Wavelength dependence of the formation of single-strand breaks and base changes in DNA by the ultraviolet radiation above 150 nm

Dose-Rate Effects in Breaking DNA Strands by Short Pulses of Extreme Ultraviolet Radiation

In this study, we examined dose-rate effects on strand break formation in plasmid DNA induced by pulsed extreme ultraviolet (XUV) radiation. Dose delivered to the target molecule was controlled by attenuating the incident photon flux using aluminum filters as well as by changing the DNA/buffer-salt ratio in the irradiated sample. Irradiated samples were examined using agarose gel electrophoresis. Yields of single- and double-strand breaks (SSBs and DSBs) were determined as a function of the incident photon fluence. In addition, electrophoresis also revealed DNA cross-linking. Damaged DNA was inspected by means of atomic force microscopy (AFM). Both SSB and DSB yields decreased with dose rate increase. Quantum yields of SSBs at the highest photon fluence were comparable to yields of DSBs found after synchrotron irradiation. The average SSB/DSB ratio decreased only slightly at elevated dose rates. In conclusion, complex and/or clustered damages other than cross-links do not appear to be induced under the radiation conditions applied in this study.

Measuring the density of DNA films using ultraviolet-visible interferometry

In order to determine a proper value for the density of dry DNA films we have used a method based upon the measurement of interference effects in transmission spectra of thin DNA layers. Our results show that the methodology is effective and the density of DNA in this state, 1.407 g/cm(3), is much lower than the commonly used 1.7 g/cm(3). Obtaining accurate values for the DNA film density will allow the optical constants for DNA to be recalculated, which were previously obtained assuming a higher DNA density. Furthermore, since our recent investigations have shown a strong dependence of the sample composition on DNA film formation and thus on its density, such a method will be important in characterizing particle interactions with DNA film and their dose dependence.

Biological responses to the simulated Martian UV radiation of bacteriophages and isolated DNA

Mars is considered as a main target for astrobiologically relevant exploration programmes. In this work the effect of simulated Martian solar UV radiation was examined on bacteriophage T7 and on isolated T7 DNA. A decrease of the biological activity of phages, characteristic changes in the absorption spectrum and in the electrophoretic pattern of isolated DNA/phage and the decrease of the amount of PCR products were detected indicating damage of isolated and intraphage T7 DNA by UV radiation. Further mechanistic insights into the UV-induced formation of intraphage/isolated T7 DNA photoproducts were gained from the application of appropriate enzymatic digestion and neutral/alkaline agarose gel electrophoresis. Our results showed that intraphage DNA was about ten times more sensitive to simulated Martian UV radiation than isolated T7 DNA indicating the role of phage proteins in the DNA damage. Compared to solar UV radiation the total amount of DNA damage determined by QPCR was about ten times larger in isolated DNA and phage T7 as well, and the types of the DNA photoproducts were different, besides cyclobutane pyrimidine dimers (CPD), double-strand breaks (dsb), and single-strand breaks (ssb), DNA-protein cross-links were produced as well. Surprisingly, energy deposition as low as 4-6 eV corresponding to 200-400 nm range could induce significant amount of ssb and dsb in phage/isolated DNA (in phage the ratio of ssb/dsb was approximately 23%/12% and approximately 32%/19% in isolated DNA). 5-8% of the CPD, 3-5% of the AP (apurinic/apyrimidinic) sites were located in clusters in DNA/phage, suggesting that clustering of damage occur in the form of multiple damaged sites and these can have a high probability to produce strand breaks. The amount of total DNA damage in samples which were irradiated in Tris buffer was reduced by a factor approximately 2, compared to samples in phosphate buffer, suggesting that some of the photoproducts were produced via radicals.

Histological Changes and Unscheduled DNA Synthesis in the Rabbit Cornea Following 213-nm, 193-nm, and 266-nm Irradiation

PURPOSE

To examine the acute outcome of corneal irradiation in adult rabbits for 193-, 213-, and 266-nm laser wavelengths.

