Antibacterial Potential of Non-Tailed Icosahedral Phages Alone and in Combination with Antibiotics.

Non-tailed icosahedral phages belonging to families Fiersviridae (phages MS2 and Qbeta), Tectiviridae (PRD1) and Microviridae (phiX174) have not been considered in detail so far as potential antibacterial agents. The aim of the study was to examine various aspects of the applicability of these phages as antibacterial agents. Antibacterial potential of four phages was investigated via bacterial growth and biofilm formation inhibition, lytic spectra determination, and phage safety examination. The phage phiX174 was combined with different classes of antibiotics to evaluate potential synergistic interactions. In addition, the incidence of phiX174-insensitive mutants was analyzed. The results showed that only phiX174 out of four phages tested against their corresponding hosts inhibited bacterial growth for > 90% at different multiplicity of infection and that only this phage considerably prevented biofilm formation. Although all phages show the absence of potentially undesirable genes, they also have extremely narrow lytic spectra. The synergism was determined between phage phiX174 and ceftazidime, ceftriaxone, ciprofloxacin, macrolides, and chloramphenicol. It was shown that the simultaneous application of agents is more effective than successive treatment, where one agent is applied first. The analysis of the appearance of phiX174 bacteriophage-insensitive mutants showed that mutations occur with a frequency of 10-3. The examined non-tailed phages have a limited potential for use as antibacterial agents, primarily due to a very narrow lytic spectrum and the high frequency of resistant mutants appearance, but Microviridae can be considered in the future as biocontrol agents against susceptible strains of E. coli in combinations with conventional antimicrobial agents.

Inactivation of Airborne Bacteria and Viruses Using Extremely Low Concentrations of Chlorine Dioxide Gas.

Infectious airborne microbes, including many pathological microbes that cause respiratory infections, are commonly found in medical facilities and constitute a serious threat to human health. Thus, an effective method for reducing the number of microbes floating in the air will aid in the minimization of the incidence of respiratory infectious diseases. Here, we demonstrate that chlorine dioxide (ClO2) gas at extremely low concentrations, which has no detrimental effects on human health, elicits a strong effect to inactivate bacteria and viruses and significantly reduces the number of viable airborne microbes in a hospital operating room. In one set of experiments, a suspension of Staphylococcus aureus, bacteriophage MS2, and bacteriophage ΦX174 were released into an exposure chamber. When ClO2 gas at 0.01 or 0.02 parts per million (ppm, volume/volume) was present in the chamber, the numbers of surviving microbes in the air were markedly reduced after 120 min. The reductions were markedly greater than the natural reductions of the microbes in the chamber. In another experiment, the numbers of viable airborne bacteria in the operating room of a hospital collected over a 24-hour period in the presence or absence of 0.03 ppm ClO2 gas were found to be 10.9 ± 6.7 and 66.8 ± 31.2 colony-forming units/m3 (n = 9, p < 0.001), respectively. Taken together, we conclude that ClO2 gas at extremely low concentrations (≤0.03 ppm) can reduce the number of viable microbes floating in the air in a room. These results strongly support the potential use of ClO2 gas at a non-toxic level to reduce infections caused by the inhalation of pathogenic microbes in nursing homes and medical facilities.

Antiviral properties of silver nanoparticles on a magnetic hybrid colloid.

Silver nanoparticles (AgNPs) are considered to be a potentially useful tool for controlling various pathogens. However, there are concerns about the release of AgNPs into environmental media, as they may generate adverse human health and ecological effects. In this study, we developed and evaluated a novel micrometer-sized magnetic hybrid colloid (MHC) decorated with variously sized AgNPs (AgNP-MHCs). After being applied for disinfection, these particles can be easily recovered from environmental media using their magnetic properties and remain effective for inactivating viral pathogens. We evaluated the efficacy of AgNP-MHCs for inactivating bacteriophage ΦX174, murine norovirus (MNV), and adenovirus serotype 2 (AdV2). These target viruses were exposed to AgNP-MHCs for 1, 3, and 6 h at 25°C and then analyzed by plaque assay and real-time TaqMan PCR. The AgNP-MHCs were exposed to a wide range of pH levels and to tap and surface water to assess their antiviral effects under different environmental conditions. Among the three types of AgNP-MHCs tested, Ag30-MHCs displayed the highest efficacy for inactivating the viruses. The ΦX174 and MNV were reduced by more than 2 log10 after exposure to 4.6 × 10(9) Ag30-MHCs/ml for 1 h. These results indicated that the AgNP-MHCs could be used to inactivate viral pathogens with minimum chance of potential release into environment.

