CYCLOBUTANE DIMERS AND (6-4)PHOTOPRODUCTS IN HUMAN CELLS ARE MENDED WITH THE SAME PATCH SIZES

The size of excision repair patches corresponding to excision of (6-4) pyrimidine-pyrimidone photoproducts and (5-5, 6-6) cyclobutane dimers have been independently determined by using bromodeoxyuridine substitution and density increases in isopycnic gradients of small DNA fragments. The two classes of photoproducts were distinguished by using (a) a xeroderma pigmentosum (XP) revertant cell line that excises (6-4) photoproducts normally, but does not excise cyclobutane dimers from bulk DNA or from an actively transcribed sequence; (b) an XP cell line containing the denV gene of bacteriophage T4, which repairs only cyclobutane dimers by a unique glycosylase mechanism, and (c) normal cells analyzed during time intervals in which cyclobutane dimer repair is the main repair process in action. The patch sizes for the two lesions were similar under all conditions and were estimated to be approximately 30-40 bases. These values are slightly large than corresponding estimates for Escherichia coli and Saccharomyces cerevisiae but close to estimates from in vitro experiments with human cell extracts. The size of 30 bases may consequently be very close to the actual distance between cleavage sites made on either side of a photoproduct during repair.     

On the Roles of Urocanic Acid in Photoimmunosuppression: Attempted Photorepair of Urocanic Acid-DNA Cyclobutane Adducts with DNA Photolyase

It has been reported that UV-induced immunosuppres-sion can be reversed by photoreactivation or exposure to T4 endonuclease V, two treatments that can repair cyclobutane pyrimidine dimers. These observations, together with the known role of urocanic acid (UA) in UV-induced immune suppression, prompted us to study the ability of DNA photolyase to repair UA-DNA cyclobutane photoadducts in single-stranded calf thymus DNA. We did not detect any release of UA, with a sensitivity implying that photolyase is at least 2900 times less active toward UA-DNA adducts than toward cis-syn thyminethymine dimers. This indicates that any reversal of photoimmunosuppression by photoreactivation cannot significantly involve cleavage of UA-DNA cyclobutane adducts.     

Spectroelectrochemistry of a photochromic [2.2]paracyclophane-bridged imidazole dimer: clarification of the electrochemical behavior of HABI

The photochromic behavior of the imidazole dimers can be attributable to the photoinduced homolytic cleavage of the C-N bond between the two imidazole rings. On the other hand, although the simultaneous formation of the imidazolyl radical and imidazole anion by the one-electron reduction of an imidazole dimer was reported, no definitive evidence for this electrochemical reaction has been demonstrated. We report the first direct evidence for the electrochemical generation of the imidazolyl radical from the radical anion of the imidazole dimer by conducting the UV-vis-NIR spectroelectrochemical analysis of the [2.2]paracyclophane-bridged imidazole dimer.     

Generation of phosphorus-centered radicals via homolytic substitution at sulfur

A novel radical domino process relying on the homolytic cleavage of P-S bonds allows the preparation of phosphorus-containing molecules through addition of P-centered radicals onto olefins. The key step of this reaction is a homolytic substitution on a sulfur atom. The scope of the reaction is broad. Diaminophosphonyl radicals whose reactivity was unknown react smoothly with olefins. Use of tin hydride can be avoided. A radical thiophosphinoylation of triple bonds has been uncovered. [reaction: see text]     

Discrimination of isomers by liquid ionization mass spectrometry with techniques of collisional activation and adduct ion formation

Liquid ionization mass spectrometry is a soft ionization technique used with liquid samples under atmospheric pressure. It facilitates the handling of reagents and the observation of ion–molecule reactions in the ion source. The differentiation of isomers by characteristic fragment ions, for example those resulting from asymmetrical cleavage of a cyclobutane ring, and by molecular adduct ion formation was studied. The samples studied were cyclobutane derivatives, alkyl 4-(3-oxo-3-pIienyl-l-aIkenyl)benzoate dimers, and reagents having two functional groups were used to produce adduct ions to clarify the difference between isomers. The reagents act on a sample molecule at two functional groups to form hydrogen bonds. Some correlations were observed between the structure of the sample and the relative abundances of molecular adduct ions and also fragment ions produced by collisionally activated dissociation.     