METHODS

Animals were randomly allocated to one of three groups and were treated with 213-nm quintupled Nd:YAG laser, a 193-nm excimer laser, or a 266-nm quadrupled Nd:YAG laser (n = 6 per group, two exposure durations). Thermal damage was assessed histologically and the extent of DNA damage estimated by measuring unscheduled DNA synthesis in corneal epithelial and stromal cells using 3H thymidine autoradiography.

RESULTS

For the 193- and 213-nm groups, irradiation did not induce thermal damage. Moreover, cells displaying unscheduled DNA synthesis represented < 4% of the total cell numbers with no difference between groups (P > .05). By contrast, the 266-nm laser led to stromal melting and vacuolation; unscheduled DNA synthesis levels were elevated over the other groups (P < .05).

CONCLUSIONS

Corneal laser ablation with the 213-nm Nd:YAG laser resulted in similarly low levels of thermal and DNA damage to those produced using the clinically accepted 193-nm excimer laser.

Photorefractive keratectomy and cataract

Fifty male albino rabbits were studied. Ten animals served as controls. Forty animals were prepared to receive photorefractive keratectomy (PRK), including anesthesia, scraping of the corneal epithelial cells, etc. Twenty of these animals then received PRK with energy delivered by excimer laser (pulse rate = 20 Hz, fluence 250 mJ/cm2; number of pulses = 6032; cumulative UV dose = 1508J/cm2). The other 20 animals were exposed to the same operating microscope light as the PRK-treated animals, but they did not receive PRK. All three groups were divided into halves: the first half was immediately analyzed at 0 time, and the second half was observed 1 year later. Samples of aqueous humor and lens were analyzed. The levels of reduced and oxidized glutathione, hydrogen peroxide, ascorbic acid, and malondialdehyde were determined. Excimer laser-induced ultrastructural modifications of the lens, verified through scanning electron microscopy, were studied at the same intervals. Immediately after PRK, the biochemical parameters studied, both in aqueous humor and in lens of treated animals, showed significant differences. One year later, the observed biochemical variations in lens were still present, whereas aqueous humor values did not significantly differ from control values. Ultrastructural abnormalities of the lens appeared only 1 year after PRK In the animals that received only the preparation for PRK the biochemical and ultrastructural differences did not significantly vary as compared to the data obtained from control animals. These findings suggest that the biochemical and ultrastructural lens alterations induced by PRK may represent events relevant to cataractogenesis in the rabbit.

The reaction of triplet 2-methyl-1,4-naphthoquinone (menadione) with DNA and polynucleotides

The photoreaction of 2-methyl-1,4-naphthoquinone (MQ, menadione) with DNA and polynucleotides in argon-saturated aqueous solution (pH 7) was studied. Results from laser flash photolysis experiments indicate that triplet quinone reacts with DNA and polyA but not detectably with polyU by one-electron oxidation of the bases of the nucleic acid with formation of the radical anion of the quinone. Irradiation of argon-saturated solutions containing MQ and DNA or polynucleotides (polyU, polyA, polyG or polyC) with 334 nm light leads to an increase in molecular weight for single-stranded DNA, polyA and to a much less extent for polyU. This finding indicates crosslink formation with quantum yields in the range of 10(-5)-10(-3).

Effects of vacuum UV and UVC radiation on dry E. coli plasmid pUC19. I. Inactivation, lacZ- mutation induction and strand breaks

Using Escherichia coli plasmid pUC19 as a test system to study the effects of radiation on DNA at the molecular level, the wavelength (160-254 nm) dependence of inactivation (loss of the ability to transform E. coli), mutation induction in the target gene lacZ and induction of single-strand breaks and double-strand breaks was investigated. The same fluences were applied for all endpoints tested. In the UVC range, the cross-sections of inactivation and mutation induction match the DNA absorption curve, whereas the cross-section for single-strand break induction deviates from the DNA curve, especially at 220 nm. In the vacuum UV range, with increasing energy of the photons, the cross-sections of inactivation and single-strand breaks increase sharply (from 190 to 160 nm by more than one order of magnitude), which is not reflected by the DNA curve. In this UV range, the shape of the action spectrum is similar to that of the absorption curve of the sugar phosphate moiety of DNA. Only after irradiation with vacuum UV at 160 nm are double-strand breaks detected. Their induction rate is about one order of magnitude lower than that of single-strand breaks at the same wavelength; however, their induction rate is at least twice that of single-strand breaks at longer wavelengths. Concerning mutation induction, the increment in the vacuum UV range is less well expressed. The data suggest the contribution of different kinds of photochemical injury to inactivation and mutation induction.