Transport and removal of bacteriophages MS2 and PhiX174 in steel slag-amended soils: column experiments and transport model analyses.

The aim of this study was to investigate the removal of bacteriophages MS2 and PhiX174 in soils amended with converter furnace steel slag. Column experiments were performed to examine the bacteriophage removal in slag-amended (slag content: 0%, 25%, and 50%) loam soils. For comparison, column experiments were also conducted with Escherichia coli. In addition, chloride (Cl) was used as a conservative tracer to determine transport characteristics. Results showed mass recoveries of Cl of 98.6 +/- 3.5%, indicating that the experiments were conducted successfully. The mass recovery of MS2 was 86.7% in no slag (100% soil), decreasing to 0% in slag contents of 25% and 50%. The mass recovery of PhiX174 decreased from 87.8% to 51.5% with increasing slag content from 0% to 50%. In the case of E. coli, the mass recoveries decreased from 47.0% to 10.5% with increasing slag content from 0% to 50%. In the transport models analyses, the HYDRUS-1D code was used to quantify the sorption parameters from breakthrough curves. For the 100% soil column, a one-site kinetic sorption model was fitted to the data, whereas a two-site kinetic sorption model was fitted for slag-amended (25% and 50% slag) soil data. Results demonstrate that the addition of steel slag to soil enhances the removal of bacteriophages due to the presence of FeO in the steel slag. However, CaO could not contribute to the bacteriophage removal in our experimental conditions because the effluent pH (7.7-8.9) in slag-amended (25% and 50% slag) soils was not high enough to promote the bacteriophage inactivation.

Nucleoside analogue mutagenesis of a single-stranded DNA virus: evolution and resistance.

It has been well established that chemical mutagenesis has adverse fitness effects in RNA viruses, often leading to population extinction. This is mainly a consequence of the high RNA virus spontaneous mutation rates, which situate them close to the extinction threshold. Single-stranded DNA viruses are the fastest-mutating DNA-based systems, with per-nucleotide mutation rates close to those of some RNA viruses, but chemical mutagenesis has been much less studied in this type of viruses. Here, we serially passaged bacteriophage X174 in the presence of the nucleoside analogue 5-fluorouracil (5-FU). We found that 5-FU was unable to trigger population extinction for the range of concentrations tested, but it negatively affected viral adaptability. The phage evolved partial drug resistance, and parallel nucleotide substitutions appearing in independently evolved lines were identified as candidate resistance mutations. Using site-directed mutagenesis, two single-nucleotide substitutions in the lysis protein E (T572C and A781G) were shown to be selectively advantageous in the presence of 5-FU. In RNA viruses, base analogue resistance is often mediated by changes in the viral polymerase, but this mechanism is not possible for X174 and other single-stranded DNA viruses because they do not encode their own polymerase. In addition to increasing mutation rates, 5-FU produces a wide variety of cytotoxic effects at the levels of replication, transcription, and translation. We found that substitutions T572C and A781G lost their ability to confer 5-FU resistance after cells were supplemented with deoxythymidine, suggesting that their mechanism of action is at the DNA level. We hypothesize that regulation of lysis time may allow the virus to optimize progeny size in cells showing defects in DNA synthesis.

Improved virus removal in ceramic depth filters modified with MgO.

Ceramic filters, working on the depth filtration principle, are known to improve drinking water quality by removing human pathogenic microorganisms from contaminated water. However, these microfilters show no sufficient barrier for viruses having diameters down to 20 nm. Recently, it was shown that the addition of positively charged materials, for example, iron oxyhydroxide, can improve virus removal by adsorption mechanisms. In this work, we modified a common ceramic filter based on diatomaceous earth by introducing a novel virus adsorbent material, magnesium oxyhydroxide, into the filter matrix. Such filters showed an improved removal of about 4-log in regard to bacteriophages MS2 and PhiX174. This is explained with the electrostatic enhanced adsorption approach that is the favorable adsorption of negatively charged viruses onto positively charged patches in an otherwise negatively charged filter matrix. Furthermore, we provide theoretical evidence applying calculations according to Derjaguin-Landau-Verwey-Overbeek theory to strengthen our experimental results. However, modified filters showed a significant variance in virus removal efficiency over the course of long-term filtration experiments with virus removal increasing with filter operation time (or filter aging). This is explained by transformational changes of MgO in the filter upon contact with water. It also demonstrates that filter history is of great concern when filters working on the adsorption principles are evaluated in regard to their retention performance as their surface characteristics may alter with use.

