Monitoring the direct and indirect damage of DNA bases and polynucleotides by using time-resolved infrared spectroscopy.

The nucleotide 5'-dGMP and polynucleotide poly(dGdC).poly(dGdC) have been irradiated by using a 200-fs, 200-nm laser pulses and spectrally characterized by using time-resolved infrared spectroscopy. Under the experimental conditions, 200-nm excitation generates both electronic excited states and radical cations through photoionization; the former decay rapidly to vibrationally hot ground state. By using infrared signatures we have been able to follow these processes, and at time scales of >1 ns we observe an infrared marker band at 1,702 cm(-1) within both 5'-dGMP and the polynucleotide assigned to a photoionized product of guanine. This transient has also been reproduced through indirect chemistry through the reaction with photogenerated carbonate radical with 5'-dGMP. The ability to use time-resolved infrared spectroscopy in this way paves the way for developing solution-phase studies to investigate both direct and indirect radiation chemistry of DNA.

Age-related changes in the induction of DNA polymerases in rat liver by gamma-ray irradiation.

DNA polymerase activities related to DNA repair were examined in the livers of young (6-month-old) and aged (27-month-old) rats irradiated with gamma-rays. The activity of DNA polymerase alpha was little changed in the livers of gamma-ray-irradiated rats, while DNA polymerases beta and gamma were induced in the livers of young and aged rats exposed by gamma-ray irradiation. These enzymes were induced from 2 to 6 h after irradiation of young and aged rats, respectively, although the induction in aged rats was weak. DNA polymerase beta activity in the livers of young rats irradiated with gamma-rays was 2-fold that in aged rats. Similarly, DNA polymerase gamma activity in the livers of young rats subjected to gamma-ray irradiation was 3-fold that in aged rats. The induction of proliferating cell nuclear antigen (PCNA) in the livers of aged rats irradiated with gamma-rays was also delayed compared with young rats. These results indicate that the decline in repair activity in aged rats leads to the accumulation of oxidative damage and DNA mutations in aged tissues.

Effects of cytosine methylation on pyrimidine dimer formation in DNA.

The relative induction of cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone photoproducts ([6-4]PD) was quantified in the duplex homopolymers polydeoxyadenosine:polydeoxythymidine, polydeoxyguanosine:polydeoxycytidine and polydeoxyguanosine:polydeoxy-5-methylcytidine irradiated with UVC or UVB radiation. Cytosine methylation significantly increased the yield of cytosine (6-4)PD after irradiation with UVC light and of cytosine CPD and (6-4)PD after irradiation with UVB light. The data suggest that CPD and (6-4)PD are preferentially induced at 5-methylcytosine bases in DNA of cells exposed to sunlight and comprise a major component of the mutation spectrum leading to the initiation of sunlight-induced skin cancer.

Preparation of insolubilized-DNA film with three-dimensional network and removal of endocrine disruptors.

A water-insolubilized film was prepared by UV irradiation on a dried DNA film. When a UV-irradiated DNA was examined using a circular dichroism spectroscopy, a double stranded structure was observed as well as that of native DNA. The UV irradiated DNA film was also accumulated intercalating reagents. These results suggested that the double stranded structure was involved in the UV irradiated DNA film with a three-dimensional network. The thymine-thymine dimer formation was suggested to be involved in the cross-linking reactions by the polymerization analysis using poly(dA)-poly(dT) and poly(dG)-poly(dC). We also demonstrate the utilization of the UV-irradiated DNA film as a functional material for the accumulation of harmful DNA intercalating pollutants in aqueous solution. These results suggested that the UV-irradiated DNA film was applicable as a functional material for medical, engineering and environmental sciences.

Fibre X-ray study of the helix-helix transitions of poly(dG-dC).poly(dG-dC).

Poly(dG-dC).poly(dG-dC) and poly(dG-m5dC).poly(dG-m5dC) present helix-helix transitions which are commonly assumed to be changes between the right-handed A- or B-DNA double helices and the left-handed Z-DNA structure. The mechanisms for such transconformations are highly improbable especially when they are supposed to be active in long polynucleotide chains organised in semicrystalline fibres. The present alternative possibility assumes that rather than the Z-DNA it is a right-handed double helix (S-DNA) which actually takes part in these form transitions. Two molecular models of this S form, in good agreement with X-ray measurements, are proposed. They present alternating C(2')-endo and C(3')-endo sugar puckering. Dihedral angles, sets of atomic co-ordinates and stereo views of the two S-DNA structures are given together with curves of calculated diffracted intensities.

