Thymidine radical formation via one-electron transfer oxidation photoinduced by pterin: Mechanism and products characterization.

UV-A radiation (320-400nm), recognized as a class I carcinogen, induces damage to the DNA molecule and its components through different mechanisms. Pterin derivatives are involved in various biological functions, including enzymatic processes, and it has been demonstrated that oxidized pterins may act as photosensitizers. In particular, they accumulate in the skin of patients suffering from vitiligo, a chronic depigmentation disorder. We have investigated the ability of pterin (Ptr), the parent compound of oxidized pterins, to photosensitize the degradation of the pyrimidine nucleotide thymidine 5'-monophosphate (dTMP) in aqueous solutions under UV-A irradiation. Although thymine is less reactive than purine nucleobases, our results showed that Ptr is able to photoinduce the degradation of dTMP and that the process is initiated by an electron transfer from the nucleotide to the triplet excited state of Ptr. In the presence of molecular oxygen, the photochemical process leads to the oxidation of dTMP, whereas Ptr is not consumed. In the absence of oxygen, both compounds are consumed to yield a product in which the pterin moiety is covalently linked to the thymine. This compound retains some of the spectroscopic properties of Ptr, such as absorbance in the UV-A region and fluorescence properties.

Time-resolved study of thymine dimer formation.

The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (<1.4 x 10-3) or the triplet state reacts with unit efficiency in less than 200 ns to yield cyclobutane dimers.

Release of unaltered bases from polycrystalline pyrimidine DNA constituents after X-irradiation and bombardment with heavy ions.

PURPOSE: The radiation-induced release of unaltered bases from the lyophilized pyrimidine DNA constituents TMP, dCMP, CMP and dCyd was determined quantitatively in order to study explicitly the direct radiation effect. MATERIALS AND METHODS: X-irradiation under an air or a nitrogen gas atmosphere and heavy ion bombardment in the beam vacuum were employed at 300 K. The release of free bases was investigated using HPLC and 1H-NMR. Dose-yield curves for free radicals of X-irradiated TMP and dCMP samples were determined by EPR spectroscopy. RESULTS: As one of the main products, the release of unaltered bases is linear with dose up to 360 kGy for X-irradiation or 200 kGy for heavy ion bombardment. The estimation of the radiation chemical yields revealed G values of about 10(-7) mol J-1. The heavy ion bombardment and X-irradiation under nitrogen effected a lower yield for base release than that for X-irradiation under air. For X-irradiation at sufficiently high doses about one order of magnitude difference in yields between bases released and free radicals formed was found. CONCLUSIONS: Compared with related findings as described in the literature, the G values from DNA are in the same order of magnitude, but from nucleosides in frozen aqueous solutions the yields of free bases are several orders of magnitude smaller.

Influence of electron scavengers on the radical formation in thymidine-5'-monophosphate and DNA in frozen aqueous solution and glasses.

Structural and quantitative effects of different electron scavenger concentrations on the free radical formation in the nucleotide thymidine-5'-monophosphate (TMP) and in deoxyribonucleic acid (DNA) after X-irradiation in frozen aqueous solution and glasses (BeF2/H2O for TMP and LiCl/H2O for DNA) at 77K are investigated. At the highest concentration used (100 mmol dm-3) about 80% (TMP) and 70% (DNA) of the radicals are scavenged compared with the control in both matrices. In TMP, allyl radicals form the major population of radicals left unscavenged at 77 K. These are shown to transform into a quintet pattern upon annealing (> or = 220 K). Analysis of various substances for quintet formation shows that a sugar-group and a C4-carbonyl group are necessary structural prerequisites. For DNA three components can be extracted from spectra obtained with different scavenger concentration in frozen solutions. There are two components in LiCl glasses, which are comparable with two of the three in frozen aqueous solution. Their potential origin is discussed in comparison with nucleotide spectra.

Reaction of cysteamine with individual DNA base radicals in gamma-irradiated nucleotides at low temperature.

An ESR investigation of the individual DNA base radicals produced by gamma-irradiation of frozen solutions of the nucleotides TMP, dCMP, dGMP and dAMP and their reactions with cysteamine upon annealing is reported. The results show that water radicals in bulk ice do not lead to the formation of DNA or cysteamine radicals. Radicals from the oxidation pathway which include the DNA base one electron oxidized radicals and their successors, G(C8)OH., A(C8)OH. and thymine dimers (.Tdi) and/or T(C6)OH; readily react with cysteamine to form RS. and ultimately RSSR-. Reactions of dGMP and dCMP radicals from the oxidation pathway with cysteamine occur at lower temperatures than those of dAMP and TMP, suggesting hole migration. Both T(C6)H. and C(N3)H. react with cysteamine to form RS. and diamagnetic products, but G(C8)H. and A(C8)H. do not. Subtraction of the anion radical T-. and its proton adduct T(C6)H. from the total radical yield of TMP (with or without cysteamine) suggests that somewhat less than half of the total TMP radicals found are a result of the oxidative pathway. Similar results are found in the other nucleotides. The total spectral intensity derived from the radicals from the oxidative pathway such as G(C8)OH., A(C8)OH. and .Tdi/T(C6)OH. are somewhat less than that for the protonated anion radicals. Only one non-base radical is identified, a sugar radical at the C(1)' site on the deoxyribose portion of dAMP. This species, S(A)., is also found to react with cysteamine or its disulfide radical anion. Analyses performed in the presence and absence of a thiol are found to allow for a clear separation of oxidative and reductive pathways.