Viral adaptation to an antiviral protein enhances the fitness level to above that of the uninhibited wild type.

Viruses often evolve resistance to antiviral agents. While resistant strains are able to replicate in the presence of the agent, they generally exhibit lower fitness than the wild-type strain in the absence of the inhibitor. In some cases, resistant strains become dependent on the antiviral agent. However, the agent rarely, if ever, elevates dependent strain fitness above the uninhibited wild-type level. This would require an adaptive mechanism to convert the antiviral agent into a beneficial growth factor. Using an inhibitory scaffolding protein that specifically blocks phiX174 capsid assembly, we demonstrate that such mechanisms are possible. To obtain the quintuple-mutant resistant strain, the wild-type virus was propagated for approximately 150 viral life cycles in the presence of increasing concentrations of the inhibitory protein. The expression of the inhibitory protein elevated the strain's fitness significantly above the uninhibited wild-type level. Thus, selecting for resistance coselected for dependency, which was characterized and found to operate on the level of capsid nucleation. To the best of our knowledge, this is the first report of a virus evolving a mechanism to productively utilize an antiviral agent to stimulate its fitness above the uninhibited wild-type level. The results of this study may be predictive of the types of resistant phenotypes that could be selected by antiviral agents that specifically target capsid assembly.

Ozone efficacy for the control of airborne viruses: Bacteriophage and norovirus models.

This study was designed to test the efficacy of an air treatment using ozone and relative humidity (RH) for the inactivation of airborne viruses. Four phages (φX174, PR772, MS2 and φ6) and one eukaryotic virus (murine norovirus MNV-1) were exposed to low ozone concentrations (1.23 ppm for phages and 0.23 ppm for MNV-1) and various levels of RH for 10 to 70 minutes. The inactivation of these viruses was then assessed to determine which of the tested conditions provided the greatest reduction in virus infectivity. An inactivation of at least two orders of magnitude for φX174, MS2 and MNV-1 was achieved with an ozone exposure of 40 minutes at 85% RH. For PR772 and φ6, exposure to the reference condition at 20% RH for 10 minutes yielded the same results. These findings suggest that ozone used at a low concentration is a powerful disinfectant for airborne viruses when combined with a high RH. Air treatment could therefore be implemented inside hospital rooms ventilated naturally.

Inhibition of peroxynitrite-mediated DNA strand cleavage and hydroxyl radical formation by aspirin at pharmacologically relevant concentrations: implications for cancer intervention.

Epidemiological studies have suggested that the long-term use of aspirin is associated with a decreased incidence of human malignancies, especially colorectal cancer. Since accumulating evidence indicates that peroxynitrite is critically involved in multistage carcinogenesis, this study was undertaken to investigate the ability of aspirin to inhibit peroxynitrite-mediated DNA damage. Peroxynitrite and its generator 3-morpholinosydnonimine (SIN-1) were used to cause DNA strand breaks in phiX-174 plasmid DNA. We demonstrated that the presence of aspirin at concentrations (0.25-2mM) compatible with amounts in plasma during chronic anti-inflammatory therapy resulted in a significant inhibition of DNA cleavage induced by both peroxynitrite and SIN-1. Moreover, the consumption of oxygen caused by 250 microM SIN-1 was found to be decreased in the presence of aspirin, indicating that aspirin might affect the auto-oxidation of SIN-1. Furthermore, EPR spectroscopy using 5,5-dimethylpyrroline-N-oxide (DMPO) as a spin trap demonstrated the formation of DMPO-hydroxyl radical adduct (DMPO-OH) from authentic peroxynitrite, and that aspirin at 0.25-2mM potently diminished the radical adduct formation in a concentration-dependent manner. Taken together, these results demonstrate for the first time that aspirin at pharmacologically relevant concentrations can inhibit peroxynitrite-mediated DNA strand breakage and hydroxyl radical formation. These results may have implications for cancer intervention by aspirin.

