Photoelectric effects of deoxyribonucleic acid

Studies have been made of the d.c. semiconductive behavior of fibers and solid gels of DNA. The semiconductive behavior under high vacuum is similar in solid gels of DNA and stretched fibers of DNA measured along and across the fiber axis. Photoelectric effects have been studied, and an action spectrum is reported which agrees with the absorption spectrum of DNA. No photoelectric effects are observed at wavelengths corresponding to the thermal energy gap. The temperature dependence of the photocurrent has been determined, and the effects of air, oxygen, and nitrogen at different pressures on the photocurrent have been measured.     

Integration Efficiency in DNA-Induced Transformation of Pneumococcus. I. a Method of Transformation in Solid Medium and Its Use for Isolation of Transformation-Deficient and Recombination-Modified Mutants

A method of transformation on solid medium especially adapted for pneumococcus has been developed. Under specific conditions, all colonies that are allowed to grow in the presence of transforming DNA for six hours give rise to transformed bacteria. Combined with replica plating this technique has been used to isolate mutants modified with regard to recombination. Most of the mutants found are transformation-defective and show a large diversity in their response to ultraviolet light. Some of these mutants have lost their ability to take up transforming DNA. One shows a reduced yield of transformants for a given quantity of DNA taken up. Mutants that manifest altered behavior with regard to marker efficiencies have also been isolated. One of these exhibits a decrease in the transformation efficiency of only the high efficiency markers and two mutants show a decrease in the transformation efficiency of the low efficiency markers.     

Cytological evidence of defective template in the fragile X chromosome

In cells of fragile X patients, the changed X segment may appear as a poorly staining region or a gap, or as a deletion, involving one or both chromatids. To find out whether the fragile site represents ah incompletely replicated DNA sequence, as has been suggested recently, we analyzed the four chromatids of methotrexate-induced endoreduplicated fragile X chromosomes. Our main observations were: (1) a deleted chromatid was never internal to a poorly staining one; (2) an endoreduplicated X chromosome with a fragile site never included a normal chromatid. These results can be explained by assuming that DNA at the fragile site, when replicated in the presence of methotrexate, may undergo defective replication and give rise to improperly packaged chromatin, appearing as a chromatid with a poorly staining region or a gap in the following metaphase. The same DNA may fail to function as a template in the following S-phase and give rise to a chromatid with a single-stranded segment, appearing as a deleted chromatid in the following metaphase.Dedicated to the memory of Professor Menashe Marcus, teacher, colleague, arid friend     

Investigating the electronic properties of silicon nanosheets by first-principles calculations

Using first-principles total energy calculations within the density functional theory (DFT), we investigated the electronic and structural properties of graphene-like silicon sheets. Our studies were performed using the LSDA (PWC) and GGS (PBE) approaches. Two configurations were explored: one corresponding to a defect-free layer (h-Si), and the other to a layer with defects (d-Si), both of which were in the armchair geometry. These sheets contained clusters of the C(n)H(m) type. We also investigated the effects of doping with group IV-A elements. Structural stability was studied by only considering positive vibration frequencies. Results showed that both h-Si and d-Si present a corrugated structure with concavity. h-Si sheets were found to be ionic (D.M. = 0.33 Debye) with an energy gap (HOMO-LUMO) of 0.77 eV in the LSDA theory and 0.76 eV in the GGS approach, while d-Si sheets were observed to be covalent (D.M. = 2.78 D), and exhibited semimetallic electronic behavior (HOMO-LUMO gap = 0.32 eV within the LSDA theory and 0.33 eV within the GGS approach). d-Si sheets doped with one carbon or one germanium preserved the polarity of the undoped d-Si sheets, as well as their semimetallic electronic behavior. However, when the sheets were doped with two C or two Ge atoms, or with one of each atom (to give Si(52)CGeH(18)), they retained the semimetallic behavior, but they changed from having ionic character to covalent character.     

