Photolysis of phosphodiester bonds in plasmid DNA by high intensity UV laser irradiation

Contribution of oxidation reactions to photo-induced damage to cellular DNA

This review article is aimed at providing updated information on the contribution of immediate and delayed oxidative reactions to the photo-induced damage to cellular DNA/skin under exposure to UVB/UVA radiations and visible light. Low-intensity UVC and UVB radiations that operate predominantly through direct excitation of the nucleobases are very poor oxidizing agents giving rise to very low amounts of 8-oxo-7,8-dihydroguanine and DNA strand breaks with respect to the overwhelming bipyrimidine dimeric photoproducts. The importance of these two classes of oxidatively generated damage to DNA significantly increases together with a smaller contribution of oxidized pyrimidine bases upon UVA irradiation. This is rationalized in terms of sensitized photooxidation reactions predominantly mediated by singlet oxygen together with a small contribution of hydroxyl radical that appear to also be implicated in the photodynamic effects of the blue light component of visible light. Chemiexcitation-mediated formation of "dark" cyclobutane pyrimidine dimers in UVA-irradiated melanocytes is a recent major discovery that implicates in the initial stage, a delayed generation of reactive oxygen and nitrogen species giving rise to triplet excited carbonyl intermediate and possibly singlet oxygen. High-intensity UVC nanosecond laser radiation constitutes a suitable source of light to generate pyrimidine and purine radical cations in cellular DNA via efficient biphotonic ionization.

RNA self-cleavage activated by ultraviolet light-induced oxidation

A novel UV-C-light-induced ribozyme activity was discovered within the highly structured 5'-genomic regions of both Hepatitis C Virus (HCV) and the related Classic Swine Fever Virus (CSFV). Cleavage is mediated by exposure to UV-C light but not by exogenous oxygen radicals. It is also very selective, occurring at base positions HCV C(79) and CSFV A(45) in some molecules and at the immediately adjacent 5'-positions HCV U(78) and CSFV U(44) in others. Among other reaction products, the majority of biochemically active products detected contained 3'-phosphate and 5'-phosphate-end groups at the newly generated termini, along with a much lower amount of 3'-hydroxyl end group. While preservation of an E-loop RNA structure in the vicinity of the cleavage site was a requisite for HCV RNA self-cleavage, this was not the case for CSFV RNA. The short size of the reactive domains (~33 nt), which are compatible with primitive RNA motifs, and the lack of sequence homology, indicate that as-yet unidentified UV-activated ribozymes are likely to be found throughout structured RNAs, thereby providing clues to whether early RNA self-cleavage events were mediated by photosensitive RNA structures.

Origin of the heterogeneous distribution of the yield of guanyl radical in UV laser photolyzed DNA

Oxidative guanine lesions were analyzed, at the nucleotide level, within DNA exposed to nanosecond ultraviolet (266 nm) laser pulses of variable intensity (0.002-0.1 J/cm(2)). Experiments were carried out, at room temperature, in TE buffer (20 mM Tris-HCl, pH 7.5; 1 mM EDTA) containing 35 mM NaCl, on 5'-end radioactively labeled double-stranded and single-stranded oligomer DNA at a size of 33-37 nucleobases. Lesions were analyzed on polyacrylamide gel electrophoresis by taking advantage of the specific removal of 8-oxodG from DNA by the formamidopyrimidine DNA glycosylase (Fpg protein) and of the differential sensitivity of 8-oxodG and oxazolone to piperidine. The quantum yields of lesions at individual sites, determined from the normalized intensities of bands, were plotted against the irradiation energy levels. Simplified model fitting of the experimental data enabled to evaluate the spectroscopic parameters characterizing excitation and photoionization processes. Results show that the distribution of guanine residues, excited to the lowest triplet state or photoionized, is heterogeneous and depends on the primary and secondary DNA structure. These findings are generalized in terms of excitation energy and charge-migration mediated biphotonic ionization. On the basis of the changes in the yield of the guanyl radical resulting from local helical perturbations in the DNA pi-stack, it can be assessed that the distance range of migration is <6-8 bp.

