Increase of positive supercoiling in a hyperthermophilic archaeon after UV irradiation.

Diverse DNA repair mechanisms are essential to all living organisms. Some of the most widespread repair systems allow recovery of genome integrity in the face of UV radiation. Here, we show that the hyperthermophilic archaeon Thermococcus nautili possesses a remarkable ability to recovery from extreme chromosomal damage. Immediately following UV irradiation, chromosomal DNA of T. nautili is fragmented beyond recognition. However, the extensive UV-induced double-stranded breaks (DSB) are repaired over the course of several hours, allowing restoration of growth. DSBs also disrupted plasmid DNA in this species. Similar to the chromosome, plasmid integrity was restored during an outgrowth period. Intriguingly, the topology of recovered pTN1 plasmids differed from control strain by being more positively supercoiled. As reverse gyrase (RG) is the only enzyme capable of inducing positive supercoiling, our results suggest the activation of RG activity by UV-induced stress. We suggest simple UV stress could be used to study archaeal DNA repair and responses to DSB.

Seabuckthron (Hippophae rhamnoides L.) leaf extract ameliorates the gamma radiation mediated DNA damage and hepatic alterations.

In vitro assessment showed that H. rhamnoides (HrLE) extract possessed free radical scavenging activities and can protect gamma (gamma) radiation induced supercoiled DNA damage. For in vivo study, Swiss albino mice were administered with HrLE (30 mg/kg body weight) for 15 consecutive days before exposing them to a single dose of 5 Gy of beta radiation. HrLE significantly prevented the radiation induced genomic DNA damage indicated as a significant reduction in the comet parameters. The lipid peroxidation, liver function enzymes, expression of phosphorylated NFkappaB (p65) and IkappaBalpha increased whereas the endogenous antioxidants diminished upon radiation exposure compared to control. Pretreatment of HrLE extract ameliorated these changes. Based on the present results it can be concluded that H. rhamnoides possess a potential preventive element in planned and accidental nuclear exposures.

Novel method for quantifying radiation-induced single-strand-break yields in plasmid DNA highlights 10-fold discrepancy.

The widely used agarose gel electrophoresis method for assessing radiation-induced single-strand-break (SSB) yield in plasmid DNA involves measurement of the fraction of relaxed-circular (C) form that migrates independently from the intact supercoiled (SC) form. We rationalized that this method may underestimate the SSB yield since the position of the relaxed-circular form is not altered when the number of SSB per DNA molecule is >1. To overcome this limitation, we have developed a novel method that directly probes and quantifies SSBs. Supercoiled (3)H-pUC19 plasmid samples were irradiated with γ-rays, alkali-denatured, dephosphorylated, and kinated with γ-[(32)P]ATP, and the DNA-incorporated (32)P activities were used to quantify the SSB yields per DNA molecule, employing a standard curve generated using DNA molecules containing a known number of SSBs. The same irradiated samples were analyzed by agarose gel and SSB yields were determined by conventional methods. Comparison of the data demonstrated that the mean SSB yield per plasmid DNA molecule of [21.2±0.59]×10(-2)Gy(-1) as measured by direct probing is ~10-fold higher than that obtained from conventional gel-based methods. These findings imply that the SSB yields inferred from agarose gels need reevaluation, especially when they were utilized in the determination of radiation risk.

Platinum nanoparticles: a promising material for future cancer therapy?

Recently, the use of gold nanoparticles as potential tumor selective radiosensitizers has been proposed as a breakthrough in radiotherapy. Experiments in living cells and in vivo have demonstrated the efficiency of the metal nanoparticles when combined with low energy x-ray radiations (below conventional 1 MeV Linac radiation). Further studies on DNA have been performed in order to better understand the fundamental processes of sensitization and to further improve the method. In this work, we propose a new strategy based on the combination of platinum nanoparticles with irradiation by fast ions effectively used in hadron therapy. It is observed in particular that nanoparticles enhance strongly lethal damage in DNA, with an efficiency factor close to 2 for double strand breaks. In order to disentangle the effect of the nano-design architecture, a comparison with the effects of dispersed metal atoms at the same concentration has been performed. It is thus shown that the sensitization in nanoparticles is enhanced due to auto-amplified electronic cascades inside the nanoparticles, which reinforces the energy deposition in the close vicinity of the metal. Finally, the combination of fast ion radiation (hadron therapy) with platinum nanoparticles should strongly improve cancer therapy protocols.

