Photosensitization of thymine nucleobase by benzophenone derivatives as models for photoinduced DNA damage: Paterno-Büchi vs energy and electron transfer processes.

Time-resolved and product studies have shown that there is a strong interaction between drugs containing the benzophenone chromophore and the free thymidine nucleoside. In quantitative terms, such an interaction is stronger for the lowest lying npi* triplet states (S-ketoprofen) than for mixed npi*-pipi* triplets (fenofibrate and fenofibric acid), as indicated by the quenching rate constants. This is consistent with a Paterno-Büchi photoreaction, where the initial step is the formation of a new bond between the excited carbonyl oxygen and one of the thymine olefinic carbons. Actually, oxetanes are obtained as photoproducts when benzophenone is irradiated in the presence of thymidine. Hence, triplet-triplet energy transfer resulting in formation of cyclobutane pyrimidine dimers, which would be thermodynamically disfavored, does not seem to play a major role. However, in DNA, the contribution of energy transfer could be higher, due to the lower energy of the thymine triplet in the biomacromolecule. These results are discussed in connection with the observed DNA damage upon photosensitization with ketoprofen, fenofibrate, and fenofibric acid.

Characterization of radiation-induced products of thymidine 3'-monophosphate and thymidylyl (3'-->5') thymidine by high-performance liquid chromatography and laser-desorption Fourier-transform mass spectrometry.

High-performance liquid chromatography (HPLC) and laser-desorption Fourier-transform mass spectrometry (LD FTMS) have been applied for direct measurements of radiation-induced products of nucleic acid constituents containing thymidine. Laser desorption FTMS could be used for the direct detection (neither hydrolyzed nor derivatized) of X ray-induced decomposition products of aqueous thymidine monophosphate. After these initial experiments, a variety of hydrogenated and hydroxylated thymine standards were acquired and examined by FTMS to assist in the identification of unknown radiation-induced decomposition products of thymine-containing nucleotides and dinucleotides. To extend these studies to dinucleotides, the radiation-induced products generated by the gamma radiolysis of thymidylyl (3'-->5') thymidine (TpT) were isolated by reverse-phase HPLC and identified by LD FTMS. Thymine and thymidine 3'-monophosphate were observed as the major products in this case. Several of the minor products of the HPLC profile were pooled in a single fraction and characterized simultaneously by LD FTMS. The resulting mass spectra indicated the presence of hydroxy-5,6-dihydrothymidine monophosphate, 5,6-dihydrothymidine monophosphate and thymidine monophosphate, thymine glycol, hydroxy-5,6-dihydrothymine, 5-hydroxy-methyluracil and 5,6-dihydrothymine. The combination of HPLC purification and LD FTMS structural characterization provides a useful tool for the direct measurement of radiation-induced products of nucleotides and dinucleotides.

Effects of the K-shell X-ray absorption of phosphorus on the scission of the pentadeoxythymidylic acid.

The scission of pentadeoxythymidylic acid, d(pT)5, by monochromatic soft X-rays on (2153 eV) and below (2147 eV) the K-shell absorption peak of phosphorus was studied as a model of strand breakage in DNA. Samples dried on glass plates were irradiated by monochromatic soft X-rays in vacuo, and the products were analysed by HPLC. The main products, in ascending order of the retention time, were thymine, 5'-dTMP, d(pT)2, d(pT)3, d(pT)4, d(pTp) and three unknown products (UK 1, 2 and 3), which were presumed to be d(pTpTp), d(pTpTpTp) and d(pTpTpTpTp), respectively. No difference between 2147 and 2153 eV irradiation in the nature of the induced products was detected, indicating that the K-shell absorption of phosphorus and the following Auger process produced the same types of products as those produced by photoabsorption at the other shells of phosphorus and at other atoms. The cross-sections for the induction of products at 2153 eV were 3.3-4.0 times larger than those at 2147 eV, the ratios of these values being scattered around the ratio (3.65) of absorbance of the sample between 2153 and 2147 eV. The dependence on the X-ray energy, however, almost disappeared after conversion from exposure to absorbed dose; the ratios of the G-values (number of products per 100 eV) of the products were 0.92-1.11. Photoabsorption at the K-shell of phosphorus induced products comparable or slightly less effectively than photoabsorption at the others. These results indicate that the K-shell absorption of phosphorus and the following Auger process do not have any characteristic effect on strand breakage in dry DNA, either qualitatively or quantitatively.

