irradiated DNA suggests that recognition of the dimer by S, is the limiting factor in its removal and dimer removal usually results from attack on the dimer containing DNA strand without the induction of a double-strand break.     

PYRIMIDINE DIMER FORMATION IN HUMAN SKIN

Cyclobutyl pyrimidine dimers are major photoproducts formed upon irradiation of DNA with ultraviolet light. We have developed a method for detecting as few as one pyrimidine dimer per million bases in about 50 ng of non-radioactive DNA, and have used this method to quantitate dimer yields in human skin DNA exposed in situ to UV. We found that UVA radiation (320–400 nm) produces detectable levels of dimers in the DNA of human skin. We also measured UVB-induced dimer yields in skin of individuals of differing sun sensitivity and found higher yields in individuals with higher UVB minimal erythema doses and greater sun sensitivity. These approaches should provide important information on damage induced in human skin upon exposure to natural or artificial sources of ultraviolet radiation.     

PYRIMIDINE DIMER FORMATION IN ULTRAVIOLET IRRADIATED TMV-RNA

Abstract— The formation of pyrimidine dimers on ultraviolet irradiation of TMV-RNA in water is demonstrated in the region from 254 nm to 302 nm. No dimer is present in either unirradiated E. coli ribosomal RNA or TMV-RNA. Dimer formation was also examined in TMV-RNA irradiated in the presence of 5times10^-6 M proflavin, in high salt, on dry ice, and in 90% methanol. No correlation of pyrimidine dimers with any biologically defined lesion is presently possible and it is suggested that dimer may not be involved in the inactivation of this material.     

PYRIMIDINE DIMER SITES ASSOCIATED WITH THE DAUGHTER DNA STRANDS IN UV-IRRADIATED HUMAN FIBROBLASTS

Abstract. Pyrimidine dimer sites associated with the newly-synthesized DNA were detected during post-replication repair of DNA in UV-irradiated human fibroblasts. These pyrimidine dimer sites were inferred from a decrease in the molecular weight of pulse-labelled DNA after treatment with an extract of Micrococcus luteus containing UV-specific endonuclease activity. In DNA synthesized immediately after irradiation the frequency of these daughter strand dimer sites was 7–20% of that in the parental DNA. Such sites were found in fibroblasts from normal donors and from xeroderma pigmentosum patients (with defects in excision-repair or post-replication repair). They were excised from the DNA of normal cells. As the time between UV-irradiation and pulse-labelling was increased, the frequency of dimer sites associated with the labelled DNA decreased. If the pulse-label was delivered 6 h after irradiation of normal cells or excision-defective xeroderma pigmentosum cells, no dimer sites were detected in the labelled DNA. It has usually been assumed that daughter-strand dimer sites were the result of recombinational exchanges. The assay procedure used in these experiments and in similar experiments of others did not distinguish between labelled DNA containing pyrimidine dimers within the labelled section, and labelled DNA which did not contain pyrimidine dimers but was attached to unlabelled DNA which did contain dimers. The latter structures would arise during normal replication immediately following UV-irradiation of mammalian cells. Calculations are presented which suggest that a significant proportion and conceivably all of the dimer sites associated with the daughter strands may have arisen in this way, rather than from recombinational exchanges as has been generally assumed.     

FLAVIN-SENSITIZED PHOTOCHEMICALLY INDUCED DYNAMIC NUCLEAR POLARIZATION DETECTION OF PYRIMIDINE DIMER RADICALS

A photochemically induced dynamic nuclear polarization (photo-CIDNP) study of carboxymethyllumiflavin-sensitized splitting of pyrimidine dimers has been carried out. In aqueous solution at high pH, an emission signal (delta 3.9 ppm) was observed from the dimer C(6)- and C(6')-protons of an N(1), N(1')-trimethylene-bridged thymine dimer (1). The dimer photo-CIDNP signal was seen only above pD 11.6 and was most intense at pD 12.9. Also observed were weak enhanced absorption signals from the product of splitting, trimethylenebis(thymine) (delta 1.7 and 7.2 ppm). In contrast, cis, syn-thymine dimer (3) gave no photo-CIDNP signals from the dimer. An enhanced absorption at 1.8 ppm, however, due to the product of splitting (thymine) was observed. It was found that dimer 1 and, to a lesser extent, dimer 3 quenched flavin fluorescence. An N(3),N(3')-dimethylated derivative of 1, however, failed to quench flavin fluorescence. Comparison of the pD profile of the dimer photo-CIDNP signal to the pKa values for thymidine dimer suggested that principally the dideprotonated dimer undergoes electron abstraction by the excited flavin.     