A comparative repair study of thymine- and uracil-photodimers with model compounds and a photolyase repair enzyme

Cyclobutane uridine and thymidine dimers with cis-syn-structure are DNA lesions, which are efficiently repaired in many species by DNA photolyases. The essential step of the repair reaction is a light driven electron transfer from a reduced FAD cofactor (FADH ) to the dimer lesion, which splits spontaneously into the monomers. Repair studies with UV-light damaged DNA revealed significant rate differences for the various dimer lesions. In particular the effect of the almost eclipsed positioned methyl groups at the thymidine cyclobutane dimer moiety on the splitting rates is unknown. In order to investigate the cleavage vulnerability of thymine and uracil cyclobutane photodimers outside the protein environment, two model compounds, containing a thymine or a uracil dimer and a covalently connected flavin, were prepared and comparatively investigated. Cleavage investigations under internal competition conditions revealed, in contrast to all previous findings, faster repair of the sterically less encumbered uracil dimer. Stereoelectronic effects are offered as a possible explanation. Ab initio calculations and X-ray crystal structure data reveal a different cyclobutane ring pucker of the uracil dimer, which leads to a better overlap of the pi*-C(4)-O(4)-orbital with the sigma*-C(5)-C(5')-orbital. Enzymatic studies with a DNA photolyase (A. nidulans) and oligonucleotides, which contain either a uridine or a thymidine dimer analogue, showed comparable repair efficiencies for both dimer lesions. Under internal competition conditions significantly faster repair of uridine dimers is observed.     

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.     

Oxidative cleavage of a cyclobutane pyrimidine dimer by photochemically generated nitrate radicals (no(3)*)

[reaction: see text] Photochemically generated nitrate radicals (NO(3)(*)) cleave the stereoisomeric N,N-dimethyl-substituted uracil cyclobutane dimers 1a-d into the monomeric uracil derivative 2 as the major reaction pathway. A preferred splitting of the syn dimers 1a,b was observed. The reaction is expected to proceed through initial one-electron oxidation with formation of an intermediate cyclobutane radical cation 11. In addition to cycloreversion, competing reaction steps of 11, which lead to the observed byproducts, are suggested.     

Efficient and selective oxidation of methyl substituted cycloalkanes by heterogeneous methyltrioxorhenium–hydrogen peroxide systems

Polymer-supported methyltrioxorhenium (MTO) systems are efficient catalysts for the oxidative functionalisation of cyclohexane and cyclopentane derivatives with H₂O₂ as oxygen donor. Using poly(4-vinyl)pyridine and poly(4-vinyl)pyridine-N-oxide as MTO supports, cycloalkanol, cycloalkanediol, cycloalkanone and ω-hydroxy methyl ketone derivatives were obtained in different yields depending on the experimental conditions. Interestingly, cycloalkane dimers were selectively recovered in acceptable to good yields when the oxidation was performed with polystyrene-microencapsulated MTO catalyst. The EPR investigation suggests that the homolytic cleavage of the CH₃–Re bond with formation of CH₃ radicals occurs inside the polystyrene capsule, indicating a possible role of methyl radical in the cycloalkane dimerisation pathway.     

1,1-Dimethylnaphthalenon-dimers as photocleavable linkers with improved two-photon-absorption efficiency and hydrolytic stability

Coumarins are well known for reversible dimer formation with wavelengths greater than 300 nm and dimer cleavage below 300 nm. In a photochemical [2+2]-cycloaddition a cyclobutane ring is formed. Formation as well as cleavage of the cyclobutane ring may be accomplished by a single-photon-absorption as well as by a two-photon-absorption triggered reaction. The coumarin system is of interest for various kinds of applications, ranging from drug delivery for ophthalmic implants to optical data storage. However, the two-photon-absorption coefficient of coumarin dimers is rather low falling in the range of 1 GM in the visible range. We present here a substitute for the coumarin dimer system which not only has an about one order of magnitude higher two-photon-absorption coefficient, but also overcomes several other problems of the coumarin dimer system. Coumarines and in particular coumarine dimers have a very limited solubility in common solvents and are susceptible to hydrolysis of the lactone ring, which leads to an undesired complexity in the photochemical cleavage reaction. The 1,1-dimethylnaphtalenone dimers introduced here show excellent stability, lead only to a single cleavage product, and have a two-photon-absorption coefficient of about 10 GM at 532 nm. These properties make the 1,1-dimethylnaphtalenone dimers a superior substitute over the well-known coumarin dimers in particular in applications where two-photon-absorption induced photocleavage is required.     