Alterations in the internucleosomal DNA helical twist in chromatin of human erythroleukemia cells in vivo influences the chromatin higher-order folding

In the present study chloroquine diphosphate, a DNA intercalating drug, was used to alter the internucleosomal DNA helical twist in chromatin of living mammalian cells. The intercalative binding of chloroquine effectively unwinds the DNA double helix and its binding is restricted to nucleosomal linker regions without noticeable disruption of nucleosomes. The results presented here imply that the alterations in the rotation angle between the adjacent nucleosomes in chromatin of eukaryotic cells in vivo significantly influences the way the chain of nucleosomes folds in higher-order chromatin structures, as evidenced by specific alterations in nuclease susceptibility of chromatin.

Exobiology, the study of the origin, evolution and distribution of life within the context of cosmic evolution: a review

The primary goal of exobiological research is to reach a better understanding of the processes leading to the origin, evolution and distribution of life on Earth or elsewhere in the universe. In this endeavour, scientists from a wide variety of disciplines are involved, such as astronomy, planetary research, organic chemistry, palaeontology and the various subdisciplines of biology including microbial ecology and molecular biology. Space technology plays an important part by offering the opportunity for exploring our solar system, for collecting extraterrestrial samples, and for utilizing the peculiar environment of space as a tool. Exobiological activities include comparison of the overall pattern of chemical evolution of potential precursors of life, in the interstellar medium, and on the planets and small bodies of our solar system; tracing the history of life on Earth back to its roots; deciphering the environments of the planets in our solar system and of their satellites, throughout their history, with regard to their habitability; searching for other planetary systems in our Galaxy and for signals of extraterrestrial civilizations; testing the impact of space environment on survivability of resistant life forms. This evolutionary approach towards understanding the phenomenon of life in the context of cosmic evolution may eventually contribute to a better understanding of the processes regulating the interactions of life with its environment on Earth.

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.

DNA damage induced by vacuum and soft X-ray photons from synchrotron radiation

The recent development of irradiation systems using synchrotron radiation (SR) as a source is enabling researchers to obtain intense monochromatic photons having a narrow bandwidth in the vacuum-UV (VUV) and soft X-ray regions. We can thus systematically study the photon energy dependence of DNA damage formation in these energy regions. The photon energy dependence provides useful information about how energy-absorbing modes--excitations, so-called superexcitations, outer- and inner-shell ionizations--affect the type and amount of DNA damage. Furthermore, low energy electrons produced by low energy photons through photoelectric interactions are useful for studying how the electron energy affects the induction of DNA damage. A report is given on the present status of the SR irradiation systems in Japan as well as some results concerning the formation of DNA damage, in vitro and in vivo, by monochromatic photons in the VUV and soft X-ray regions.

Photolesions and biological inactivation of plasmid DNA on 254 nm irradiation and comparison with 193 nm laser irradiation