Effect of the photocatalytic activity of TiO(2) on plasmid DNA

We investigated the photodynamic DNA strand-breaking activity of TiO(2). A solution of super-coiled pBR 322 DNA was irradiated with 5 J/cm(2) of UVA in the presence of TiO(2) and the products were analyzed by using gel electrophoresis. The ratio of open-circular DNA to super-coiled circular DNA was calculated from the resulting peak areas as a DNA strand-breaking index (SBI). The SBI of anatase-structure TiO(2) (band gap=3.23 eV) was greater than that of rutile structure (band gap=3.06 eV), and the level of SBI correlated with the photocatalytic activity for degradation of 2-propanol. The inhibitory effects of active oxygen scavengers, including DMSO, glutathione and histidine, on the DNA strand-breaking activity were examined. All of the scavengers except ascorbic acid showed inhibitory effects, as did several polyhydric alcohols including mannitol, a well-known hydroxyl radical scavenger. These results suggest that the photodynamic DNA strand-breaking activity of TiO(2) is due to active oxygen species, especially hydroxyl radicals. Polyhydric alcohols showed an inverse correlation between the inhibitory effect on DNA strand-breaking activity and the octanol/water partition coefficient (logP).     

Pollen DNA repair after treatment with the mutagens 4-nitroquinoline-1-oxide, ultraviolet and near-ultraviolet irradiation, and boron dependence of rapair

Summary Irradiation of dry, mature pollen from Petunia hybrida with near-ultraviolet light from an erythemal-sunlamp gave rise to a repair-like, unscheduled DNA synthesis during the early stages of in vitro germination. Like that brought about by farultraviolet light from a germicidal lamp, this DNA synthesis is enhanced by hydroxyurea added to the germination medium, and reduced by photoreactivating light given after ultraviolet irradiation and before germination begins. It is concluded that pollen, often receiving considerable exposure to sunlight, has, in addition to the protection afforded by the ultraviolet filtering effect of yellow pigments, also the capacity to repair ultraviolet produced changes in DNA, by both photoreactivation and dark repair processes.Because mature Petunia pollen is arrested at the G₂ stage of the cell cycle, germinating pollen provides us with a highly synchronous plant tissue with a very low background of DNA replicative synthesis suitable for sensitive measurement of DNA repair synthesis. Thus we have shown that 4-nitroquinoline-1-oxide, at concentrations greater than 0.001 mM, gives rise to an unscheduled DNA synthesis which is enhanced by hydroxyurea. Like that induced by ultraviolet radiation, the chemical mutagen brings about DNA repair only during the early stages of pollen germination, and further it has been possible to show that repair ceases at about the time that generative cell division and pollen tube elongation begins.Boron addition enhances both ultraviolet and 4-nitroquinoline-1-oxide induced repair synthesis. By delaying the chemical mutagen initiation of repair until after germination has begun, we have been able to show that boron is most beneficial during the first hour of germination. It is postulated that this is achieved through an as yet unknown effect of boron on the supply of precursors before pollen cell metabolism is fully committed to pollen tube synthesis later in the germination period.     

Electron and photon spectra for three gadolinium-based cancer therapy approaches

Some recent neutron capture therapy research has focused on using compounds containing the element gadolinium, which produces internal conversion and Auger cascade electrons. The low-energy, short-range Auger electrons are absorbed locally and increase cell killing dramatically as the gadolinium compounds are introduced into the cell nucleus and bind to the DNA. Detailed electron and photon spectra are needed for biophysical modeling and Monte Carlo calculations of damage to DNA. This paper presents calculated electron and photon spectra for three cases: thermal neutron absorption by (157)Gd, the beta-particle decay of (159)Gd, and the K-shell photoelectric event in gadolinium. The Monte Carlo sampling of atomic and nuclear transitions for each of the three cases was used to calculate a large number of representative decays. The sampled decays were used to determine average emissions and energy deposited in small spheres of tissue. The kinetic energy nuclear recoil from gamma-ray and electron emissions was calculated and found to be more than 10 eV for 26% of all (157)Gd neutron capture reactions.     

A band model for melanin deducted from optical absorption and photoconductivity experiments

Natural and synthetic melanins have been studied by optical absorption and photoconductivity measurements in the range 200--700 nm. Both optical absorption and photoconductivity increase in the ultraviolet region, and a negative photoconductivity was observed with a maximum near 500 nm. This behaviour has been interpreted by the band model of amorphous materials and an "optical gap" of 3.4 eV has been determined.     