Efficiency and pattern of UV pulse laser-induced RNA-RNA cross-linking in the ribosome

Escherichia coli ribosomes were irradiated with a KrF excimer laser (248 nm, 22 ns pulse) with incident pulse energies in the range of 10-40 mJ for a 1 cm2 area, corresponding to fluences of 4.5 to 18 x 10(9) W m(-2), to determine strand breakage yields and the frequency and pattern of RNA-RNA cross- linking in the 16S rRNA. Samples were irradiated in a cuvette with one laser pulse or in a flow cell with an average of 4.6 pulses per sample. The yield of strand breaks per photon was intensity dependent, with values of 0.7 to 1.3 x 10(-3) over the incident intensity range studied. The yield for RNA-RNA cross-linking was 3 x 10(-4) cross-links/photon at the intensity of 4.5 x 10(9) W m(-2), an approximately 4-fold higher yield per photon than obtained with a transilluminator. The cross-link yield/photon decreased at higher light intensities, probably due to intensity-dependent photoreversal. The pattern of cross-linking was similar to that observed with low intensity irradiation but with four additional long-range cross-links not previously seen in E.coli ribosomes. Cross- linking frequencies obtained with one laser pulse are more correlated to internucleotide distances than are frequencies obtained with transilluminator irradiation.

Wavelength dependence of ultraviolet-induced DNA damage distribution: involvement of direct or indirect mechanisms and possible artefacts

DNA damage profiles have been established in plasmid DNA using purified DNA repair enzymes and a plasmid relaxation assay, following exposure to UVC, UVB, UVA or simulated sunlight (SSL). Cyclobutane pyrimidine dimers (CPDs) are revealed as T4 endonuclease V-sensitive sites, oxidation products at purine and pyrimidine as Fpg- and Nth-sensitive sites, and abasic sites are detected by Nfo protein from Escherichia coli. CPDs are readily detected after UVA exposure, though produced 10(3) and 10(5) times less efficiently than by UVB or UVC, respectively. We demonstrate that CPDs are induced by UVA radiation and not by contaminating UVB wavelengths. Furthermore, they are produced at doses compatible with human exposure and are likely to contribute to the mutagenic specificity of UVA [E. Sage et al., Proc. Natl. Acad. Sci. USA 93 (1996) 176-180]. Oxidative damage is induced with a linear dose dependence, for each region of the solar spectrum, with the exception of oxidized pyrimidine and abasic sites, which are not detectable after UVB irradiation. The distribution of the different classes of photolesions varies markedly, depending on wavelengths. However, the unexpectedly high yield of oxidative lesions, as compared to CPDs, by UVA and SSL led us to investigate their production mechanism. An artificial formation of hydroxyl radicals is observed, which depends on the material of the sample holder used for UVA irradiation and is specific for long UV wavelengths. Our study sheds light on a possible artefact in the production of oxidative damage by UVA radiation. Meanwhile, after eliminating some potential sources of the artefact ratios of CPDs to oxidized purine of three and five upon irradiation with UVA and SSL, respectively, are still observed, whereas these ratios are about 140 and 200 after UVC and UVB irradiation.

Long-range oxidative damage to DNA: effects of distance and sequence

INTRODUCTION

Oxidative damage to DNA in vivo can lead to mutations and cancer. DNA damage and repair studies have not yet revealed whether permanent oxidative lesions are generated by charges migrating over long distances. Both photoexcited *Rh(III) and ground-state Ru(III) intercalators were previously shown to oxidize guanine bases from a remote site in oligonucleotide duplexes by DNA-mediated electron transfer. Here we examine much longer charge-transport distances and explore the sensitivity of the reaction to intervening sequences.