Laser-induced modification of DNA and Poly[A,G] at guanine moiety using acetone as photosensitizer.

The interactions of triplet acetone with polyadenylic acid (Poly[A]), polyguanylic acid (Poly[G]), polyadenylic-guanylic acid (Poly[A,G]) and single-stranded DNA (ssDNA) were investigated in neutral aqueous solution using KrF (248 nm) laser flash photolysis. The transient absorption spectra and kinetics of DNA and polynucleotides obtained under acetone sensitization demonstrated that the predominant transient species was guanine radical. These novel findings have offered time-resolved evidence for photochemical modification of DNA and Poly[A,G] at guanine moiety.

Oxidative damage to 5-methylcytosine in DNA.

Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl group yields 5-hydroxymethyluracil. Oxidation of the 5,6 double bond of cytosine yields cytosine glycol, which decomposes to 5-hydroxycytosine, 5-hydroxyuracil and uracil glycol, all of which are repaired in DNA by Escherichia coli endonuclease III. We now describe the products of oxidation of 5-methylcytosine in DNA. Poly(dG-[3H]dmC) was gamma-irradiated or oxidized with hydrogen peroxide in the presence of Fe3+ and ascorbic acid. The oxidized co-polymer was incubated with endonuclease III or 5-hydroxymethyluracil-DNA glycosylase, to determine whether repairable products were formed, or digested to 2'-deoxyribonucleosides, to determine the total complement of oxidative products. Oxidative attack on 5-methylcytosine resulted primarily in formation of thymine glycol. The radiogenic yield of thymine glycol in poly(dG-dmC) was the same as that in poly(dA-dT), demonstrating that 5-methylcytosine residues in DNA were equally susceptible to radiation-induced oxidation as were thymine residues.

Photochemistry of DNA and related biomolecules: quantum yields and consequences of photoionization.

The reactions of nucleic acids and constituents, which can be induced by laser UV irradiation, are described. Emphasis is placed on the quantum yields of various stable photoproducts of DNA and model compounds upon irradiation at 193, 248, 254 or 266 nm. In particular, those quantum yields and processes are discussed which involve photoionization as the initial step and occur in aqueous solution under well defined conditions, e.g. type of atmosphere. The efficiencies of some photoproducts, with respect to photoionization using irradiation at 193 or 248 nm, are presented. Radical cations of nucleobases are important sources of damage of biological substrates since they can cause lesions other than dimers and adducts, e.g. strand breakage, abasic sites, crosslinks or inactivation of plasmid and chromosomal DNA. While competing photoreactions, such as hydration, dimerization or adduct formation, diminish the selectivity of the photoionization method, a combination with model studies on pyrimidine- and purine-containing constituents of DNA has brought about an enhanced insight into the reaction mechanisms. The knowledge concerning the lethal events in plasmid and cellular DNA has been greatly improved by correlation with the chemical effects obtained by gamma-radiolysis, vacuum-UV (< 190 nm) and low-intensity irradiation at 254 nm.

Metal-ion assisted, radiation-induced conversion of B- to Z-DNA in poly (dGdC) and two natural DNAs.

Metal-ion assisted, gamma-radiation-induced B-Z conformation changes have been observed with UV and circular dichroism spectroscopy for poly (dGdC), calf thymus and herring testis DNA. These conformational changes are similar to those induced by increasing multivalent metal ion concentrations in DNA containing alternating purine and pyrimidine base sequences. In both the metal-ion-induced and the metal-ion-assisted, radiation-induced conformation changes, the conversions were from the right-handed B-DNA to the left-handed Z-DNA conformation. It is proposed that radiation-induced DNA strand breaks markedly reduce the high activation energy barrier in the metal ion-driven B-Z conformation conversion and allow much smaller metal ion concentrations to induce this conversion than in the absence of strand breaks. The biological importance of such radiation-induced conformational changes is discussed in terms of the potential significance of the Z-DNA conformation in the control of the DNA transcription process.

Damage to uracil- and adenine-containing bases, nucleosides, nucleotides and polynucleotides: quantum yields on irradiation at 193 and 254 nm.