Enzymatic analysis of isomeric trithymidylates containing ultraviolet light-induced cyclobutane pyrimidine dimers. I. Nuclease P1-mediated hydrolysis of the intradimer phosphodiester linkage.

Our recent findings suggest that enzymatic hydrolysis of the intradimer phosphodiester bond may constitute the initial step in the repair of UV light-induced cyclobutane pyrimidine dimers in human cells. To examine the susceptibility of this phosphodiester linkage to enzyme-mediated hydrolysis, the trinucleotide d-Tp-TpT was UV-irradiated and the two isomeric compounds containing a cis-syn-cyclobutane dimer were isolated by high performance liquid chromatography and treated with various deoxyribonucleases. Snake venom phosphodiesterase hydrolyzed only the 3'-phosphodiester group in the 5'-isomer (d-T less than p greater than TpT) but was totally inactive toward the 3'-isomer (d-TpT less than p greater than T). In contrast, calf spleen phosphodiesterase only operated on the 3'-isomer by cleaving the 5'-internucleotide bond. Kinetic analysis revealed that (i) the activity of snake venom phosphodiesterase was unaffected by a dimer 5' to a phosphodiester linkage, (ii) the action of calf spleen phosphodiesterase was partially inhibited by a dimer 3' to a phosphodiester bond, and (iii) Escherichia coli phr B-encoded DNA photolyase reacted twice as fast with d-T less than p greater than TpT as with d-TpT less than p greater than T. Mung bean nuclease, nuclease S1, and nuclease P1 all cleaved the 5'-internucleotide linkage, but not the intradimer phosphodiester bond, in d-TpT less than p greater than T. Both phosphate groups in d-T less than p greater than TpT were refractory to mung bean nuclease or nuclease S1. Incubation of d-T less than p greater than TpT with nuclease P1, however, generated the novel compound dT less than greater than d-pTpT containing a severed intradimer phosphodiester linkage. Accordingly, nuclease P1 represents the first purified enzyme known to hydrolyze an intradimer phosphodiester linkage.

Enzymatic analysis of isomeric trithymidylates containing ultraviolet light-induced cyclobutane pyrimidine dimers. II. Phosphorylation by phage T4 polynucleotide kinase.

Phage T4 polynucleotide kinase (EC 2.7.1.78) proved incapable of catalyzing the phosphorylation of thymidylyl-(3'----5')-thymidine containing either a cis-syn-cyclobutane pyrimidine dimer (d-T less than p greater than T) or a 6-4'-[pyrimidin-2'-one]pyrimidine photoproduct (d-T[p]-T), and similarly the UV-modified compounds of (dT)3 bearing either photoproduct at their 5'-end (d-T less than p greater than TpT and d-T[p]TpT). In contrast, the 3'-structural isomers of these trinucleotides (d-TpT less than p greater than T and d-TpT[p]T) were phosphorylated at the same rate as the parent compound. These phosphorylatable lesion-containing oligonucleotides are quantitatively released from UV-irradiated poly(dA):poly(dT) by enzymatic hydrolysis with snake venom phosphodiesterase and alkaline phosphatase (Liuzzi, M., Weinfeld, M., and Paterson, M. C. (1989) J. Biol. Chem. 264, 6355-6363). By combining this digestion regimen with phosphorylation by polynucleotide kinase and [gamma-32P]ATP, pyrimidine dimers were quantitated at the fmol level following exposure of poly(dA):poly(dT) and herring sperm DNA to biologically relevant UV fluences. The rate of dimer induction in the synthetic polymer, approximately 10 dimers/10(6) nucleotides/Jm-2, was in close agreement with that obtained by conventional methods. Dimers were induced at one-fourth of this rate in the natural DNA. Further treatment of the phosphorylated oligonucleotides derived from irradiated herring sperm DNA with nuclease P1 released the labeled 5'-nucleotide, thus permitting analysis of the nearest-neighbor bases 5' to the lesions. We observed a ratio for pyrimidine-to-purine bases of almost 6:1, implicating tripyrimidine stretches as hotspots for UV-induced DNA damage.

Intramolecular H atom abstraction from the sugar moiety by thymine radicals in oligo- and polydeoxynucleotides.