RESULTS

Oxidative damage was examined in a series of DNA duplexes containing a pendant intercalating photooxidant. These studies revealed a shallow dependence on distance and no dependence on the phasing orientation of the oxidant relative to the site of damage, 5'-GG-3'. The intervening DNA sequence has a significant effect on the yield of guanine oxidation, however. Oxidation through multiple 5'-TA-3' steps is substantially diminished compared to through other base steps. We observed intraduplex guanine oxidation by tethered *Rh(III) and Ru(III) over a distance of 200 A. The distribution of oxidized guanine varied as a function of temperature between 5 and 35 degrees C, with an increase in the proportion of long-range damage (> 100 A) occurring at higher temperatures.

CONCLUSIONS

Guanines are oxidized as a result of DNA-mediated charge transport over significant distances (e.g. 200 A). Although long-range charge transfer is dependent on distance, it appears to be modulated by intervening sequence and sequence-dependent dynamics. These discoveries hold important implications with respect to DNA damage in vivo.

Photocross-linking of nucleic acids to associated proteins

Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.

Depopulation of highly excited singlet states of DNA model compounds: quantum yields of 193 and 245 nm photoproducts of pyrimidine monomers and dinucleoside monophosphates

Formation of uracil and orotic acid photodimers, uridine and 5'-UMP photohydrates, TpT photodimers and (6-4)photoproducts, dCpT photohydrates and (6-4)photoproducts and UpU, CpC and CpU photohydrates were studied in neutral deoxygenated aqueous solution at room temperature upon irradiation at either 193 or 254 nm. The photoproducts were identified and quantified and the contribution from photoionization to substrate decomposition, using lambda irr = 193 nm, was separated. The ratio of the quantum yields of respective stable products, eta = phi 193/phi 254, is indicative of the yield of internal conversion from the second to the first excited singlet state, S2-->S1. For the observed photodimers eta decreases from 0.94 for uracil to 0.7 for TpT and further to 0.55 for orotic acid. For the (6-4)photoproducts of TpT and dCpT eta = 0.5-0.8 and for the photohydrates in the cases of UpU, CpC, CpU and dCpT eta ranges from 0.55 to 1.

Adjacent guanines as preferred sites for strand breaks in plasmid DNA irradiated with 193 nm and 248 nm UV laser light

193 nm UV laser light induces single strand breaks as well as double strand breaks in plasmid DNA. The frequency of strand breaks is increased at sites where at least two guanine or, less frequently, a guanine and an adenine are adjacent to each other. 248 nm UV laser light induces predominantly single strand breaks with a less pronounced preference for guanine clusters. At both wavelengths, the presence of oxygen does not change the pattern of strand breaks, but in the presence of nitrous oxide, selectivity is lost; this is attributable to the production of the hydroxyl radical. These findings can be explained by a model in which the propagation of a radical or an electron hole along the DNA helix competes kinetically with the strand cleavage reaction. The difference in selectivity at the two different wavelengths is ascribed to the preferential light absorption by the purine bases at 193 nm.

193 nm light induces single strand breakage of DNA predominantly at guanine

Irradiation of DNA with 193 nm light results in monophotonic photoionization, with the formation of a base radical cation and a hydrated electron (phi PI = 0.048-0.065). Although > 50% of the photoionization events initially occur at guanine in DNA, migration of the "hole" from the other bases to guanine occurs to yield predominantly its radical cation or its deprotonated form. From sequence analysis, the data reveal that 193 nm light induces single strand breaks (ssb) in double-stranded DNA preferential 3' to a guanine residue. However, it has previously been reported that 193 nm light yields very low yields of ssb (< 2% of the yield of e-aq). The distribution of these ssb at guanine is nonrandom, showing a dependence on the neighboring base moiety. The efficiency of ssb formation at nonguanine sites is estimated to be at least one order of magnitude lower. The preferred cleavage at guanine is consistent with migration and localization of the electron loss center at guanine. It is argued that singlet oxygen and the photoionized phosphate group of the sugar moiety are not major precursors to ssb. At present, the mechanisms of strand breakage are not known although a guanine radical or one of its products remain potential precursors.