CIDNP DETECTED FLASH PHOTOLYSIS OF cis–syn 1,3 DIMETHYLTHYMINE DIMER

Abstract— Theanthraquinone–2-sulfonate photo-sensitized splitting of cis-syn 1,3-dimethylthymine dimer gives rise to large CIDNP effects in the reaction product 1,3-dimethylthymine. The polarization originates from a radical ion pair formed by electron transfer from the dimer to the triplet state sensitizer. In a deoxygenated solution the sign of the polarization of theC–6 proton is reversed compared to the predicted one on account of the CIDNP sign rules. In an aerated solution the correct sign is observed. This can be accounted for by assuming reduction of the lifetime of the radical pair in the presence of oxygen. The time-resolved photo-CIDNP technique was used to study the time dependence of the 1,3-dimethylthymine signal. To account for this time-dependence a cation radical disproportionation reaction is proposed.     

P-AMINOBENZOIC ACID CAN SENSITIZE THE FORMATION OF PYRIMIDINE DIMERS IN DNA: DIRECT CHEMICAL EVIDENCE

Thymine-containing photoproducts with chromatographic properties similar to those of cyclobutyl pyrimidine dimers can be formed in [³H]-thymine-labeled DNA in solution by 313 nm ultraviolet radiation in the presence of para-aminobenzoic acid (PABA), a compound used in sunscreen preparations. In the absence of PABA, similar fluences of 313 nm radiation do not produce significant numbers of these photoproducts. The thymine-containing photoproducts can be reversed by 254 nm radiation so that the tritium label migrates with the mobility of thymine monomer, a behavior characteristic of thymine-containing cyclobutyl pyrimidine dimers. This result supports previous, but less direct, data from other laboratories indicating that PABA can sensitize dimer formation in the DNA of bacterial and mammalian cells.     

Unusual Stabilization of Dication Diradical Intermediate of Dizinc(II) Porphyrin Dimer

We have demonstrated here how the nature of a metal ion controls the reactivity of a metalloporphyrin π‐cation radical. One‐electron oxidations of diethylpyrrole‐bridged dicopper(II) and dipalladium(II) porphyrin dimers using iodine as an oxidant result in the formation of strongly interacting cofacial mixed‐valent π‐cation radical dimers. The mixed‐valent cation radical so generated being highly reactive drives a spontaneous and rapid transformation to form an indolizinium‐fused chlorin‐porphyrin heterodimer. In sharp contrast to this, similar addition of iodine leads to 1e‐oxidation of dizinc(II) porphyrin dimer, which is followed by a second oxidation to produce a dication diradical complex. The axial coordination of iodine upon 1e‐oxidation of dizinc(II) porphyrin dimer lowers the overall oxidation potential of the system, and thereby, making the second oxidation easily accessible. This has resulted in the stabilization of a dication diradical complex, in which two porphyrin π‐cation radicals undergo electronic communication through the bridging pyrrole group. Interestingly, despite being well‐separated from each other, the two radical spins undergo strong antiferromagnetic coupling to form a diamagnetic compound. The conjugation also leads to a change in identity of the bridge, which further highlights the critical role played by the bridge in the electronic communication between the two rings. DFT calculations clearly support the experimental observations.     

Excitonic interactions in covalently-linked porphyrin dimers

We have studied the absorption spectra, emission spectra, and fluorescence excitation polarization spectra of a series of free base and diprotonated etioporphyrin-I dimers covalently linked through (CH₂)_n bridges, n = 0–8. The absorption spectra of the n = 0 and n = 1 dimer show red shifts, which are largest (≈15 mm) for the Soret band of the n = 0 dimer. The Soret bands of the diprotonated dimers n = 0–3 show splitting (≈500–1000 cm^?1) which can be interpreted by an exciton model assuming a reasonable geometry. The fluorescence spectra and quantum yields are similar to that of the monomer, except for the same red shift seen in absorption; however, the n = 0 diprotonated dimer shows an anomalo vibronic structure. The fluorescence excitation polarization spectra for the n = 0 and the n = 1 dimers differ substantially from the monomer; dimers n ? 3 have fluorescence excitation polarization spectra that suggest that some of the excitation stays localized in one moiety while the r hops to the dimer partner.     

