Nonlinear laser photophysics, photochemistry and photobiology of nucleic acids

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.

Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking

Interactions of DNA with structural proteins such as histones, regulatory proteins, and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The in vivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved little progress has been achieved in the crosslinking step. Because of its low efficiency the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" crosslinking agent. Efficient biphotonic crosslinking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein crosslinks in vitro model systems and cells.

Singlet-Triplet States Interaction Regions in DNA/RNA Nucleobase Hypersurfaces

The present study provides new insight into the intrinsic mechanisms for the population of the triplet manifold in DNA nucleobases by determining, at the multiconfigurational CASSCF/CASPT2 level, the singlet-triplet states crossing regions and the main decay paths for their lowest singlet and triplet states after near-UV irradiation. The studied singlet-triplet interacting regions are accessible along the minimum energy path of the initially populated singlet bright (1)ππ* state. In particular, all five natural DNA/RNA nucleobases have, at the end of the main minimum energy path and near a conical intersection of the ground and (1)ππ* states, a low-energy, easily accessible, singlet-triplet crossing region directly connecting the lowest singlet and triplet ππ* excited states. Adenine, thymine, and uracil display additional higher-energy crossing regions related to the presence of low-lying singlet and a triplet nπ* state. These funnels are absent in guanine and cytosine, which have the bright (1)ππ* state lower in energy and less accessible nπ* states. Knowledge of the location and accessibility of these regions, in which the singlet-triplet interaction is related to large spin-orbit coupling elements, may help to understand experimental evidence such as the wavelength dependence measured for the triplet formation quantum yield in nucleobases and the prevalence of adenine and thymine components in the phosphorescence spectra of DNA.

Soluble sunscreens fully protect E. coli from disinfection by electrohydraulic discharges

We show that the ultraviolet radiation emitted, rather than the thermal/pressure shocks or the chemical species that are generated in these events, is the lethal agent that inactivates Escherichia coli colonies exposed to electrohydraulic discharges, EHD. Disinfection is completely suppressed in the presence of <100 mg L(-1) of 2,2'-dihydroxy-4,4'-dimethoxybenzophenone-5,5'-disulfonic acid, BP9, a commercial water-soluble sunscreen. Viable bacteria decay by logit kinetics with the number of EHD. The fact that the slopes of the logit plots depend inversely on BP9 concentration, and vanish above approximately 30 mg BP9 L(-1), is direct evidence that E. coli is exclusively sterilized by UV radiation in these experiments. Present LD50 photon doses are about 10(3) times larger than those required from low-power germicidal lamps, indicating that high-intensity radiation is able to further promote into inactive channels the lower excited state(s) of nucleic acids responsible for DNA damage. The present study confirms the existence of a significant trade-off between photon efficiency and radiative power in bacterial disinfection by UV light.

Escherichia coli disinfection by electrohydraulic discharges

We study the survival of single-strain Escherichia coli colonies in aqueous media exposed to 5.5 kV, 90 kA electrohydraulic discharges (EHD). The probability of survival (Pn) of a 4 x 10(7) cfu mL(-1) E. coli population after n consecutive EHDs follows a logit distribution: In(Pn/ 100 - Pn) = 1.329 - 1.579 ln n with r2 = 0.993 that corresponds to lethal doses of LD50 = 2.2 and LD90 = 10.5 EHDs. Considering that the reactor is thoroughly mixed during each discharge and that LD50 = 0.9 values are nearly independent of E. coli concentrations in the range of 2 x 10(3) < or = E coli/cfu mL(-1) < or = 3 x 10(6), we ascribe the nonexponential Pn decay of single-strain E. coli colonies to a shielding phenomenon where inactive cells protect the successively smaller numbers of viable cells in the EHD. The qualitatively similar concentration dependence observed for survival under 254 nm of radiation, in contrast with the lower resistance of denser colonies to 20 kHz power ultrasound and the delayed onset of extracellular beta-D-galactosidase activity in bacterial populations already decimated by EHDs, support the view that UV radiation is the dominant disinfection agent generated by electrohydraulic discharges.