A band model for melanin deduced from optical absorption and photoconductivity experiments

Natural and synthetic melanins have been studied by optical absorption and photoconductivity measurements in the range 200–700 nm. Both optical absorption and photoconductivity increase in the ultraviolet region, and a negative photoconductivity was observed with a maximum near 500 nm. This behaviour has been interpreted by the band model of amorphous materials and an “optical gap” of 3.4 eV has been determined.     

Radical-pair energetics and decay mechanisms in reaction centers containing anthraquinones, naphthoquinones or benzoquinones in place of ubiquinone

In reaction centers from Rhodobacter sphaeroides (formerly called Rhodopseudomonas sphaeroides), light causes an electron-transfer reaction that forms the radical pair state (P+I-, or PF) from the initial excited singlet state (P) of a bacteriochlorophyll dimer (P). Subsequent electron transfer to a quinone (Q) produces the state P+Q-. Back electron transfer can regenerate P from P+Q-, giving rise to 'delayed' fluorescence that decays with approximately the same lifetime as P+Q-. The free-energy difference between P+Q- and P can be determined from the initial amplitude of the delayed fluorescence. In the present work, we extracted the native quinone (ubiquinone) from Rps. sphaeroides reaction centers, and replaced it by various anthraquinones, naphthoquinones, and benzoquinones. We found a rough correlation between the halfwave reduction potential (E1/2) of the quinone used for reconstitution (as measured polarographically in dimethylformamide) and the apparent free energy of the state P+Q- relatively to P. As the E1/2 of the quinone becomes more negative, the standard free-energy gap between P+Q- and P decreases. However, the correlation is quantitatively weak. Apparently, the effective midpoint potentials (Em) of the quinones in situ depend subtly on interactions with the protein environment in the reaction center. Using the value of the Em for ubiquinone determined in native reaction centers as a reference, and the standard free energies determined for P+Q- in reaction centers reconstituted with other quinones, the effective Em values of 12 different quinones in situ are estimated. In native reaction centers, or in reaction centers reconstituted with quinones that give a standard free-energy gap of more than about 0.8 eV between P+Q- and P*, charge recombination from P+Q- to the ground state (PQ) occurs almost exclusively by a temperature-insensitive mechanism, presumably electron tunneling. When reaction centers are reconstituted with quinones that give a free-energy gap between P+Q- and P* of less than 0.8 with quinones that give a free-energy gap between P+Q- and P* of less than 0.8 eV, part or all of the decay proceeds through a thermally accessible intermediate. There is a linear relationship between the log of the rate constant for the decay of P+Q- via the intermediate state and the standard free energy of P+Q-. The higher the free energy, the faster the decay. The kinetic and thermodynamic properties of the intermediate appear not to depend strongly on the quinone used for reconstitution, indicating that the intermediate is probably not simply an activated form of P+Q-.(ABSTRACT TRUNCATED AT 400 WORDS)     

Repair of DNA strand breaks after gamma-irradiation of protoplasts isolated from cultured wild carrot cells

We have isolated protoplasts of cultured wild carrot (Daucus carota L.) cells, lysed them directly on top of alkaline sucrose gradients, and measured single-stranded DNA of molecular weight 1·10⁸ by velocity sedimentation. DNA sedimentation studies on γ-irradiated protoplasts indicate that the energy absorbed in DNA per strand break is 85 eV in air and 260 eV in nitrogen. Isolated wild carrot protoplasts can repair 50% of the DNA strand breaks within 5 min after a dose of 20 krad, and by 1 h none can be detected.     