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.

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 in glasses at 77 K: high energy ionizing radiation versus UV electron ejection

Most in the field of ionizing radiation damage to DNA in frozen aqueous solutions agree that two major types of radical ions are formed, i.e. G+/A+ and T-/C-. The main evidence stems from EPR and strand break studies. Fluid solutions exposed to laser light are known to give G+ and esolv- with low yields of single strand breaks. We have explored this contrast by photoionizing DNA solutions at 77 K, in the expectation that this would prevent the formation of esolv- and hence that the results might be similar to those for high energy radiation. They are not: the results show only the formation of G+ (or) (A+), the fate of the ejected electrons is unclear except for sodium perchlorate glasses when they react to give O-.

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.

The role of DNA damage in PM2 viral inactivation by methylene blue photosensitization

This study investigates the importance of DNA damage in viral inactivation by phenothiazines and light. Phenothiazines, including methylene blue (MB), toluidine blue and azure B are of particular interest because of their ability to bind to nucleic acids in vitro. Initial studies employing phages T7, MS2 and PM2 indicated that both DNA and RNA phages as well as enveloped and nonenveloped phages can be inactivated by phenothiazine photosensitization. PM2, which contains a lipid-protein bilayer and supercoiled DNA, was used for the mechanistic studies to model blood-borne viruses. Viral DNA damage was assessed following treatment of phage to known levels of viral inactivation by extracting the DNA and analyzing for both direct and piperidine-catalyzed strand cleavage by gel electrophoresis. DNA strand cleavage was found to be both sensitizer concentration and light dose dependent. Both viral inactivation and DNA damage were found to be oxygen-dependent events. In parallel experiments, strand cleavage of isolated PM2 DNA treated with MB and light was also found to be oxygen dependent, in contrast to some previous reports. Transfection studies, which measure the infectivity of the extracted viral DNA, indicated that DNA from MB-treated phage was just as capable of generating progeny virus as the untreated controls. It was therefore concluded that the observed DNA damage is not correlated with loss of phage infectivity.

Photochemical alterations in DNA revealed by DNA-based liquid crystals

The preparations of chicken erythrocyte linear double-stranded DNA and superhelical plasmid pBR322 DNA were irradiated by continuous low-intensity UV radiation (I = 25-50 W/m2, lambda = 254 nm) as well as by high-intensity picosecond laser UV radiation (I = 10(11)-10(13) W/m2, lambda = 266 nm). The effect of DNA secondary structure alterations on the formation of liquid-crystalline dispersions from UV-irradiated DNA preparations was studied. It was shown that in the case of linear DNA, watching the disappearance of abnormal optical activity characteristic for cholesteric liquid crystal we managed to detect the presence of photochemical alterations in DNA irradiated by low-intensity UV radiation at an absorbed energy of more than 20 quanta per nucleotide. In the case of superhelical DNA using enzyme treatment of liquid-crystalline dispersions and monitoring the appearance of abnormal optical activity, we detected the presence of photochemical alterations in DNA molecules after low-intensity UV irradiation at an absorbed energy of less than 4 quanta per nucleotide. Under the latter approach using picosecond UV laser irradiation at three different light intensities we were able to distinguish the different mechanisms of fine alterations in DNA secondary structure at an absorbed energy value of about 3 quanta per nucleotide.

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)

Upper excited state photochemistry of DNA

The quantum yields for cyclobutylpyrimidine dimers, alkali-labile sites, and frank strand breaks in double-stranded DNA have been measured using low-intensity radiation at 199.8, 217.8, and 239.5 nm from a Raman-shifted frequency quadrupled Nd:YAG laser. The quantum yield for cyclobutylpyrimidine dimers was also measured using 254 nm radiation from a low-pressure mercury lamp. The quantum yield for cyclobutylpyrimidine dimers is constant within a factor of two between 254 and 199.8 nm except for 239.5 nm, indicating that upper excited singlet states of bases convert efficiently to the lowest singlet state. The quantum yields for alkali-labile sites and frank strand breaks both increase as the wavelength decreases but follow different patterns. These results indicate that alkali-labile sites from a higher excited state of the base, whereas frank strand breaks form by excitation of the sugar-phosphate backbone.