Hydroxyl radical addition to uracil (U) has been suggested to lead to strand breaks in polyuridylic acid, an occurrence attributed in part to H atom abstraction by .U-OH radicals from the ribose moiety [D.G.E. Lemaire et al., Int. J. Radiat. Biol. 45, 351-358 (1984)]. We have investigated this particular reaction by means of the hydroxyl radical-induced products of thymine (T), pT, TpT, TpTpT, polythymidylic acid (poly-T), (T + dR) poly-dA.poly-T, and a mixture of T and 2-deoxyribose (dR). The major monomeric product of .T-OH in TpT, TpTpT, poly-T, and poly-dA.poly-T was found to be 5-hydroxy-6-hydrothymine (H-T-OH), while that in T, pT, and T plus dR was thymine glycol (HO-T-OH). These results indicated that the intramolecular H atom abstraction from a nearby sugar (in this case, deoxyribose) moiety by base radicals, i.e., .T-OH, occurs in oligo- and polydeoxynucleotides of T. In poly-T, the yield of H-T-OH is not much greater than in TpT or TpTpT, indicating that the abstraction of an H atom from the sugar moiety of a nucleotide subunit further than two nucleotides along the chain may not be significant. Additionally, a corresponding decrease in the yield of HO-T-OH with an increase in the yield of H-T-OH suggests that the formations of these two types of thymine products are competitive.

Two-dimensional 1H NMR study of two cyclobutane type photodimers of thymidylyl-(3'----5')-thymidine.

2D NMR spectroscopy and J coupling constant analysis are applied to resolve the structure of two photoproducts of thymidylyl-(3'----5')-thymidine. These products are cyclobutane type thymine dimers possessing the cis-syn (the predominant one) and trans-syn geometry. The cis-syn is formed in an ANTI-ANTI conformation about the N-glycosyl linkages and resembles the normal base-stacked configuration. The glycosidic conformation in solution of the 5' terminal fragment differs from the crystal in which the less common SYN conformation is observed. In this isomer only the sugar pucker of the 3' terminal fragment is changed substantially with respect to the dinucleotide. The trans-syn isomer is formed in a SYN-ANTI glycosidic conformation. In this isomer the sugar puckers of both deoxyribose rings are affected and a preference for a pure 2'-endo conformation is observed.

Photoreversal-dependent release of thymidine and thymidine monophosphate from pyrimidine dimer-containing DNA excision fragments isolated from ultraviolet-damaged human fibroblasts.

To elucidate the enzymatic excision-repair process operative on cyclobutane-type pyrimidine photodimers in human dermal fibroblasts, we have examined excised dimer-containing material recovered in the trichloroacetic acid soluble fraction from far-ultraviolet-irradiated (254 nm, 40 J m-2) and incubated (24 h) cell cultures. The excised DNA photoproducts were found in oligonucleotide fragments with an estimated mean chain length of approximately 3.7 bases. Exposure of these isolated excision fragments, labeled with [3H]thymidine (dT), to a secondary, dimer-photoreversing fluence of far-UV (5.5 kJ m-2) resulted in the release of free dT and thymidine monophosphate (TMP). Photorelease of these two radioactive species was measured by high-performance liquid chromatography, with TMP being detected as the increase in dT following bacterial alkaline phosphatase treatment. These data imply that the photoliberated dT and TMP moieties were attached to the excision fragments solely by the cyclobutane ring of the dimer. No evidence was obtained for the photoliberation of free thymine, thus corroborating a conclusion reached by others that the excision of dimers in human cells is not initiated by scission of an intradimer N-glycosyl bond. The sum of the tritium label recovered in dT plus TMP corresponded to approximately 40% of that disappearing from thymine-containing dimers on photoreversal, suggesting that in about 80% of the isolated excision fragments the dimer is located at one end of the oligonucleotide and contains a break in its internal phosphodiester bond.(ABSTRACT TRUNCATED AT 250 WORDS)

Radiation chemistry of a dinucleoside monophosphate and its sequence isomer.

A combination of high-performance liquid chromatography (HPLC) and nuclear magnetic resonance (NMR) spectroscopy was used to analyze the products of X-irradiated aqueous solutions of the dinucleoside monophosphate thymidylyl(3'-5')-2'-deoxyadenosine, d(TpA), and its sequence isomer 2'-deoxyadenylyl(3'-5')thymidine, d(ApT). The products of d(TpA) include both bases and nucleotides and a variety of thymine modifications of d(TpA) including the two cis and two trans glycol stereoisomers, two cis monohydroxy derivatives, an N-formamide derivative, and the hydroxymethyl derivative. Attention is focused on using NMR spectral features to distinguish among the various stereoisomers. The radiation chemistry of d(ApT) is also explored and differences in product formation compared with d(TpA) are described, particularly the formation of two products involving modification of adenine base. The potential of the HPLC-NMR approach to the study of radiation chemistry in DNA model compounds is discussed.