Mechanistic aspects of radiation-induced free radical formation in frozen aqueous solutions of DNA constituents: consequences for DNA?

Frozen aqueous solutions of 1 M thymidine-5'-monophosphate were X-irradiated 77 K. The free radicals formed were analyzed by electron spin resonance spectroscopy between 77 K and about 260 K and were shown to result nearly exclusively from electron reaction at 77 K forming the thymine base anion, which converts into the well known 5-thymyl radical upon annealing. Primary oxidation of the substrate was not detectable. A minority species denoted TOH., which appeared at about 200 K, was suggested to result from OH. addition to carbon C6 of the base, perhaps via intermediate oxidation involving H2O2 or from direct reaction of OH. with the base. Another minority species at 77 K up to about 150 K, which was strongly enhanced by H2O2, was shown to be the allyl radical formed by reaction of the OH. with the methyl group. Support for this was given from experiments using BeF2 glasses. The possible spectral features for the cation of dTMP were extracted from aqueous pastes of the Ca2+ salt at 77 K. The mechanistic aspects derived from the results are in conflict with previous assumptions and are discussed for DNA model compounds and DNA.

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.

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.

Formation of radiation-induced cross-links between thymine and tyrosine: possible model for cross-linking of DNA and proteins by ionizing radiation.

A model for radiation-induced cross-linking of DNA and proteins has been developed. It is based on initial formation of free radicals on a DNA base, i.e., thymine, and on an amino acid, i.e., tyrosine. It was demonstrated that interaction of these radicals is highly favored as measured by their kinetics and the cross-linked products. The gas chromatography-mass spectrometry methodology used for the identification of the thymine-tyrosine cross-links is suggested as an experimental approach in the measurements of biological cross-links.

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.

The use of capillary gas chromatography-mass spectrometry for identification of radiation-induced DNA base damage and DNA base-amino acid cross-links.

Application of capillary gas chromatography-mass spectrometry (GC-MS) to isolation and identification of radiation-induced DNA base damage including DNA base-amino acid crosslinks is reported. gamma-Irradiated samples of thymine (thy), thymidine (dT), thymidine-5'-monophosphate (pdT), cytosine(cyt),2'-deoxycytidine (dC), 2'-deoxycytidine-5'-monophosphate (pdC), and mixtures of thy, dT and pdT with tyrosine were used as model systems. Trimethylsilylation was used as the derivatization method. Samples containing nucleosides and nucleotides were first subjected to hydrolysis with formic acid or hydrochloric acid to remove sugar or sugar-phosphate moieties, then trimethylsilylated and analyzed by GC-MS. Trimethylsilyl derivatives of radiation-induced monomeric and dimeric products of the model systems mentioned above were shown to have excellent GC properties and easily interpretable mass spectra. The presence of the molecular ion (M+.) and a characteristic (M-CH3)+ ion in the mass spectra facilitated structural elucidation. The complementary use of tert.-butyldimethylsilyl derivatives was also demonstrated. These derivatives provided an intense characteristic (M-57)+ ion in their mass spectra, which may be used to corroborate the molecular weight and to monitor the corresponding compounds in a complex mixture by means of selected-ion monitoring. All gas chromatograms and mass spectra obtained are discussed in detail.

[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.

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.

Radiation-induced reactions of thymine, thymidine and thymidine-5'-monophosphate in aqueous solutions.

Radiochemical reactivities of thymine (T), thymidine (Td), thymidine-3' and 5'-monophosphates (3'-, 5'-TMP) and thymidylyl (3' leads to 5') thymidine (TpT) varied in the following order: [A] T (G-value for decomposition, 1.81) less than Td (2.14) less than 3'-TMP = TpT (2.51) less than 5'-TMP (2.76) in deaerated aqueous solution; [B] TpT (2.82) less than T (3.17) congruent to Td (3.18) less than 3'-TMP (3.49) less than 5'-TMP (3.65) in N2O-saturated aqueous solution; [C] T (2.70) congruent to TpT (2.73) less than Td (2.81) less than 3'-TMP = 5'-TMP (3.47) in deaerated aqueous solution containing sodium formate.