Photoreactions, such as base release and decomposition of the base moiety, induced by either 20 ns laser pulses at 193 nm or continuous 254 nm irradiation, were studied for a series of uracil and adenine derivatives in neutral aqueous solution. The quantum yield of chromophore loss (phi cl) depends significantly on the nature of the nucleic acid constituent and the saturating gas (Ar, N2O or O2). In the case of polynucleotides the destruction of nucleotides was measured by high-performance liquid chromatography after hydrolysis; the quantum yields (phi dn) are comparable to those of chromophore loss or larger. The phi cl and phi dn of 0.04-0.1 for poly(U) and poly(dU), obtained for both wavelengths of irradiation, are due to processes originating from the lowest excited singlet state, i.e. formation of photohydrates and photodimers, and a second part from photoionization using lambda irr = 193 nm. Irradiation at 193 nm effectively splits pyrimidine dimers and thus reverts them into monomers. The quantum yield for release of undamaged bases (phi br) from nucleosides, nucleotides and polynucleotides upon irradiation at 254 nm is typically phi br = (0.1-1) x 10(-4). Breakage of the N-glycosidic bond is significantly more efficient for lambda irr = 193 nm, e.g. phi br = 1.1 x 10(-3), 0.8 x 10(-3), 4.3 x 10(-3) and 0.5 x 10(-3) for poly(A), poly(dA), poly(U) and poly(dU) in Ar-saturated solution, respectively. Enhanced phi values for lambda irr = 193 nm, essentially for adenine and its derivatives, are caused by photoprocesses that are initiated by photoionization.

Excision of ultraviolet-induced photoproducts of 5-methylcytosine from DNA.

Transition mutations at DNA 5-methylcytosines, congregated at CpG islands, are implicated in the etiogenesis of human diseases. Formation of 5-methylcytosine hydrate (5-methyl-6-hydroxy-5,6-dihydrocytosine) by hydration of the 5,6 double bond of 5-methylcytosine has been suggested as an intermediate in a possible mechanism of deamination to thymine. Ultraviolet irradiation of DNA yields pyrimidine hydrates, which are removed by repair glycosylases. We have identified 5-methylcytosine photoproducts following their excision from DNA by E. coli endonuclease III. Poly(dG-[3H]5-medC):poly(dG-[3H]5-medC) was irradiated and reacted with the enzyme. Radiolabeled photoproduct releases were directly proportional to irradiation doses and enzyme concentrations. These were identified as cis-thymine hydrate (6-hydroxy-5,6-dihydrothymine) and trans-thymine hydrate. Recovery of thymine hydrates is consistent with hydration of pyrimidines. Subsequent heating (which converts thymine hydrates to thymines) and chemical sequencing of an irradiated, 3' end-labeled, synthetic DNA strand demonstrated the appearance of thymine at the 5-methylcytosine site. These results demonstrate a mechanism for deamination of DNA 5-methylcytosine via hydration of the 5,6 double bond, putatively yielding 5-methylcytosine hydrate; this deaminates to thymine hydrate, and loss of water yields thymine formation at the 5-methylcytosine site. Identification of these DNA 5-methylcytosine modified moieties indicates a possible molecular mechanism for the frequent transition mutations found at CpG loci.

Protonation of nucleobase anions in gamma-irradiated DNA and model systems. Which DNA base is the ultimate sink for the electron?

Electron spin resonance (ESR) spectroscopy has been used to investigate irreversible protonations of the nucleobase anions in gamma-irradiated frozen aqueous solutions of dGMP-dCMP, polyG-polyC, poly[dGdC].poly[dGdC], dAMP-dTMP, poly[dAdT].poly-[dAdT] and DNA itself. Analysis of the ESR spectra at a dose of 22 kGy shows that fractional conversion of total radicals to carbon-protonated species on annealing is in the order: dAMP-dTMP (43%) > pdAdT = DNA (23%) > dGMP.dCMP (15%) > poly-dGdC.polydGdC (6%) > polyG.polyC (3%). Two hydrogen addition radicals make contributions to the polyG.polyC, poly-[dGdC].poly[dGdC] and dGMP.dCMP spectra in H2O on annealing. They are those formed by protonations at C6 of the cytosine anion radical, C(C6)H., and at C8 of the guanine anion radical, G(C8)H.. Computer analysis reveals that anion protonation reaction in dGMP.dCMP results in mainly C(C6)H., whereas protonation reaction in polyG.polyC and poly[dGdC].poly-[dGdC] yields mainly G(C8)H.. In dAMP.dTMP and poly[dAdT].poly[dAdT] as in DNA itself, the only DNA base found to undergo an irreversible protonation at a carbon site is thymine, resulting in T(C6)H.. The conversion of DNA anion to T(C6)H. is found to be dependent on dose. At low doses (5 kGy), about 30% conversion to T(C6)H. is found, whereas at high doses (94 kGy), only 13% conversion is found. The dose dependence is ascribed in part to ion radical recombinations whose probabilities are increased at high doses. A consideration of the rates of protonations of the purine and pyrimidine anion radicals as well as the differences in electron affinities suggest carbon protonation reactions of DNA base anions in irradiated stacked double-strand DNA at 37 degrees C would be predominantly at thymine and perhaps guanine, whereas in single-strand DNA all bases would contribute.