Phototoxicity of phenylenediamine hair dye chemicals in Salmonella typhimurium TA102 and human skin keratinocytes.

Phenylenediamines (PD) are dye precursors used to manufacture hair dyes. The three PDs, 1,2-,1,3-, and 1,4-PD and three chlorinated PDs, 4-chloro-1,2-PD, 4-chloro-1,3-PD, and 4,5-dichloro-1,2-PD were studied for their mutagenic effect in Salmonella typhimurium TA 102, cytotoxicity in human skin keratinocyte cells, and for DNA cleavage. The results show that all six compounds are not toxic/mutagenic in TA 102 bacteria or skin cells, and do not cause DNA cleavage in PhiX 174 phage DNA. If the same tests are carried out by exposing them to light irradiation concurrently, all three chlorinated PDs cause mutation in TA 102 bacteria and single strand cleavage in PhiX174 phage DNA. This indicates that chlorination of the PDs makes these compounds more photochemically active and produces reactive species that cause DNA damage and mutation. For the photocytotoxicity test in skin cells, it appears there is no such structure-activity relationship. Two chlorinated PDs and two non-chlorinated PDs are cytotoxic at a fairly high concentration (1000microM) upon exposure to light irradiation.

In situ ammonia production as a sanitation agent during anaerobic digestion at mesophilic temperature.

AIM: To measure the sanitizing effect of mesophilic (37 degrees C) anaerobic digestion in high ammonia concentrations produced in situ. METHODS AND RESULTS: Indicator organisms and salmonella were transferred to small-scale anaerobic batch cultures and D-values were calculated. Batch cultures were started with material from two biogas processes operating at high (46 mmol l(-1)) and low (1.6 mmol l(-1)) ammonia concentration. D-values were shortened from c. 3 days to <1 day for the bacteria. MS2 had the same D-value (1.3 days) independent of ammonia concentration whereas PhiX174 and 28B were faster inactivated in the control (1.1 and 7.9 days) than in the high ammonia (8.9 and 39 days) batch cultures. CONCLUSION: Running biogas processes at high levels of ammonia shortens the time to meet EU regulation concerning reduction of salmonella and enterococci (5 log). Unless a minimum retention time of 2 days, post-treatment digestion is needed to achieve sufficient sanitation in continuous biogas processes. SIGNIFICANCE AND IMPACT OF THE STUDY: Running mesophilic biogas processes at high ammonia level produces residue with a high fertilizer value. With some stipulations concerning management parameters, such processes provide a method of bacterial sanitation without preceding pasteurization of the incoming organic waste.

Interactions between viruses and goethite during saturated flow: effects of solution pH, carbonate, and phosphate.

Metal oxides have great potential for controlling the fate and transport of viruses in the subsurface and water-treatment systems. The processes, however, are subject to solution chemistry. In this study, a number of column experiments were conducted to examine the effects of solution pH and anions (carbonate and phosphate) on attachment, transport, and inactivation of two bacteriophages (phiX174 and MS-2) in goethite-coated sand medium. Removal of both viruses on goethite-coated sand increased as solution pH decreased from 9.3 to 7.5, due mostly to virus inactivation. MS-2, a relatively hydrophobic virus with a lower isoelectric point (3.9), was more sensitive to the change of solution pH than phiX174, a relatively hydrophilic virus with a higher isoelectric point (6.6), in terms of their attachment and inactivation on goethite. About 90% of the MS-2 particles removed by goethite (accounting for 81% of the total input) were inactivated at pH 7.5, whereas all of the removed MS-2 particles (accounting for 10% of the total input) still remained infectious at pH 9.3. In comparison, approximately 74% of the goethite-bound phiX174 particles (accounting for 95% of the total input) lost their infectivity at pH 7.5, in contrast to a complete recovery at pH 9.3 (accounting for 65% of the total input) when the columns were eluted using a beef extract solution (pH 9.5). Presence of phosphate (20 mM H(2)PO(4)(-)) in input solution reduced virus attachment and appeared to protect the viruses from being inactivated during transport; this effect was more significant on MS-2 than on phiX174. Specifically, approximately 29% of the phiX174 particles and approximately 49% of MS-2 particles injected into the column were removed during transport. Mass recovery data showed that no phiX174 was inactivated in the presence of phosphate, whereas about 38% of the MS-2 particles attached on goethite lost their infectivity. Conversely, presence of carbonate on goethite increased virus attachment and inactivation due to contribution of additional attachment sites from protonated surface groups of the carbonate ions that were adsorbed on goethite. About 70% of the total input viruses (both phiX174 and MS-2) were removed during transport, of which 35% phiX174 and 85% MS-2 were eventually inactivated.