Cysteine-rich cyanopeptide beta2 from Spirulina fusiformis exhibits plasmid DNA pBR322 scission prevention and cellular antioxidant activity.

Isolation of three different active peptides from C-phycocyanin (C-pc) beta chain of S. fusiformis and their biological properties are reported. Phycocyanin peptide beta fraction 2 (cyanopeptide beta 2) facilitated both antioxidant and plasmid DNA strand scission prevention activity due to higher cysteine moieties in the isolated peptide. The peptide significantly scavenged the free radicals like 1-1,-diphenyl-2-picryl hydrazyl and ferric reducing ability of plasma, increased the absorbance values in reducing power and also showed the higher trolox equivalent antioxidant capacity values in total reactive antioxidant potentials assay. Cyanopeptide beta 2 also inhibited reactive oxygen species induced DNA pBR322 damage in dose dependent manner along with free radical scavenging properties suggesting the role in the DNA integrity which is also evident by DNA binding activity of peptide. In addition, the generation of reactive oxygen species (ROS) was dose dependent (10 and 20 ng/ml) and significantly quenched by cyanopeptide beta2 in human fibroblast cell line TIG 3-20. In vitro cell scratch injury assay demonstrated the capacity of cyanopeptide beta2 in cell migration in to wounded area suggesting fibroblast proliferation and migration. The results suggest that cyanopeptide beta2 can be a free radical scavenger and effective peptide for future biomedical applications like wound healing, atherosclerosis, cell redox potential and hypoxia.

A radiation target method for size determination of supercoiled plasmid DNA.

Supercoiled DNA plasmids were exposed in the frozen state to high-energy electrons. Surviving supercoiled molecules were separated from their degradation products (e.g., open circle and linear forms) by agarose gel electrophoresis and subsequently quantified by staining and image analysis. Complex survival curves were analyzed using radiation target theory, yielding the radiation-sensitive mass of each form. One of the irradiated plasmids was transfected into cells, permitting radiation analysis of gene expression. Loss of this function was associated with a mass much smaller than the entire plasmid molecule, indicating a lack of energy transfer in amounts sufficient to cause structural damage along the DNA polynucleotide. The method of radiation target analysis can be applied to study both structure and function of DNA.

Gold nanoparticles enhance DNA damage induced by anti-cancer drugs and radiation.

The chemotherapeutic agent cisplatin was chemically linked to pGEM-3Zf(-) plasmid DNA to produce a cisplatin-DNA complex, Gold nanoparticles, which bind electrostatically to pure DNA, could also be added to this complex. Dry films of pure plasmid DNA and DNA-cisplatin, DNA-gold nanoparticles and DNA-cisplatin-gold nanoparticles complexes were bombarded by 60 keV electrons. The yields of single- and double-strand breaks were measured as a function of exposure by electrophoresis. From a comparison of such yields from the different type of films, we found that the binding of only one gold nanoparticle to a plasmid-cisplatin complex containing 3197 base pairs increases by a factor of 3 the efficiency of the chemotherapeutic agent cisplatin to produce double-strand breaks in irradiated DNA. Furthermore, adding two cisplatin molecules and one gold nanoparticle to DNA enhances radiation-induced DSBs by a factor of 7.5. A number of phenomena could contribute to this huge enhancement, including the higher density of low-energy electrons and reactive species around the gold nanoparticles and the weakening of bonds adjacent to cisplatin in the DNA backbone. The addition of gold nanoparticles to cisplatin and other platinum agents may therefore provide interesting avenues of research to improve the treatment of cancer by concomitant chemoradiation.

Resonant formation of DNA strand breaks by low-energy (3 to 20 eV) electrons.

Most of the energy deposited in cells by ionizing radiation is channeled into the production of abundant free secondary electrons with ballistic energies between 1 and 20 electron volts. Here it is shown that reactions of such electrons, even at energies well below ionization thresholds, induce substantial yields of single- and double-strand breaks in DNA, which are caused by rapid decays of transient molecular resonances localized on the DNA's basic components. This finding presents a fundamental challenge to the traditional notion that genotoxic damage by secondary electrons can only occur at energies above the onset of ionization, or upon solvation when they become a slowly reacting chemical species.

Nanoscale detection of ionizing radiation damage to DNA by atomic force microscopy.