Plasmid pTZ18R and calf thymus DNA in aerated neutral aqueous solution were irradiated by continuous 254 nm light. The quantum yields are phi ssb = 4.0 x 10(-5) and phi dsb = 1.4 x 10(-6) for single- and double-strand break formation, respectively, phi br = 2.3 x 10(-5) for base release, phi dn = 2.1 x 10(-3) for destruction of nucleotides, and phi icl approximately phi lds approximately 1 x 10(-6) for interstrand cross-links and locally denatured sites, respectively. The presence of Tris-HCl/ethylenediaminetetraacetic acid (10:1, pH 7.5) buffer strongly reduces phi ssb. The corresponding phi values, obtained on employing pulsed 193 nm laser irradiation, are much larger than those using lambda irr = 254 nm. This is ascribed to a contribution of chemical reactions induced by photoionization, which is absent for 254 nm irradiation. The quantum yields of inactivation of plasmid DNA (lambda irr = 254 nm) were measured by transformation of the Escherichia coli strains AB1157 (wild type), phi ina (1157) = 1.6 x 10(-4), AB1886 (uvr-), phi ina (1886) = 4.2 x 10(-4), AB2463 (rec-), phi ina (2463) = 4.1 x 10(-4) and AB2480 (uvr- rec-), phi ina (2480) = 3.1 x 10(-3). The quantum yields of inactivation of plasmid DNA are compared with those of the four E. coli strains (denoted as chromosomal DNA inactivation) obtained from the literature. The results for E. coli strain AB2480 show that the chromosomal DNA and the plasmid DNA are both inactivated by a single pyrimidine photodimer per genome.(ABSTRACT TRUNCATED AT 250 WORDS)

Photolesions in DNA upon 193 nm excitation

Aqueous solutions of plasmid (pBR322 and pTZ18R) and calf thymus DNA were excited by 20 ns laser pulses at 193 nm. The quantum yields of single-and double-strand break formation, interstrand cross-links, locally denatured sites, (6-4)photoproducts and biological inactivation (phi ssb, phi dsb, phi icl, phi lds, phi 6-4 and phi ina, respectively) were measured. The quantum yields are virtually independent of intensity, demonstrating a one-quantum process. The obtained values in aerated neutral solution in the absence of additives are phi ssb approximately 1.5 x 10(-3), phi dsb approximately 0.06 x 10(-3) (dose: 10-200 J m-2), phi icl approximately phi lds approximately 0.1 x 10(-3) and phi 6-4 = 0.5 x 10(-3). Both phi ssb and phi dsb decrease strongly with increasing concentrations of TE buffer (0.01-10 mM). Biological inactivation of the pTZ18R plasmid was determined from the transformation efficiency of Escherichia coli bacteria strains AB1157, AB1886 uvr and AB2480 uvr rec; the phi ina values are 1.4 x 10(-3), 2.1 x 10(-3) and 3 x 10(-3), respectively. The monoexponential survival curves in all cases show that a single damage site leads to inactivation (one single hit). The biological consequences of different photoproducts are discussed.

Wavelength dependence (150-290 nm) of the formation of the cyclobutane dimer and the (6-4) photoproduct of thymine

The action cross sections for the formation of the cyclobutane dimer and the (6-4) photoproduct of thymine as well as the absorption cross sections of thymine were determined in the wavelength region between 150 and 290 nm. Thymine films sublimed on glass plates were irradiated by monochromatic photons in a vacuum; the induced photoproducts were quantitatively analyzed by high-performance liquid chromatography (HPLC). Under our conditions, two major peaks appeared on the HPLC chromatograms of irradiated samples. The two peaks were identified as being the cis-syn cyclobutane dimer and the (6-4) photoproduct, based on their HPLC retention times, absorption spectra in the effluent, and photochemical reactivity. The fractions of the two photoproducts increased linearly with the fluence at low fluences over the entire wavelength range. Their action cross sections were determined by the slopes of the linear fluence response curve at 10 nm intervals between 150 and 290 nm. The two action spectra showed a similar wavelength dependence and had a maximum at 270 nm as well as two minor peaks at 180 and 220 nm, at which wavelengths the peaks of the absorption spectrum of thymine sublimed on a CaF2 crystal plate appeared. The quantum yields had relatively constant values of around 0.008 for the dimer and 0.013 for the (6-4) photoproduct above 200 nm, decreasing to 0.003 and 0.006, respectively, at 150 nm as the wavelength became shorter.