UV irradiation of nucleic acids: formation, purification and solution conformational analysis of the '6-4 lesion' of dTpdT.

Irradiation of dTpdT with 300 kJ/m2 of 254 nm produces numerous photo-products, one of which labeled dT6pd4T[1] was purified by HPLC. dT6pd4T has a UV spectrum (H20, pH 7) with lambda max = 326 nm and lambda min = 265 nm, and a P-31 NMR resonance at -3.46 ppm (normal dTpdT occurs at -4.01 ppm; TMP, 30 degrees C). 2-D COSY NMR spectra facilitated proton resonance assignments and 2-D NOESY spectra aided analysis of spatial orientation. Carbon-13 and proton-coupled P-31 NMR spectra of dT6pd4T were also obtained. These analyses indicate: C5=C6 of dT6p- is saturated and the -pd4T base is more aromatic; the dT6p- base possesses a configuration of 5R, 6S; dT6p- and -pd4T have anti-type glycosidic conformations; furanose conformation of dT6p- is mainly C3'-endo and that of -pd4T exists in a C3'-endo in equilibrium C3'-exo; exocyclic bonds gamma (C5'-C4'), beta (05'-C5') and epsilon (C3'-03') are non-classical rotamers; dihedral angle about epsilon (C3'-03') is smaller relative to dTpdT.

Radiation-induced formation of thymine-thymine crosslinks.

The formation of dimers upon gamma-irradiation of thymine, thymidine and thymidine-5'-monophosphate in N2O-saturated aqueous solution is reported. A method using capillary gas chromatography-mass spectrometry was developed for their separation and identification. Quantitative measurements reveal that about 50 per cent of OH adduct radicals of thymine undergo dimerization.

Production of thymine base damage in ultrasound-exposed EMT6 mouse mammary sarcoma cells.

Mouse mammary sarcoma cells, line EMT6/Ro, were exposed for 1 min to 1 MHz continuous wave ultrasound over a range of intensities from 0.5 to 30 W/cm2 (spatial peak). The presence of thymine base damage (TBD) products of the 5,6-dihydroxydihydrothymine type was determined by an alkali degradation assay. Production of damage was found to be greatest (approximately 2.7 X 10(-3%) t'/T) at an intensity of 10 W/cm2 and fell off rapidly above and below this intensity. The amount of base damage produced at 10 W/cm2 ultrasound was approximately equivalent to the damage produced by a gamma-ray absorbed dose of 12 krad. Assay of cells immediately after sonication at 10 W/cm2 showed that approximately 14% of the cells had been lysed. Tests showed that it was the DNA of the intact cells, however, which sustained all of the TBD. Survival data demonstrated that of the remaining unlysed cell population approximately 5% were viable, whereas cells exposed to 12 krad showed no survival. Additionally, cells were exposed for up to 5 min at 5 W/cm2. An increase in TBD was demonstrated with increasing time of exposure such that the rate of production at 5 min was approximately three times greater than that of a 1-min exposure. TBD was found to be completely suppressed when cells were sonicated at 10 W/cm2 for 2 min under 4 bar of hydrostatic pressure. Addition of the radical scavengers beta-MEA and cystamine eliminated TBD but had minimal effect on survival. The pressure and scavenger experiments demonstrate that TBD results from cavitation-induced free radicals. Based on the values for both the half-life and diffusion distance of such radicals, our results indicate that at least part of the bubble collapse occurs intracellularly.

[Modeling the effects of radiation damage to DNA and the genetic risk of radionuclide decay. Dehydrogenation of pyrimidine nucleotides during decay of incorporated 3H]. / Modelirovanie éffektov radiatsionnykh povrezhdenii DNK i geneticheskaia opasnost' raspada radionuklidov. Degidrirovanie pirimidinovykh nukleotidov pri raspade inkorpororovannogo 3H.

Dehydrogenation of DNA pyrimidine nucleotides in thymine positions 5 and 6 and cytosine position 5 is not a drastic lethal damage. Moreover, dehydrogenation of DNA in thymine positions 5 and 6 is not an effective mutagenic lesion. DNA dehydrogenation in cytosine position 5 has proved to be a pronounced mutagenic damage. As to induction of point mutations, 3H is not more harmful than external gamma-radiation given in equivalent doses.