Comparing the spectroscopic and electrochemical properties of ruthenium and osmium complexes of the tridentate polyazine ligands 2,2′:6′,2″-terpyridine and 2,3,5,6-tetrakis(2-pyridyl)pyrazine

A number of osmium and ruthenium complexes of the tridentate ligands 2,2′:6′,2″-terpyridine (tpy) and 2,3,5,6-tetrakis(2-pyridyl)pyrazine (tpp) have been prepared and characterized by our laboratory. All these complexes possess metal based oxidations and ligand based reductions localized on each polyazine ligand. Polymetallic complexes bridged by the tpp ligand exhibit two sequential tpp based reductions prior to the reduction of other polyazine ligands in these complexes. The spectroscopy of these complexes is dominated by ligand based π-π^* transitions in the ultraviolet and MLCT (metal-to-ligand charge transfer) bands terminating on each polyzine ligand in the visible. For the complexes reported herein the lowest lying optical transitionis a M → BL CT band. For most of the complexes reported, occupation of this excited state gives rise to an observable emission at room temperature. For ruthenium complexes of these tridentate ligands, the presence of a low-lying LF state shortens the excited state lifetimes of these chromophores. This gives rise to ruthenium complexes that display shorter excited state lifetimes than the analogous osmium based systems. Incorporation of tpp based chromophores into polymetallic frameworks leads to the production of bimetallic species with long-lived excited states, 100 ns at room temperature. This makes these chromophores good candidates for the development of stereochemically defined supramolecular complexes. It is possible to measure an electrochemical HOMO-LUMO energy gap and a correlation between this electrochemically measured energy gap and the spectroscopic energy associated with this HOMO→LUMO transition are reported herein (HOMO== highest occupied molecular orbital, LUMO = lowest unoccupied molecular orbital).     

An infrared spectroscopy study of the molecular structure changes of DNA after electron and ultraviolet irradiation

Samples of calf thymus DNA and two different leukemic leukocyte DNA's in the solid state have been irradiated (at 300°K) with 800 keV electrons and 4.9 eV (2537Å) ultraviolet rays. The subsequent effects on the DNA's have been studied using infrared spectroscopy as the probe for radiation-produced molecular alterations. The region of the infrared spectrum studied covered the wave number range from 4000 cm⁻¹ to 300 cm⁻¹. Our results indicate that under electron and ultraviolet irradiation, the prominent infrared active absorption peaks of all three DNA's are altered. The infrared results of our ultraviolet irradiation of DNA indicate that similar molecular bonds are broken as for the case of DNA irradiated with 800 keV electrons. The results indicate that up to high doses, calf thymus DNA is more sensitive to electron irradiation than the leukemic leukocyte DNA's. The infrared active absorption peaks of the two leukemic leukocyte DNA's respond similarly to electrons. The ultraviolet results indicate some difference between calf thymus DNA and the two leukocyte DNA's in their response to 4.9 eV light.     

The effect of ultraviolet irradiation on collagen-fold formation

1. A study has been made of the effect of ultraviolet irradiation, in the presence of air and nitrogen, on the conformational changes taking place in cooled solutions of gelatin prepared from thermally denatured neutral-salt-soluble collagen. 2. The increase in negative rotation and viscosity at 15 degrees for irradiated and thermally denatured solutions of collagen becomes less as the irradiation time is increased. 3. The principal effect of ultraviolet irradiation is the fission of the primary collagen peptide chains, eventually yielding chain lengths incapable of stabilizing a helical structure. 4. Irradiation in both air and nitrogen results in a loss of tyrosine, histidine and phenylalanine, with more denaturation occurring in the presence of nitrogen.     

The Roles of Structural Order and Intermolecular Interactions in Determining Ionization Energies and Charge‐Transfer State Energies in Organic Semiconductors

The energy landscape in organic semiconducting materials greatly influences charge and exciton behavior, which are both critical to the operation of organic electronic devices. These energy landscapes can change dramatically depending on the phases of material present, including pure phases of one molecule or polymer and mixed phases exhibiting different degrees of order and composition. In this work, ultraviolet photoelectron spectroscopy measurements of ionization energies (IEs) and external quantum efficiency measurements of charge‐transfer (CT) state energies (E_CT) are applied to molecular photovoltaic material systems to characterize energy landscapes. The results show that IEs and E_CT values are highly dependent on structural order and phase composition. In the sexithiophene:C₆₀ system both the IEs of sexithiophene and C₆₀ shift by over 0.4 eV while E_CT shifts by 0.5 eV depending on molecular composition. By contrast, in the rubrene:C₆₀ system the IE of rubrene and C₆₀ vary by ≤ 0.11 eV and E_CT varies by ≤ 0.04 eV as the material composition varies. These results suggest that energy landscapes can exist whereby the binding energies of the CT states are overcome by energy offsets between charges in CT states in mixed regions and free charges in pure phases.     