The detection and quantification of ionizing radiation damage to DNA at a single-molecule level by atomic force microscopy (AFM) is reported. The DNA damage-detection technique combining supercoiled plasmid relaxation assay with AFM imaging is a direct and quantitative approach to detect gamma-ray-induced single- and double-strand breaks in DNA, and its accuracy and reliability are validated through a comparison with traditional agarose gel electrophoresis. In addition, the dependence of radiation-induced single-strand breaks on plasmid size and concentration at a single-molecule level in a low-dose (1 Gy) and low-concentration range (0.01 ng microL(-1)-10 ng microL(-1)) is investigated using the AFM-based damage-detection assay. The results clearly show that the number of single-strand breaks per DNA molecule is linearly proportional to the plasmid size and inversely correlated to the DNA concentration. This assay can also efficiently detect DNA damage in highly dilute samples (0.01 ng microL(-1)), which is beyond the capability of traditional techniques. AFM imaging can uniquely supplement traditional techniques for sensitive measurements of damage to DNA by ionizing radiation.

5-Methyltetrahydrofolate inhibits photosensitization reactions and strand breaks in DNA.

The known functions of folate are to support one-carbon metabolism and to serve as photoreceptors for cryptochromes and photolyases. We demonstrate that 5-methyltetrahydrofolate (5-MTHF, the predominant folate in plasma) is also a potent, near diffusion limited, scavenger of singlet oxygen and quencher of excited photosensitizers. Both pathways result in decomposition of 5-MTHF, although ascorbate can protect against this loss. In the absence of photosensitizers, 5-MTHF is directly decomposed only very slowly by UVA or UVB. Although synthetic folic acid can promote DNA damage by UVA, submicromolar 5-MTHF inhibits photosensitization-induced strand breaks. These observations suggest a new role for reduced folate in protection from ultraviolet damage and have bearing on the hypothesis that folate photodegradation influenced the evolution of human skin color.

DNA double-strand breaks induced by decay of (123)I-labeled Hoechst 33342: role of DNA topology.

PURPOSE: To determine double-strand-break (DSB) yields produced by decay of minor-groove-bound (123)I-labeled Hoechst 33342 ((123)IEH) in supercoiled (SC) and linear (L) forms of pUC19 DNA, to compare strand-break efficiency of (123)IEH with that of (125)IEH, and to examine the role of DNA topology in DSB induction by these Auger electron emitters. MATERIALS AND METHODS: Tritium-labeled SC and L pUC19 DNA were incubated with (123)IEH (0-10.9 MBq) at 4 degrees C. After (123)I had completely decayed (10 days), samples were analyzed on agarose gel, and single-strand-break (SSB) and DSB yields were measured. RESULTS: Each (123)I decay in SC DNA produces a DSB yield of 0.18 +/- 0.01. On the basis of DSB yields for (125)IEH (0.52 +/- 0.02 for SC and 1.62 +/- 0.07 for L, reported previously) and dosimetric expectations, a DSB yield of approximately 0.5 (3 x 0.18) per (123)I decay is expected for L DNA. However, no DSB are observed for the L form, even after approximately 2 x 10(11) decays of (123)I per microg DNA, whereas a similar number of (125)I decays produces DSB in approximately 40% of L DNA. CONCLUSION: (123)IEH-induced DSB yield for SC but not L DNA is consistent with the dosimetric expectations for Auger electron emitters. These studies highlight the role of DNA topology in DSB production by Auger emitters and underscore the failure of current theoretical dosimetric methods per se to predict the magnitude of DSB.

Photochemical methods to assay DNA photocleavage using supercoiled pUC18 DNA and LED or xenon arc lamp excitation.

Methods for the study of DNA photocleavage are illustrated using a mixed-metal supramolecular complex [{(bpy)(2)Ru(dpp)}(2)RhCl(2)]Cl(5). The methods use supercoiled pUC18 plasmid as a DNA probe and either filtered light from a xenon arc lamp source or monochromatic light from a newly designed, high-intensity light-emitting diode (LED) array. Detailed methods for performing the photochemical experiments and analysis of the DNA photoproduct are delineated. Detailed methods are also given for building an LED array to be used for DNA photolysis experiments. The Xe arc source has a broad spectral range and high light flux. The LEDs have a high-intensity, nearly monochromatic output. Arrays of LEDs have the advantage of allowing tunable, accurate output to multiple samples for high-throughput photochemistry experiments at relatively low cost.