Effect of pH on one-electron oxidation chemistry of organoselenium compounds in aqueous solutions

Pulse radiolysis coupled with absorption detection has been employed to study one-electron oxidation of selenomethionine (SeM), selenocystine (SeCys), methyl selenocysteine (MeSeCys), and selenourea (SeU) in aqueous solutions. Hydroxyl radicals (*OH) in the pH range from 1 to 7 and specific one-electron oxidants Cl2*- (pH 1) and Br2*- (pH 7) have been used to carry out the oxidation reactions. The bimolecular rate constants for these reactions were reported to be in the range of 2 x 10(9) to 10 x 10(9) M(-1) s(-1). Reactions of oxidizing radicals with all these compounds produced selenium-centered radical cations. The structure and stability of the radical cation were found to depend mainly on the substituent and pH. SeM, at pH 7, produced a monomer radical cation (lambdamax approximately 380 nm), while at pH 1, a dimer radical cation was formed by the interaction between oxidized and parent SeM (lambdamax approximately 480 nm). Similarly, SeCys, at pH 7, on one-electron oxidation, produced a monomer radical cation (lambdamax approximately 460 nm), while at pH 1, the reaction produced a transient species with (lambdamax approximately 560 nm), which is also a monomer radical cation. MeSeCys on one-electron oxidation in the pH range from 1 to 7 produced monomer radical cations (lambdamax approximately 350 nm), while at pH < 0, the reaction produced dimer radical cations (lambdamax approximately 460 nm). SeU at all the pH ranges produced dimer radical cations (lambdamax approximately 410 nm). The association constants of the dimer radical cations of SeM, MeSeCys, and SeU were determined by following absorption changes at lambdamax as a function of concentration. From these studies it is concluded that formation of monomer and dimer radical cations mainly depends on the substitution, pH, and the heteroatoms like N and O. The availability of a lone pair on an N or O atom at the beta or gamma position results in monomer radical cations having intramolecular stabilization. When such a lone pair is not available, the monomer radical cation is converted into a dimer radical cation which acquires intermolecular stabilization by the other selenium atom. The pH dependency confirms the role of protonation on stabilization. The oxidation chemistry of these selenium compounds is compared with that of their sulfur analogues.     

PHOTOCHEMISTRY, PHOTOPHYSICS, AND MECHANISM OF PYRIMIDINE DIMER REPAIR BY DNA PHOTOLYASE

Abstract— DNA photolyases photorepair pyrimidine dimers (PyroPyr) in DNA as well as RNA and thus reverse the harmful effects of UV-A (320–400 nm) and UV-B (280–320 nm) radiations. Photolyases from various organisms have been found to contain two noncovalently bound cofactors; one is a fully reduced flavin adenine dinucleotide (FADH^-) and the other, commonly known as second chromophore, is either methenyltetrahydrofolate (MTHF) or 8-hydroxydeazaflavin (8-HDF). The second chromophore in photolyase is a light-harvesting molecule that absorbs mostly in the near-UV and visible wavelengths (300–500 nm) with its high extinction coefficient. The second chromophore then transfers its excitation energy to the FADH^-. Subsequently, the photoexcited FADH^- transfers an electron to the Pyr<>Pyr generating a dimer radical anion (Pyr<>Pyr^-) and a neutral flavin radical (FADH^-). The Pyr<>Pyr^- is very unstable and undergoes spontaneous splitting followed by a back electron transfer to the FADH^-. In addition to the main catalytic cofactor FADH^-, a Trp (Trp277 in Escherichia coli ) in apophotolyase, independent of other chromophores, also functions as a sensitizer to repair Pyr <> Pyr by direct electron transfer.     

PHOTOSENSITIZED SPLITTING OF PYRIMIDINE DIMERS BY INDOLE DERIVATIVES AND BY TRYPTOPHAN-CONTAINING OLIGOPEPTIDES AND PROTEINS

Abstract— Indole derivatives including tryptophan can be used as photosensitizers of the splitting of pyrimidine dimers. The reaction can take place in frozen aqueous solutions as well as in fluid medium. Electron transfer from the indole ring to the dimer appears to be involved in the photosensitized reaction. Solvated electrons produced by flash photolysis in the presence of indoles or by pulse radiolysis are also able to split thymine dimers.
The splitting of pyrimidine dimers in DNA can be photosensitized by indole derivatives such as serotonin and by tryptophan-containing oligopeptides. Several methods including fluorescence and nuclear magnetic resonance have been used to show that the indole ring of these oligopeptides is able to stack with bases in nucleic acids. These stacked complexes are involved in the photosensitized reaction.
The splitting of pyrimidine dimers in DNA has also been photosensitized by the protein coded by gene 32 of phage T4 which binds strongly and cooperatively to single-stranded DNA. The mechanism of the splitting reaction as well as the possible use of this reaction to investigate the role of tryptophan residues in the binding of proteins to nucleic acids are discussed.