Radiation damage in DNA: possible role of higher triplet states

Triplet states of deoxyribose are expected to dissociate efficiently into radicals, leading to strand breaks. Such states could be excited by slow secondary electrons (A) or result from ion recombination in spurs containing two or more ion pairs (B). Estimates of the efficiencies of these processes are presented and the mechanisms discussed in the light of recent work with electrons, vacuum ultraviolet (VUV) photons, and X rays. Route B could play a significant role in producing double-strand breaks, while route A may be a better approach to characterizing the process experimentally.

Differential remodeling of the HIV-1 nucleosome upon transcription activators and SWI/SNF complex binding

Here we have examined HIV-1 nucleosome remodeling upon the binding of transcription factors and the SWI/SNF complex using a novel approach. The approach combines UV laser protein-DNA crosslinking, electrophoretic mobility-shift analysis and DNase I protection analysis with immunochemical techniques. It was found that single activator-bound HIV-1 nucleosomes exhibit very weak perturbation in histone NH(2) tail-DNA interactions. However, the simultaneous binding of the transcription activators Sp1, NF-kB1, LEF-1 and USF synergistically increased the release of histone NH(2) tails from nucleosomal DNA. In contrast, the binding of SWI/SNF complex to HIV-1 nucleosome disrupted structured histone domain-DNA contacts, but not histone NH(2) tail-DNA interactions. Stable remodeled nucleosomes, (obtained after detachment of SWI/SNF), displayed identical structural alterations with those bound to SWI/SNF. These results demonstrate a different in vitro remodeling of the HIV-1 nucleosome upon the binding of multiple transcription activators and of SWI/SNF complex.

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.

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.

Photophysical properties of the photosensitizer pheophorbide a studied at high photon flux densities

The photophysical properties of pheophorbide a (Pheo a) under two-step laser activation were investigated. For the first time quantum yields of higher excited state formation were calculated. It was shown that the quantum yields of the formation of these states depend strongly on the pulse duration of the excitation source. The nonlinear properties of Pheo a are quite different in dependence on the excitation wavelength but the quantum yields of the higher excited state formation in both cases (lambda exc = 337 nm and lambda exc = 667 nm) rise up increasing the photon flux density of the laser light up to 10(26) phot cm-2 s-1. A further increase of the photon flux density has no effect on the quantum yields.

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.

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.

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.

Model studies for the direct effect of high-energy irradiation on DNA. Mechanism of strand break formation induced by laser photoionization of poly U in aqueous solution

Laser flash photolysis of polyuridylic acid (poly U) in anoxic aqueous solutions leads to biphotonic photoionization of the uracil moiety followed by the formation of single strand breaks (ssb). The rate constant for ssb formation (1.0 s-1, obtained from the slow component of conductivity increase at 23 degrees C and pH 6.8) increases with decreasing pH to 235 s-1 at pH 3.5. The activation energy (pre-exponential factor) was measured to be 66 kJ mol-1 (5 X 10(11) s-1) at pH 6.8. Addition of dithiothreitol (DTT) or glutathione (GSH) prevents ssb formation by reacting with a poly U intermediate (rate constant = 1.2 X 10(6) and 0.16 X 10(6) dm3 mol-1 s-1, respectively). Since with OH radicals as initiators very similar data have been obtained for the kinetics of ssb formation and for the reaction with DTT, we conclude that photoionization of the uracil moiety in poly U leads eventually to the same chemical pathway for ssb formation as that induced by OH radicals. Furthermore, we propose that protection by DTT and GSH occurs via H donation to the C-4' radicals of the sugar moiety of DNA and to the C-4' and the C-2' radicals of poly U.

Laser biology and medicine

The substantial repertoire of laser radiation--its coherence, range of intensity and frequency, controlability of focal area and of beam length--has been comprehensively explored in the contexts of micro- and macro-diagnostics of cells, biochemical kinetics, therapy and surgery.