Effect of Photoreactivation on the Filling of Gaps in Deoxyribonucleic Acid Synthesized After Exposure of Escherichia coli to Ultraviolet Light

Daughter-strand gaps in deoxyribonucleic acid (DNA) synthesized after exposure of excision-deficient Escherichia coli to ultraviolet light are filled during subsequent incubation in buffer, and the rate of filling is increased when the incubation in buffer is carried out in the presence of 360-nm light. It is concluded that daughter-strand discontinuities are prevented from being rapidly sealed in the dark not because of some structural feature of the daughter-strand but because of the presence of a pyrimidine dimer on the opposite (parental) strand. "Photoreactivation-stimulated gap filling" is dependent on the polA(+) and recA(+) but not the exrA(+) genes. It is suggested that the removal of the dimer allows gap-filling by DNA polymerase I and polynucleotide ligase. The recA(+) gene may be needed at a very early stage, possibly for gap stabilization.     

Immunochemical studies on the correlation between conformational changes of DNA caused by ultraviolet irradiation and manifestation of antigenicity.

The conformational changes of double-stranded DNA induced during irradiation with ultraviolet, were immunologically investigated. These studies revealed that at least two distinct antigenic sites were induced in the irradiated DNA molecule, giving rise to two different antibodies specific for ultraviolet-irradiated (uv) DNA and thermally denatured DNA-like structure, and these were demonstrable using radioimmunoassay and double diffusion tests. A series of experiments, including melting profile, fluorescence intensity of the ethidium bromide complex and chromatographic behavior on hydroxyapatite, performed on the antigenically active uvDNA indicated that the duplex structure of DNA separated irregularly during irradiation. Furthermore, the data showed that the conformational determinants of uvDNA are located on the exposed single-stranded regions.     

Senescence of human fibroblasts after psoralen photoactivation is mediated by ATR kinase and persistent DNA damage foci at telomeres

Cellular senescence is a phenotype that is likely linked with aging. Recent concepts view different forms of senescence as permanently maintained DNA damage responses partially characterized by the presence of senescence-associated DNA damage foci at dysfunctional telomeres. Irradiation of primary human dermal fibroblasts with the photosensitizer 8-methoxypsoralen and ultraviolet A radiation (PUVA) induces senescence. In the present study, we demonstrate that senescence after PUVA depends on DNA interstrand cross-link (ICL) formation that activates ATR kinase. ATR is necessary for the manifestation and maintenance of the senescent phenotype, because depletion of ATR expression before PUVA prevents induction of senescence, and reduction of ATR expression in PUVA-senesced fibroblasts releases cells from growth arrest. We find an ATR-dependent phosphorylation of the histone H2AX (gamma-H2AX). After PUVA, ATR and gamma-H2AX colocalize in multiple nuclear foci. After several days, only few predominantly telomere-localized foci persist and telomeric DNA can be coimmunoprecipitated with ATR from PUVA-senesced fibroblasts. We thus identify ATR as a novel mediator of telomere-dependent senescence in response to ICL induced by photoactivated psoralens.     

Inhibition of DNA replication by hydroxyurea and caffeine in an ultraviolet-irradiated human fibroblast cell line

DNA replication in human fibroblasts with normal excision repair was investigated after ultraviolet irradiation and incubation with caffeine or hydroxyurea. The DNA synthesized soon after irradiation had a reduced size, but that synthesized later was near normal size. When caffeine was present before labeling, it reduced the size of DNA synthesized but when added after labeling it was without effect. When irradiated cells were allowed to grow, labeled DNA increased in size steadily for 60 min to a maximum that was below control and dose-dependent. Further growth resulted in a transition of some label to parental DNA sizes, but a large fraction remained permanently blocked at smaller sizes producing bimodal distributions of DNA. The steady increase in size was inhibited by hydroxyurea. Removing cells from hydroxyurea resulted in increases similar to or slightly slower than those observed immediately after labeling, and this protocol did not permit cells to acquire any induced or enhanced capacity to replicate damaged DNA.