Mutagen-induced changes in cellular deoxycytidine triphosphate and thymidine triphosphate in Chinese hamster ovary cells.

Deoxynucleoside triphosphate concentrations in Chinese hamster ovary cell lines, CHO-K1 and Mut 8-16, were examined following exposure of cells to UV or dimethylsulfate. Marked decreases in dCTP were observed 2 hr after exposure to both mutagens. In contrast, dTTP concentrations increased with increased cell killing after exposure to UV but not after exposure to dimethylsulfate. Examination of DNA synthesis in permeabilized cells in the presence of excess concentrations of dNTP substrates suggests that excess dCTP enhances replication while excess of dTTP inhibits replication. We therefore ask whether the increase in the dTTP/dCTP ration in mutagenized whole cells either contributes to or prolongs induced inhibition of replication. In addition we proposed that such an induced dNTP imbalance may also contribute to an increase in mutations by enhancing the probability for base-misincorporation.

[Molecular nature of the mutations in gene ADE2 in Saccharomyces cerevisiae yeasts. III. Determination of the correlation of the GC AT pairs in genes ADE1 and ADE2]. / Izuchenie molekuliarnoi prirody mutatsii v gene ADE2 u drozhzhei Saccharomyces cerevisiae. Soobshchenie III. Opredelenie sootnosheniia par GTs i AT v genakh ADE1 i ADE2.

Lethal and mutagenic effects and the nature of mutations induced by decay of 32P incorporated into yeast cell DNA as 32P-deoxyguanosine monophosphate (32PdGMP) and 32P-thymidine monophosphate (32P-TMP), were studied. The lethal efficiency per 32P decay is independent of a labelled nucleotide incorporated into DNA. However, the mutagenic efficiency in ADE1, ADE2 genes per 32P decay is approximately 3 times greater for 32PdGMP than for 32P-TMP. This suggests that ADE1, ADE2 genes contain about 3 times more GC base pairs than AT pairs. Variations in a relative frequencies of GC leads to AT and AT leads to GC transitions were obtained depending upon a nucleotide labelled.

Formation of an adenine-thymine photoadduct in the deoxydinucleoside monophosphate d(TpA) and in DNA.

A photoadduct is formed between the adenine (A) and thymine (T) bases of the deoxydinucleoside monophosphate d(TpA) when it is irradiated at 254 nanometers in aqueous solution. Treatment of the photoadduct with acid converts it specifically into a fluorescent hydrolysis product, C7H7N3O, incorporating the position-8 carbon of adenine and the methyl group of thymine. Isolation of the fluorescent hydrolysis product from acid hydrolyzates of oligo- and polydeoxyribonucleotides has shown that the photoadduct is formed by ultraviolet irradiation of d(pTpA), d(TpApT), d(TpApTpA), poly(dA-dT), and both single- and double-stranded DNA.

Transfer of radiation-induced spins from deoxyribonucleic and thymidylic acids to propyl gallate.

When calf thymus deoxyribonucleic acid (DNA), propyl gallate (PG) and their five molecular mixtures (with PG content of 1, 2, 5, 10 and 20%) are irradiated with gamma-rays in dry state in vacuum at 296 degrees K, the ESR spectra of all molecular mixtures differ strikingly from those of DNA, but bear a close resemblance to those of PG. The spin yield in the PG contained in these mixtures is two to three orders of magnitude higher than that in the case of PG irradiated separately. Furthermore, on the basis of the relative saturation characteristics of ESR spectra, these molecular mixtures behave more like PG than like DNA. It may be inferred that the radiation-induced spins could be transferred from DNA to PG. With r representing the molar ratio of nucleotides to PG, we have found a good linear correlation between the transfer ratio (TR) and square root of r. One PG molecule could protect at least 68 nucleotides in the duplex DNA chain, and thereby the minimal range of spin transfer is estimated at 115 A. Results obtained from irradiation at 77 degrees K show that PG exerts no protective effect on DNA, so DNA sustains an irreversible damage. It is thought that the spin transfer from DNA to PG is exclusively due to a hydrogen transfer mechanism. We have also demonstrated the transfer of radiation-induced spins from both thermally denatured DNA and TMP to PG. The former process can be ascribed primarily to the hydrogen transfer mechanism, whereas the latter, as in the case of native DNA, exclusively to this mechanism.