Explicit and implicit solvation of radical ions: the cycloreversion of CPD dimers

The electron transfer catalyzed cycloreversion of cyclobutane pyrimidine dimers is the key step in repair of light-induced DNA lesions catalyzed by the enzyme CPD photolyase. The formation of the CPD radical anion was found to be strongly solvent dependent due to a specific hydrogen bond that stabilizes the valence bound state over the dipole bound state of the additional electron. The effect of solvation on the vertical and adiabatic electron affinity of uracil and uracil dimers as well as on the mechanism of the cycloreversion of the uracil dimer radical anion is explored for three model systems that include explicit solvent molecules at the B3LYP/6-311++G^∗∗/B3LYP/6-31+G^∗ level of theory. The second solvation shell is described using the implicit C-PCM solvation model. These calculations indicate an effectively barrierless mechanism. These results are in agreement with the available experimental data for the reaction energies and isotope effects. It is also shown that a single hydrogen bond donor is a sufficient minimal model for the first solvation shell by adequately describing the stabilization of the valence bound state of the radical anion through hydrogen bonding. The relationship of these model systems with the enzymatic reaction catalyzed by DNA photolyase is also discussed.     

Thermal [2 + 2] cycloreversion of a cyclobutane moiety via a biradical reaction

The nature of the Woodward-Hoffmann-forbidden, thermal activated cycloreversion mechanism of cyclobutane has long been the subject of speculation and intense research. We were now able to prove the theoretically postulated biradicalic mechanism directly from radical scavenging reactions and electron paramagnetic resonance (EPR) experiments on [2 + 2] heterodimers of 5-fluoro-1-heptanoyluracil and 7-methoxy-1,1-dimethylnaphthalenon. The dimers show both the "allowed" photochemically as well as the "forbidden" thermally triggered [2 + 2] cycloreversion of the cyclobutane ring. The quantum efficiency of the photochemical cleavage is about 1%. The thermal cycloreversion reaction is independent from solvent and occurs at low activation energies of about 13 kcal/mol, even in the solid state. The radical scavenger and EPR results are further supported by the finding, that the reaction products are solely the educts for the anti-head-to-tail heterodimer. But for the syn-head-to-head heterodimer two additional products are observed, which require a sufficiently stable biradical intermediate to facilitate the required intramolecular rearrangements. Because of the surprisingly high lifetime of the radical species of these heterodimers it was possible to prove the long-discussed biradical mechanism experimentally.     

Photochemistry of nitroso derivatives in solution—XXX: Temperature effects on radical additions to terpenes and reactions of 2-ammonium nitrosoalkanes

Temperature effects on aminium radical initiated photoaddition to three monoterpenes were investigated. Photoaddition of N-nitrosopiperidine to camphene and pinenes gave the α-piperidinium tertiary-nitrosoalkanes as the primary adducts derived from 1,2-addition; the additions to pinenes required a low temperature (?40°) to suppress the cyclobutane ring opening pathway of the C-radical intermediate. Since the functional groups of these α-piperidinium nitrosoalkanes could assume cis-coplanar configuration, they underwent a facile cleavage reaction to give the corresponding oximes and immonium salts. As the photolysis temperature was raised, in the addition to pinenes, the cyclobutane ring opening pathway progressively dominated the reaction giving increasing amounts of 8-nitroso-p-menthene derivatives which underwent solvolysis and elimination reactions. A mechanistic interpretation in favor of the homolytic ring opening process from the C-radical intermediate is presented. The results established a diagnostic rule for stepwise addition to olefins. An efficient preparation of tricyclene from a commercial camphene sample was appended.     

Radical-driven dissociation of odd-electron peptide radical ions produced in 157 nm photodissociation

Odd-electron a+1 radical ions generated in the 157 nm photodissociation of peptide ions were investigated in an ion trap mass spectrometer. To localize the radical, peptide backbone amide hydrogens were replaced with deuterium. When the resulting radical ions underwent hydrogen elimination, no H/D scrambling was obvious, suggesting that without collisional activation, the radical resides on the terminal α-carbon. Upon collisional excitation, odd-electron radical ions dissociate through two favored pathways: the production of a-type ions at aromatic amino acids via homolytic cleavage of backbone C_α-C(O) bonds and side-chain losses at nonaromatic amino acids. When aromatic residues are not present, nonaromatic residues can also lead to a-type ions. In addition to a-type ions, serine and threonine yield c _n−1 and a _n−1+1 ions where n denotes the position of the serine or threonine. All of these fragments appear to be directed by the radical and they strongly depend on the amino acid side-chain structure. In addition, thermal fragments are also occasionally observed following cleavage of labile Xxx-Pro bonds and their formation appears to be kinetically competitive with radical migration.     

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.     

REPAIR OF CYCLOBUTANE DIMERS AND (6–4) PHOTOPRODUCTS IN ICR 2A FROG CELLS

Abstract— The removal of cyclobutane dimers and Pyr(6–4)Pyo photoproducts from the DNA of UV-irradiated ICR 2A frog cells was determined by radioimmunoassay. In the absence of photoreactivat-ing light, 15% of the cyclobutane dimers and 60% of the (6–4) photoproducts were removed 24 h post-irradiation with 10 J m⁻², Exposure to 30 kJ m⁻² photoreactivating light resulted in removal of 80% of the cyclobutane dimers and an enhanced rate of repair of (6–4) photoproducts, resulting in a loss of 50% of these lesions in 3 h. The preferential removal of (6–4) photoproducts by excision repair resembles previously published data for mammalian cells.     