Influence of primary structure on initial free radical products trapped in A:T polydeoxynucleotides X-irradiated at 4 K.

EPR measurements were made at Q-band microwave frequencies on powder samples pressed into pellets and X-irradiated at 4 K. Measurements were made at 4 K after no anneal, then after a 77 K anneal, and then after a 300 K anneal. In poly(dA):poly(T) the free radical distribution is approximately a simple sum of the distributions in the separate homopolymers. In poly(dA-T) the free radical distribution differs from that of poly(dA):poly(T). The clearest difference is that in poly-(dA):poly(T) the concentration of one-electron-reduced thymine (Tre.) is reduced relative to the total radical concentration. On warming the thymine-containing samples from 77 K to room temperature, the Tox. radical disappears and the (T-H5'). radical appears. Also, the Tre. radical disappears and the (T + H6). radical appears. There are three main conclusions. First, little or no transfer of free radicals between strands is needed to explain the data. Second, when A and T are interstacked, either the Tre. radical is less stable against recombination than other radical products or radical transfer occurs to an adjacent adenine. Third, in the poly- and oligonucleotides, the Tox. radical is a likely precursor to the (T-H5'). radical.

Room-temperature steady-state fluorescence properties of poly(dG-dC).poly(dG-dC).

We report the steady-state fluorescence properties of the alternating polynucleotide poly(dG-dC).poly(dG-dC) in low-salt solution at room temperature for excitation at the Hg lines 265, 280 and 297 nm. Its fluorescence spectrum peaks at about 325 nm and, within the experimental error, its shape does not change significantly with the excitation wavelength. The fluorescence anisotropy is found to decrease strongly for short-wavelength excitation, a behavior which is very similar to that exhibited by free guanine. In view of the fact that the anisotropy for free cytosine is virtually constant at the aforementioned three excitation wavelengths, the results suggest that in this polynucleotide the emission stems from guanine. The values of the fluorescence quantum yield for the three excitation wavelengths are found to be very low, 0.8 x 10(-5), 0.8 x 10(-5), and 2.8 x 10(-5), respectively; these are compatible with transfer of energy from the lower-energy electronic state of guanine, before vibronic relaxation is established, to cytosine. Upon denaturation, the fluorescence spectrum becomes very broad and the fluorescence quantum yield increases; these observations support the authenticity of the emission from the nondenatured polynucleotide.

[The inhibition by the tumor necrosis factor of the death and DNA fragmentation of lymphoid cells in irradiated rats]. / Ingibirovanie faktorom nekroza opukholi gibeli i fragmentatsii DNK limfoidnykh kletok obluchennykh krys.

The influence of a tumor necrosis factor, administered 16 h before irradiation of rats, on the radiation response of thymus and bone marrow cells has been investigated. Three and 6 h after irradiation the following indices were analyzed: the number of apoptotic cells in the thymus; the accumulation of polydeoxyribonucleotides and the appearance of single-strand breaks in DNA of bone marrow and thymus cells; and the electrophoretic properties of thymocyte DNA. The injection of a tumor necrosis factor reduced the number of polydeoxyribonucleotides, inhibited internucleosome DNA fragmentation, and did not influence the formation of single-strand breaks in DNA.

Formation and stability of repairable pyrimidine photohydrates in DNA.