Laser cross-linking of proteins to nucleic acids: photodegradation and alternative photoproducts of the bacteriophage T4 gene 32 protein

Pulsed laser cross-linking provides a means of introducing a covalent bond between proteins and the nucleic acids to which they are bound. This rapid cross-linking effectively traps the equilibrium that exists at the moment of irradiation and thus allows examination of the protein-nucleic acid interactions that existed. Laser irradiation may also induce photodestruction of protein and we have used the bacteriophage T4 gene 32 protein to investigate this phenomenon. Our results show that both nonspecific and specific photoproducts can occur, specifically at wavelengths where the peptide backbone of proteins is known to absorb. These results demonstrate that nonspecific photodegradation can be correlated with the formation of a specific photodegradation product. The formation of this product was monitored to show that product yield is nonlinearly dependent on laser power and wavelength. We have also investigated an unexpected photoproduct whose formation is dependent on the length of the polynucleotide to which the gene 32 protein binds and that further demonstrates the complexities of analyzing protein-nucleic acid interactions through the use of UV laser cross-linking. These data provide essential information for the establishment of appropriate conditions for future studies that use UV cross-linking of protein-nucleic acid complexes.

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.

Dissociation of a model DNA compound dApdA by monochromatic soft X-rays in solids and comments on the high selectivity for 3' breakage in the phosphoester bond

The dissociation products of dApdA (2'-deoxyadenylyl-(3'-5')-2'-deoxyadenosine) irradiated in the solid state by highly monochromatic soft X-rays (energy resolution, less than 10(-3) near the K-edge of phosphorus were analysed using thin-layer chromatography. The major chemical species identified were adenine base and 5'-dAMP in approximately equal amounts, indicating that the dissociation occurred between the 3' carbon (C3') of deoxypentose and its adjacent phosphorus over the energy range of 2.147-2.167 keV, including the K-edge resonance absorption of phosphorus at 2.153 keV. In conjunction with the accumulated data on the degradation of dApdA and related oligonucleotides by vacuum-UV radiation (above 7 eV), which generally indicate a simple, selective dissociation at the 3' side of the deoxypentose as observed with the soft X-rays, an hypothesis is presented on the molecular mechanism of radiation-induced breakage of phosphoester bonds that led to the selective 3' breakage, based on the differential flexibility of torsion angles of C3'-O3'-P and C4'-C5'-O5'-P groups in relation to those of the sugar ring.

The distribution of UV damage in the lacI gene of Escherichia coli: correlation with mutation spectrum

We have determined the UV (254 nm) damage distribution in the transcribed and non-transcribed strands of the i-d region of the Escherichia coli lacI gene. The locations of replication blocking lesions were revealed as termination sites of T7 DNA polymerase and/or T4 DNA polymerase 3'-5' exonuclease. Termination products, i.e. both cyclobutane pyrimidine dimers and 6-4 photoproducts, were resolved and analysed on an automated DNA sequencer. These two major photoproducts are not randomly distributed along the gene, but occur in clusters, in longer runs of pyrimidines. We also have compared the UV damage distribution with the previously reported UV-induced base substitutions in the same region. Mutational hotspots, in both repair-deficient and repair-proficient strains of E. coli, are all located in stretches of pyrimidines, and thus correlate well with the distribution of photolesions. One mutational hotspot in the wild-type strain may reflect the high frequency of closely opposed lesions. To explain the other mutational hotspots, we propose that the repair of UV lesions is impaired due to the local conformation of the DNA, which might deviate from the B-form. This hypothesis is supported by the excess of mutational hotspots in pyrimidine runs in the Uvr+ strain compared to Uvr-. Runs of pyrimidines thus represent both damage- and mutation-prone sequences following UV treatment.