Strand breakage in poly(C), poly(A), single- and double-stranded DNA induced by nanosecond laser excitation at 193 nm

Single- and double-stranded calf thymus DNA and two polynucleotides (0.4 mM) were studied in aqueous solution at pH approximately 7 using pulsed, 20 ns laser excitation at 193 nm. Monophotonic ionization of the nucleic acids is suggested from the linear dependences of the concentration of ejected electrons and the number of single- and double-strand breaks (ssb, dsb, respectively) on laser intensity (IL) in the range (0.2-3) x 10(6) W cm-2. The quantum yields of formation of hydrated electrons (phi e-) and ssb and dsb (phi ssb and phi dsb) are therefore independent of IL. In contrast, under 248 nm excitation these quantum yields increase linearly with IL under otherwise comparable conditions. Nevertheless, several effects and mechanistic implications are analogous using lambda exc = 193 and 248 nm. For polycytidylic acid, poly(C), in Ar-saturated solution for example, the efficiency of ssb per radical cation (eta RC = phi ssb/phi e-) is similar to the efficiency of ssb per OH radical (eta OH). For polyadenylic acid, poly(A), and single- and double-stranded DNA eta RC (lambda exc = 193 nm) is significantly smaller than eta OH. The ratio phi ssb (N2O)/phi ssb (Ar) is approximately 2 for poly(C), approximately 4 for poly(A) approximately 10 for DNA; the conversion of hydrated electrons into OH radicals in N2O-saturated solution and smaller eta RC than eta OH values in the case of DNA account for these results. For double-stranded DNA phi dsb does not depend on IL but increases linearly with the dose, indicating an accumulative effect of two ssb to generate one dsb. The critical distance for this event is 60-85 phosphoric acid diester bonds.

Wavelength dependent formation of thymine dimers and (6-4) photoproducts in DNA by monochromatic ultraviolet light ranging from 150 to 365 nm

We investigated the wavelength dependence of cyclobutane thymine dimer and (6-4)photoproduct induction by monochromatic UV in the region extending from 150 to 365 nm, using an enzyme-linked immunosorbent assay with two monoclonal antibodies. Calf thymus DNA solution was irradiated with 254-365 nm monochromatic UV from a spectrograph, or with 220-300 nm monochromatic UV from synchrotron radiation. Thymine dimers and (6-4)photoproducts were fluence-dependently induced by every UV below 220 nm extending to 150 nm under dry condition. We detected the efficient formation of both types of damage in the shorter UV region, as well as at 260 nm, which had been believed to be the most efficient wavelength for the formation of UV lesions. The action spectra for the induction of thymine dimers and (6-4)photoproducts were similar from 180 to 300 nm, whereas the action spectrum values for thymine dimer induction were about 9- and 1.4-fold or more higher than the values for (6-4)photoproduct induction below 160 nm and above 313 nm, respectively.

Single- and double-strand break formation in double-stranded DNA upon nanosecond laser-induced photoionization

Double-stranded (ds) calf thymus DNA (0.4 mM), excited by 20 ns laser pulses at 248 nm, was studied in deoxygenated aqueous solution at room temperature and pH 6.7 in the presence of a sodium salt (10 mM). The quantum yields for the formation of hydrated electrons (phi c-), single-strand breaks (phi ssb) and double-strand breaks (phi dsb) were determined for various laser pulse intensities (IL). phi c- and phi ssb increase linearly with increasing IL; however, phi ssb has a tendency to reach saturation at high IL (greater than 5 X 10(6) Wcm-2). The ratio phi ssb/phi c-, representing the number of ssb per radical cation, is about 0.08 at IL less than or equal to 5 X 10(6) Wcm-2. For comparison, the number of ssb per OH radical reacting with dsDNA is 0.22. On going from argon to N2O saturation, phi ssb and phi dsb become larger by factors of approximately 5 and 10-15, respectively. This enhancement is produced by attack on DNA bases by OH radicals generated by N2O-scavenging of the photoelectrons. While phi ssb is essentially independent of the dose (Etot), phi dsb depends linearly on Etot in both argon- and N2O-saturated solutions. The linear dependence of phi dsb implies a square dependence of the number of dsb on Etot. This portion of dsb formation is explained by the occurrence of two random ssb, generated within a critical distance (h) in opposite strands. For both argon- and N2O-saturated solutions h was found to be of the order of 40-70 phosphoric acid diester bonds. On addition of electron scavengers such as 2-chloroethanol (or N2O plus t-butanol), phi dsb is similar to that in neat, argon-saturated solutions. Thus, hydrated electrons are not involved in the chemical pathway leading to laser-pulse-induced dsb of DNA.