Ultraviolet irradiation of poly(dG-dC) and poly(dA-dU) in solution produces pyrimidine hydrates that are repaired by bacterial and mammalian DNA glycosylases [Boorstein et al. (1989) Biochemistry 28, 6164-6170]. Escherichia coli endonuclease III was used to quantitate the formation and stability of these hydrates in the double-stranded alternating copolymers poly(dG-dC) and poly(dA-dU). When poly(dG-dC) was irradiated with 100 kJ/m2 of 254-nm light at pH 8.0, 2.2% of the cytosine residues were converted to cytosine hydrate (6-hydroxy-5,6-dihydrocytosine) while 0.09% were converted to uracil hydrate (6-hydroxy-5,6-dihydrouracil). To measure the stability of these products, poly(dG-dC) was incubated in solution for up to 24 h after UV irradiation. Cytosine hydrate was stable at 4 degrees C and decayed at 25, 37, and 55 degrees C with half-lives of 75, 25, and 6 h. Uracil hydrate produced in irradiated poly(dA-dU) was stable at 4 degrees C and at 25 degrees C and decayed with a half-life of 6 h at 37 degrees C and less than 0.5 h at 55 degrees C. Uracil hydrate and uracil were also formed in irradiated poly(dG-dC). These experiments demonstrate that UV-induced cytosine hydrate may persist in DNA for prolonged time periods and also undergo deamination to uracil hydrate, which in turn undergoes dehydration to yield uracil. The formation and stability of these photoproducts in DNA may have promoted the evolutionary development of the repair enzyme endonuclease III and analogous DNA glycosylase/endonuclease activities of higher organisms, as well as the development of uracil-DNA glycosylase.

Formation of alpha-deoxyadenosine in polydeoxynucleotides exposed to ionizing radiation under anoxic conditions.

When poly(dA), poly(dA-dT), and salmon testis DNA were gamma-irradiated under nitrogen, the major deoxyadenosine damage product (excluding liberated adenine) was identified as the alpha-anomer of deoxyadenosine. The yields of alpha-deoxyadenosine from poly(dA), poly(dA-dT), and salmon testis DNA irradiated with a dose of 500 Gy under anoxic conditions were 1.5, 1.3, and 1.3%, respectively. No alpha-deoxyadenosine was detected after irradiation under oxic conditions. The presence of nucleotides with the alpha-configuration at the anomeric carbon atom in the DNA chain may have a significant effect on its tertiary structure and possibly modify its biological activity.

Extensive photodimerization of non-adjacent pyrimidines.

In a prior study we found that non-adjacent thymidyl residues in the single-stranded alternating copolymer poly[d(G-T)] are subject to photodimerization by germicidal lamp irradiation (lambda max 254 nm). The maximum yield of this photoproduct was 1% of the total thymine of poly[d(G-T)]. We now report that dimer formation in this polymer is increased to 10 to 40% thymine as dimer between non-adjacent pyrimidines, using near-ultraviolet irradiation (lambda max 310 nm) with or without acetone triplet-sensitization. As previously observed for 254 nm irradiation, dimer formation was nearly absent in double-stranded poly[d(G-T).d(C-A)]. These observations extend prior findings by demonstrating high-yield dimerization between non-adjacent pyrimidines via direct irradiation at environmentally relevant wavelengths (greater than or equal to 280 nm), and are potentially relevant to the mechanism of the ultraviolet light-induced targeted -1 frameshift mutation.

UV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activities.

Escherichia coli endonuclease III and mammalian repair enzymes cleave UV-irradiated DNA at AP sites formed by the removal of cytosine photoproducts by the DNA glycosylase activity of these enzymes. Poly(dG-[3H]dC) was UV irradiated and incubated with purified endonuclease III. 3H-Containing material was released in a fashion consistent with Michaelis-Menten kinetics. This 3H material was determined to be cytosine by chromatography in two independent systems and microderivatization. 3H-Containing material was not released from nonirradiated copolymer. When poly(dA-[3H]dU) was UV irradiated, endonuclease III released 3H-containing material that coeluted with uracil hydrate (6-hydroxy-5,6-dihydrouracil). Similar results are obtained by using extracts of HeLa cells. There results indicate that the modified cytosine residue recognized by endonuclease III and the mammalian enzyme is cytosine hydrate (6-hydroxy-5,6-dihydrocytosine). Once released from DNA through DNA-glycosylase action, the compound eliminates water, reverting to cytosine. This is consistent with the known instability of cytosine hydrate. The repairability of cytosine hydrate in DNA suggests that it is stable in DNA and potentially genotoxic.