Base release from DNA and polynucleotides upon 193 nm laser excitation

Release of bases form calf thymus DNA and three polynucleotides, induced by 20 ns excitation at 193 nm in aqueous solution at pH 7, was detected by HPLC. The quantum yields of formation of free bases (phi B) from double-stranded DNA (0.4 mM) are independent of intensity, indicating a one-quantum mechanism of N-glycosidic bond cleavage. The phi B values increase in the order guanine, thymine, adenine, cytosine, the latter being phi C approximately 7 x 10(-4) for double-stranded DNA under Ar and O2. The larger phi B values in N2O-saturated solution, e.g., phi C = 1.2 x 10(-3), are ascribed to additional base release via OH-adduct radicals. The phi B values of homopolynucleotides increase in the order poly(G), poly(A) and poly(C), e.g. phi C = 7 x 10(-3) under Ar, as do the efficiencies for base release per radical cation (eta B). A comparison of the eta B values with the efficiencies of single-strand breakage for poly(C), poly(A) and DNA shows a similar trend; both are markedly larger for pyrimidines than for purines. Pathways to undamaged bases, initiated from base radical cations, are proposed.

Two-quantum photoprocesses in DNA under picosecond laser UV irradiation at 216 and 270 nm

It is demonstrated that at high power picosecond laser irradiation of 216 and 270 nm, two-quantum photodestructions of the DNA secondary structure, such as interstrand covalent crosslinks, "weak" crosslinks, and B----C conformational transition, take place. Thermal effects do not contribute to the observed effects.

Effects of ultraviolet laser radiation on Venezuelan equine encephalomyelitis virus

The effects of usual low-intensity continuous (lambda = 254 nm, I = 10 W/m2) UV radiation and high-intensity laser nanosecond (lambda = 266 nm, tau p = 10 ns, I = 10(9) W/m2) or picosecond (lambda = 266 nm, tau p = 23 ps, I = 10(12) W/m2) UV radiation on Venezuelan equine encephalomyelitis virus (a member of the Togaviridae family) were compared. The quantum yields of infectivity inactivation, pyrimidine dimer formation and RNA-protein crosslinking were determined.

Formation of single and double strand breaks in DNA ultraviolet irradiated at high intensity

The induction of single-strand breaks (SSB) by two quantum processes in DNA is well established. We now report that biphotonic processes result in double-strand breaks (DSB) as well. pUC19 and bacteriophage M13 RF DNA were irradiated using an excimer laser (248 nm) at intensities of 10(7), 10(9), 10(10) and 10(11) W/m2 and doses up to 30 kJ/m2. The proportion of DNA as supercoil, open circular, linear and short fragments was determined by gel electrophoresis. Linear molecules were noted at fluences where supercoiled DNA was still present. The random occurrence of independent SSB in proximity to each other on opposite strands (producing linear DNA) implies introduction of numerous SSB per molecule in the sample. If so, supercoiled DNA that has sustained no SSB should not be observed. A model accounting for the amounts of supercoiled, open circular, linear and shorter fragments of DNA due to SSB, DSB and Scissions (opposition of two independently occurring SSB producing an apparent DSB) was developed, our experimental data and those of others were fit to the model, and quantum yields determined for SSB and DSB formation at each intensity. Results showed that high intensity laser radiation caused an increase in the quantum yields for both SSB and DSB formation. The mechanism of DSB formation is unknown, and may be due to simultaneous cleavage of both strands in one biphotonic event or the biased introduction of an SSB opposite a preexisting SSB, requiring two biphotonic events.