Computational studies on the cyclization of polycyclic aromatic hydrocarbons in the synthesis of curved aromatic derivatives.

Computational studies on the cyclization reactions of some polycyclic aromatic hydrocarbons (PAHs) were performed at the DFT level. Compounds C26H14 and C24H14, which show the connectivity of C60 fullerene fragments, were chosen as suitable models to study the formation of curved derivatives by six- or five-membered ring formation, upon oxidation to their radical cations. Four possible pathways for the cyclization process were considered: a) initial C-C bond formation to afford a curved derivative, followed by dehydrogenation; b) homolytic C-H cleavage prior to cyclization; c) initial concerted H2 elimination and subsequent cyclization; and d) deprotonation of the radical cations prior to cyclization. Computed reaction and activation energies for these reactions show that direct cyclization from radical cations (pathway a) is the lowest-energy mechanism. The formation of five-membered rings is somewhat more favourable than benzannulation. After new cycle formation, homolytic C-H dissociation to afford the corresponding cations is the most favourable process. These cations react with H* without barrier to give H2* Intermediate deprotonations are strongly disfavoured. The relatively low activation energies compared with carbon cage rearrangements suggest that ionization of PAHs can be used for the tailored preparation of nonplanar derivatives from suitable precursors.     

DNA REPAIR IN THE VARIABLE PLATYFISH (Xiphophorus variatus) IRRADIATED in vivo WITH ULTRAVIOLET B LIGHT

Abstract— Dark- and light-dependent DNA repair processes were studied in vivo in the variable platyfish, Xiphophorus vuriatus . Excision (dark) repair of the (6–4) photoproduct was more efficient than that of the cyclobutane dimer with ∼ 70% of the (6–4) photoproducts reniovcd by 24 h post-UVB radiation compared to ∼30% of the cyclobutane dimers. Exposure to photoreactivating light resulted in rapid loss of most (>90%) of the cyclobutane dimers and increased excision repair of the (6–4) photoproduct. Preexposure to photoreactivating light 8 h prior to UVB radiation increased the rate of photoreactivation two-fold.     

Density Functional Studies on Thromboxane Biosynthesis: Mechanism and Role of the Heme‐Thiolate System

Reaction mechanisms for the isomerization of prostaglandin H₂ to thromboxane A₂, and degradation to 12‐L‐hydroxy‐5,8,10‐heptadecatrienoic acid (HHT) and malondialdehyde (MDA), catalyzed by thromboxane synthase, were investigated using the unrestricted Becke‐three‐parameter plus Lee–Yang–Parr (UB3LYP) density functional level theory. In addition to the reaction pathway through Fe^IV‐porphyrin intermediates, a new reaction pathway through Fe^III‐porphyrin π‐cation radical intermediates was found. Both reactions proceed with the homolytic cleavage of endoperoxide O? O to give an alkoxy radical. This intermediate converts into an allyl radical intermediate by a C? C homolytic cleavage, followed by the formation of thromboxane A₂ having a 6‐membered ring through a one electron transfer, or the degradation into HHT and MDA. The proposed mechanism shows that an iron(III)‐containing system having electron acceptor ability is essential for the 6‐membered ring formation leading to thromboxane A₂. Our results suggest that the step of the endoperoxide O? O homolytic bond cleavage has the highest activation energy following the binding of prostaglandin H₂ to thromboxane synthase.     

Insight in DNA Repair of UV‐induced Pyrimidine Dimers by Chromatographic Methods

UV‐induced formation of pyrimidine dimers in DNA is a major deleterious event in both eukaryotic and prokaryotic cells. Accumulation of cyclobutane pyrimidine dimers and pyrimidine (6‐4) pyrimidone photoproducts can lead to cell death or be at the origin of mutations. In skin, UV induction of DNA damage is a major initiating event in tumorigenesis. To counteract these deleterious effects, all cell types possess DNA repair machinery, such as nucleotide excision repair and, in some cell types, direct reversion. Different analytical approaches were used to assess the efficiency of repair and decipher the enzymatic mechanisms. We presently review the information provided by chromatographic methods, which are complementary to biochemical assays, such as immunological detection and electrophoresis‐based techniques. Chromatographic assays are interesting in their ability to provide quantitative data on a wide range of damage and are also valuable tools for the identification of repair intermediates.