Binding and photocleavage of DNA by mixed ligand Co(III) and Ni(II) complexes of thiophene[2, 3-b] quinoline and phenanthrolie/bipyridine.

In order to systematically perform an experimental and theoretical study on DNA binding and photocleavage properties of transition metal complexes of the type [M(L)2(L1)](PF6)n x xH2O (where M = Co(III) or Ni(II), L = 1,10-phenanthroline or 2.2' bipryidine, L1 = Thiophene [2,3-b] quinoline (qt), n = 3 or 2 and x = 5 or 2) have been synthesized and characterized by elemental analysis, IR, 1H NMR, UV and magnetic susceptibility data. The DNA-binding properties of these complexes have been investigated with UV-Vis, viscosity measurements, thermal denaturation and cyclic voltametric studies. It is experimentally found that all the complexes are bound to DNA via intercalation in the order [Co(bpy)2(qt)](PF6)3 > [Co(phen)2(qt)](PF6)3 > [Ni(phen)2(qt)](PF6)2 > [Ni(bpy)2(qt)](PF6)2. The photocleavage studies with pUC19 DNA shows that all these complexes promoted the conversion of SC form to NC form in absence of 'inhibitors'.

Gamma rays and bleomycin nick DNA and reverse the DNase I sensitivity of beta-globin gene chromatin in vivo.

The active beta-globin genes in chicken erythrocytes, like all active genes, reside in large chromatin domains which are preferentially sensitive to digestion by DNase I. We have recently proposed that the special structure of chromatin in active domains is maintained by torsional stress in the DNA (Villeponteau et al., Cell 39:469-478, 1984). This hypothesis predicts that nicking of the DNA within any such chromosomal domain in vivo will relax the DNA and lead to loss of the special DNase I-sensitive state. Here we have tested this prediction by using gamma irradiation and bleomycin treatment to cleave DNA within intact chicken embryo erythrocytes. Both treatments cause reversal of DNase I sensitivity. Moreover, reversal occurs at approximately one nick per 150 kilobase pairs for both agents despite their entirely unrelated modes of cell penetration and DNA attack. These results suggest that the domain of DNase I sensitivity surrounding the beta-globin genes comprises 150 kilobase pairs of chromatin under torsional stress and that a single DNA nick in this region is sufficient to reverse the DNase I sensitivity throughout the entire domain.

Damage to plasmid DNA induced by low energy carbon ions.

The damage induced in supercoiled plasmid DNA molecules by 1-6 keV carbon ions has been investigated as a function of ion exposure, energy and charge state. The production of short linear fragments through multiple double strand breaks has been demonstrated and exponential exposure responses for each of the topoisomers have been found. The cross section for the loss of supercoiling was calculated to be (2.2 +/- 0.5) x 10(-14) cm(2) for 2 keV C(+) ions. For singly charged carbon ions, increased damage was observed with increasing ion energy. In the case of 2 keV doubly charged ions, the damage was greater than for singly charged ions of the same energy. These observations demonstrate that ion induced damage is a function of both the kinetic and potential energies of the ion.

A comprehensive analysis of direct and photosensitized attenuation of Toxoplasma gondii tachyzoites.

In the present work, we have evaluated the effect of three different types of radiation: UVC (254±5nm), UVA (365±20nm) and visible (420±20nm) on different morphological and biological functions of Toxoplasma gondii tachyzoites. Briefly, UVC and UVA showed an inhibitory effect on parasite invasion in a dose-dependent manner. UVC showed the strongest effect inducing both structural damage (antigens) and functional inhibition (i.e., invasion and replication). On its own, visible light induces a quite distinctive and selective pattern of parasite-attenuation. This type of incident radiation inhibits the replication of the parasite affecting neither the capability of invasion/attachment nor the native structure of proteins (antigens) on parasites. Such effects are a consequence of photosensitized processes where phenol red might act as the active photosensitizer. The potential uses of the methodologies investigated herein are discussed.

Enhancement of the photokilling effect of TiO2 in photodynamic therapy by conjugating with reduced graphene oxide and its mechanism exploration.