The role of ground state complexation in the electron transfer quenching of methylene blue fluorescence by purine nucleotides

The effect of three purine nucleotides on the fluorescence of methylene blue in aqueous buffer has been investigated. Guanosine-5'-monophosphate (GMP) and xanthosine-5'-monophosphate cause fluorescence quenching while adenosine-5'-monophosphate causes a red shift in the fluorescence maximum. All three nucleotides form ground state complexes with the nucleotides as indicated by absorption spectroscopy. The fluorescence changes at nucleotide concentrations less than 30 mM are best described by a static mechanism involving the formation of non-fluorescent binary and ternary complexes in competition with dimerization of the dye. Quenching of the fluorescence decay (tau = 368 ps) at high GMP concentrations (10-100 mM) occurs at the rate of diffusion. The mechanism of fluorescence quenching may involve electron transfer within the singlet excited dye-nucleotide complex although published values of the oxidation potentials of various purine derivatives would suggest that all three nucleotides should cause quenching. Evidence for electron transfer was obtained from flash photolysis experiments in which 100 mM GMP was found to cause the appearance of a long lived transient species absorbing in the region expected for semimethylene blue.

Transients of uracil and thymine derivatives and the quantum yields of electron ejection and intersystem crossing upon 20 ns photolysis at 248 nm

Transients of uracil and a series of 17 correlated pyrimidines, e.g. methylated bases, nucleosides, nucleotides, and polyuridylic acid [poly(U)] were studied after 248 nm excitation by 20 ns laser pulses. The transient absorption spectra in aqueous solution at room temperature reveal the triplet state and the hydrated electron (e-aq), while the corresponding radical cation could not be observed at pH 6-7. Fast loss of the chromophore in the 260-290 nm range within 0.1 microsecond was observed in aqueous solution in some cases [e.g. poly(U), 5'-UMP, uridine, uracil] and in others (thymine, thymidine) virtually not. This photobleaching is assigned to formation of the photohydrate. The concentration of e-aq shows a quadratic dependence on the laser pulse intensity (IL) in the range (0.2-2) x 10(7) W cm-2 and the quantum yield of electron ejection (phi c-) thus depends linearly on IL. This behaviour, suggesting that the photoionization involves a two-step absorption process, was found for poly(U) and all pyrimidine monomers examined. At a constant IL value of 2 x 10(7) W cm-2, phi c- ranges from 3 x 10(-3) for 1,3-dimethylthymine to 4 x 10(-2) for poly(U). The triplet state shows a much larger transient absorbance (delta A, typically in a broad range, e.g. 290-500 nm) than that of the neutral radical resulting from the radical cation. The triplet state in organic solvents (acetonitrile and ethanol) shows generally a significantly larger delta A value than in aqueous solution. The estimated quantum yields of intersystem crossing at room temperature are compared with those of phosphorescence at -196 degrees C.

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.

Sequence-specificity of the alkali-sensitive lesions induced in DNA by high-intensity ultraviolet laser radiation

The action of high-intensity (10(9)-10(12) W/m2) UV (266 nm) laser radiation pulses (duration ca 10 ns or ca 40 ps) on liquid aqueous solutions of DNA is known to cause not only single- but also two-quantum modification of nucleic bases. The action of hot piperidine on the laser-irradiated DNA results in non-random splitting of polynucleotide chain. Hence, at least some of the modified nucleoside residues are alkali-sensitive lesions (ASLs). The distribution of ASLs along the DNA chain shows that the position of these lesions corresponds with pyrimidines in the PyPy sequences (similar to those formed via single-quantum conversions) as well as with deoxyguanosine residues. The last ASLs result from two-quantum reactions and occur much more efficiently than the direct photo-induced cleavage of the internucleotide (phosphodiester) bond. It has been shown with fragments of plasmids pUC18, pUC19 and pBR322 (total length over 600 base pairs) that the relative efficiency of ASLs at deoxyguanosine sites depends on the primary structure context and can differ by an order of magnitude. The highest efficiency of modification is observed when a purine is 3' neighbour to the 2'-deoxyguanosine, i.e. at 5'-GPu-3' sites. However, considerable variations in the modification efficiency were also found in these sequences.

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.