Photochemistry of DNA using 193 nm excimer laser radiation

Photoproducts in double-stranded DNA induced by 193 nm radiation have been investigated. Double-stranded, supercoiled pBR322 DNA in buffered aqueous solution was exposed to varying fluences of 193 nm radiation from an ArF excimer laser. The quantum yields for formation of cyclobutylpyrimidine dimers, frank strand breaks and alkali labile sites were calculated from the conversion of supercoiled (Form I) DNA to relaxed (Form II) DNA after treatment with Micrococcus luteus dimer-specific endonuclease, no treatment, or treatment with alkali and heat, respectively. The quantum yields were 1.65 (+/- 0.03) X 10(-3) for pyrimidine dimers, 9.4 (+/- 3.2) X 10(-5) for frank strand breaks and 9.6 (+/- 3.6) X 10(-5) for alkali labile sites. The quantum yields for pyrimidine dimers and strand breaks and alkali labile sites were not affected by 10 nM mannitol. The relative quantum yields for these DNA photoproducts induced by 193 nm radiation differed markedly from those produced by 254 nm radiation.

Cytotoxicity and mutagenicity of excimer laser radiation

Excimer laser radiation at 193 nm, 248 nm and 308 nm cause DNA photochemistry. The photobiological effects resulting from exposure of cells to 308 nm and 248 nm radiation appear to be the same as those obtained using low irradiance CW sources at similar wavelengths. This indicates that the high irradiances available from the excimer laser cause the same DNA photochemistry as the lower-irradiance CW sources. Excimer laser radiation at 193 nm causes less cytotoxicity than predicted based on the DNA absorption spectrum. This may result from absorption of 193 nm radiation by protein present between the cell surface, and nuclear DNA, or from less efficient DNA photochemistry using 193 nm radiation. In vitro assays indicate that DNA-damaging effects resulting in cytotoxicity decrease in the order 248 nm greater than 308 nm greater than 193 nm.

Action spectrum for the induction of single-strand breaks in DNA in buffered aqueous solution in the wavelength range from 150 to 272 nm: dual mechanism

The induction of single-strand breaks by vacuum-u.v. and far-u.v. radiations (150 nm-272 nm) in plasmid Col E1 DNA in buffered aqueous solution was studied by agarose gel electrophoresis. The results indicated that the mechanisms of DNA strand-break induction are different in the two u.v. regions: above 210 nm the direct excitation of DNA seemed to be the main cause; below 180 nm the photolysis of solvent water seemed to be essential. The demonstration of a systematic protection at 160 nm and not at 209 nm by OH scavengers, such as ethyl alcohol, potassium iodide and D-mannitol, supports the involvement of OH radicals in the vacuum-u.v. region.

Enzymatic quantification of strand breaks of DNA induced by vacuum-UV radiation

HindIII-digested plasmid DNA dried on an aluminum plate was irradiated by vacuum-UV at 160 and 195 nm using a synchrotron irradiation system. A change induced in the DNA, presumably a single strand break, was quantified by the aid of the strand break-derived stimulation of poly(ADP-ribose) synthetase activity. The end group of strand breaks so induced was recognized by the enzyme as effectively as that by DNase I treatment, suggesting a nicking as the major lesion inflicted on the DNA. The fluence (UV) dependent stimulation of poly(ADP-ribose) synthetase activity was much higher upon 160 nm irradiation than upon 195 nm irradiation.