As a promising next-generation photodynamic therapy (PDT) photosensitizer, TiO2 nanoparticles (NPs) has gained great attention due to its higher efficiency. Yet, its application in PDT is strongly limited by its UV light response range. In this work, TiO2 NPs conjugated with reduced graphene oxide (RGO-TiO2) composites were successfully prepared by hydrothermal reduction method. They were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR), Transmission electron microscope (TEM), Brunauer-Emmett-Teller (BET), UV-vis spectroscopy and X-ray photoelectron spectroscopy (XPS). Superior adsorption and killing efficiency under UV-A light or visible light were achieved in the presence of the RGO rather than that of unmodified TiO2. The optimal photocatalytic activity was obtained when modified proportion was 0.2 (RGO:TiO2). Dark cytotoxicity was observed using 0-500µgmL-1 RGO-TiO2 during long incubation time. In parallel, following exposure of human hepatocellular carcinoma cell line (HepG2 cells) to RGO-TiO2 and UV-A or visible light irradiation, a marked decrease in the ratio of the super-coiled DNA, mitochondrial membrane potential (MMP), and the oxidative damage effects, as well as increased the apoptosis rate and intracellular calcium concentration were observed. Moreover, photocatalytic RGO-TiO2 composites killed the HepG2 cells by apoptosis pathway. The results suggested that RGO-TiO2 composites were an excellent candidate as a PDT photosensitizer in the near future.

Efficient photoinduced DNA damage by coralyne.

The photoinduced DNA damage by the berberine derivative coralyne is presented. The irradiation of coralyne in the presence of plasmid DNA namely, pBR322, leads to remarkably fast DNA damage by single-strand cleavage, as determined by agarose-gel electrophoresis. Even upon exposure to sunlight, almost all of the supercoiled plasmid is converted to the open circular form in less than a minute [c(pBR322) = 3.5 x 10(-9) M; c(coralyne) = 4.3 x 10(-5) M]. The efficiency of the DNA strand cleavage is not decreased in the presence of radical-trapping reagents such as tert-butanol or DMSO. Moreover, the extent of the DNA damage is the same under aerobic conditions and at reduced oxygen concentration. Thus, the formation of reactive intermediates such as hydroxyl radicals or singlet oxygen is excluded. These results show that the exposure of coralyne and derivatives thereof to light, even with moderate light intensity, needs to be avoided during experiments in which their biological activity is assessed by plasmid unwinding assays.

Analysis of inhibition of DNA replication in irradiated cells using the SV40-based in vitro assay of DNA replication.

The mechanisms of inhibition of DNA replication after DNA damage through the activation of the S-phase checkpoint have been the focus of several investigations over the last 40 yr. Recent studies have identified several components of this checkpoint response and there is strong interest in its biochemical characterization. Helpful for the delineation of the mechanism of the S-phase checkpoint is the observation that factors inhibiting DNA replication in vivo can be found in active form in extracts prepared from irradiated cells, when these are tested using the simian virus 40 (SV40) assay for in vitro DNA replication. In this assay, replication of plasmids carrying the minimal origin of SV40 DNA replication is achieved in vitro using cytoplasmic cell extracts and SV40 large tumor antigen (TAg) as the only noncellular protein. Here, we describe protocols developed to measure in vitro DNA replication with the purpose of analyzing its regulation after exposure to DNA damage. The procedures include the preparation of components of the in vitro DNA replication reaction including cytoplasmic extracts from cells that have sustained DNA damage. The assay is powerful but is limited by the fact that initiation steps carried out by the TAg in vitro may have different cellular determinants.

Repair of oxidative DNA damage by amino acids.

Guanyl radicals, the product of the removal of a single electron from guanine, are produced in DNA by the direct effect of ionizing radiation. We have produced guanyl radicals in DNA by using the single electron oxidizing agent (SCN)2-, itself derived from the indirect effect of ionizing radiation via thiocyanate scavenging of OH. We have examined the reactivity of guanyl radicals in plasmid DNA with the six most easily oxidized amino acids cysteine, cystine, histidine, methionine, tryptophan and tyrosine and also simple ester and amide derivatives of them. Cystine and histidine derivatives are unreactive. Cysteine, methionine, tyrosine and particularly tryptophan derivatives react to repair guanyl radicals in plasmid DNA with rate constants in the region of approximately 10(5), 10(5), 10(6) and 10(7) dm3 mol(-1) s(-1), respectively. The implication is that amino acid residues in DNA binding proteins such as histones might be able to repair by an electron transfer reaction the DNA damage produced by the direct effect of ionizing radiation or by other oxidative insults.