Phosphorescence of nucleic acids and DNA components at 77 K

The emission spectra of nucleic acids, pyrimidine and purine nucleotides, nucleosides and bases and a series of pyrimidine derivatives were obtained using UV light excitation in glasses (ethanol and 2:1 mixtures of ethylene glycol and water (EG-H2O); also partly in butyronitrile and 2-methyltetrahydrofuran) at 77 K. The quantum yields of fluorescence phi f and phosphorescence phi p of some 30 compounds are presented; for several substituted uracils they are reported for the first time. The values cover a range from phi f = 0.0002 and phi p = 0.001 for uracil in ethanol to phi f = 0.50 for guanosine in acidic ethanol and phi p = 0.095 for guanosine-5'-monophosphate in EG-H2O (pH 6-7). The phosphorescence lifetime tau p at 77 K ranges from about 0.3 s (uracil moiety) to 3 s (adenine moiety). The measured tau p, phi f and phi p values are compared with those available in the literature.

Two-quantum UV photochemistry of nucleic acids: comparison with conventional low-intensity UV photochemistry and radiation chemistry

The action of high-intensity laser u.v. radiation on nucleic acid molecules and their constituents in vitro and in vivo is compared with the results of low-intensity u.v. photolysis and gamma-radiolysis.

Irradiation of the template with high-intensity (pulse-laser) ultraviolet light results in DNA-polymerase termination events at deoxyguanosine residues

During primer elongation by Escherichia coli DNA-polymerase I large fragments on the template were irradiated with UV laser pulses at an intensity greater than or equal to 10(10) W/m2. In addition to the termination events at photoproducts typical of low-intensity UV irradiation, termination is observed before deoxyguanosine residues. The effect of the UV light intensity on the ratio of termination efficiencies before dPy and dG suggests that the termination of polymerization before deoxyguanosine residues results from the formation of photoproducts yielded by two-quantum reactions. The results obtained herein, together with data published previously, imply that photomodification of dG residues is the major two-quantum reaction under the action of high-intensity UV radiation on DNA.

Photosensitized reactions of poly(U) with tris(2,2'-bipyridyl)ruthenium(II) and peroxydisulfate

The reactions of polyuridylic acid [poly(U)] with Ru(bpy)3(3+) [Ru(III)] and SO4.-, following UV and visible light irradiation of Ru(bpy)3(2+) [Ru(II)] in the presence of S2O8(2-), were studied in an argon-saturated aqueous solution using time-resolved absorption and conductivity methods. The kinetics of the Ru(III) conversion to Ru(II) in the presence of poly(U) was monitored spectroscopically either in the absence of SO4.- [rapid mixing with Ru(III)] or in its presence (after laser flash excitation, lambda exc = 353 nm). The conversion of Ru(III) to Ru(II) is complete at a [nucleotide]/[sensitizer] (N/S) ratio greater than or equal to 10 (rate constant k = 12 s-1) for rapid mixing and at N/S greater than or equal to 6 (k = 15 s-1 at N/S = 10) after laser pulsing. Conductivity measurements following the laser pulse revealed a fast conductivity increase (risetime less than 10 micros), due to the formation of charged species and protons. A slower increase in the 0.1-0.5 s range was observed for poly(U) but it is considerably smaller for poly(dU) and absent in uracil containing monounits. The slow increase is unaffected by pH changes in the 3.5-7 range, markedly reduced in the 7-9 range and is replaced by a slight decrease in conductivity in buffered solutions. An explanation is that poly(U)-bound excited Ru(II) reacts with S2O8(2-) forming Ru(III) and SO4.- as oxidizing species both of which react with poly(U) bases. The resulting base radicals react with Ru(III) or the ligands in the ruthenium complex, producing protons which give rise to the slow conductivity increase (k = 15 s-1 at N/S = 10). The formation of single-strand breaks and the ensuing release of condensed counterions does not appear to contribute significantly to the slow conductivity signal. At N/S less than 10 the observed rate and extent of Ru(III)--Ru(II) conversion and of the slow proton production vary markedly with the N/S ratio.