Capillary isoelectric focusing of native and inactivated microorganisms.

The research of microorganisms includes the development of methods for the inactivation of viruses and other microbes. It also means to efficiently eliminate the infectivity of microorganisms without damage of their integrity and structure. According to the results of the last 5 years the capillary electromigration techniques appear to be very perspective for the comparison of the methods applicable for inactivation in the diagnostics and study of the pathogens. In this paper we suggest the capillary isoelectric focusing of the model microorganisms, Escherichia coli, Staphylococcus epidermidis, Candida albicans and bacteriophage PhiX 174, native or inactivated by different procedures. UV detection and fluorometric detection for the dynamically modified microbes by pyrenebutanoate on the basis of the non-ionogenic tenside were used here. Isoelectric points of native and/or dynamically modified microorganisms and other properties were compared with those obtained after microorganisms inactivation. The segmental injection of the sample pulse enabled the reproducible and efficient capillary isoelectric focusing in different pH gradients. The low-molecular-weight pI markers were used for tracing of the pH gradient.

Solar photocatalytic disinfection of E. coli and bacteriophages MS2, ΦX174 and PR772 using TiO2, ZnO and ruthenium based complexes in a continuous flow system.

The performance of photocatalytic treatment processes were assessed using different photocatalysts against E. coli and bacteriophages MS2, ΦX174 and PR772, in a recirculating continuous flow compound parabolic collector system under real sunlight conditions. Suspended TiO2 and ZnO nanoparticle powders and Tris(2,2'-bipyridyl)dichlororuthenium(II) hexahydrate in solution were tested separately, as well as in combination, using E. coli. For a 3-log reduction of E. coli in distilled water, inactivation rates in terms of cumulative dose were in the order Ru(bpy)3Cl2>(TiO2 & Ru(bpy)3Cl2)>(ZnO & Ru(bpy)3Cl2)>ZnO>TiO2>photolysis. Reactivation of E. coli was observed following all trials despite the detection limit being reached, although the reactivated colonies were observed to be under stress and much slower growing when compared to original colonies. Treatment with Ru(bpy)3Cl2 was also compared against standard photolysis of bacteriophages MS2, ΦX174 and PR772 with the order of photolytic inactivation for a 3-log reduction in terms of cumulative UV-A dose being ΦX174>PR772>MS2. However, MS2 was found to be the most susceptible bacteriophage to treatment with Ru(bpy)3Cl2, with complete removal of the phage observed within the first 15min of exposure. Ru(bpy)3Cl2 also significantly improved inactivation rates for PR772 and ΦX174.

[Comparison on resistance of bacteriophages to sodium dichloroisocyanurate in laboratory].

OBJECTIVE: To scan the most resistable bacteriophage as an indicator in disinfection tests, and to study the resistance of bacteriophage T4, Phichi 174D, and f2 to the sodium dichloroisocyanurate (NaDCC) in laboratory. METHODS: The virucidal activity of NaDCC against bacteriophage T4, Phichi 174D, and f2 were assessed by suspension test. The neutralizer was selected and be appraised by test of neutralizer. Bacteriophage T4, Phichi 174D, and f2 were detected and enumerated by the double-agar-layer plaque technique. RESULTS: (1) With 150 mg/L of available chlorine of NaDCC solution, within a contact time of 40 minutes, or 300 mg/L, 5 minutes, the reductions of bacteriophage T4 achieved the "disinfection" level [log(10) inactivation value or log(10) reduction value of bacteriophage T4 (log(10)No-log(10)Nt) > or = 4.00 log(10)]. (2) With 300 mg/L of available chlorine of NaDCC solution, within a contact time of 5 minutes, or 400 mg/L, 3 minutes, the reductions of bacteriophage Phichi 174D achieved the "disinfection" level. (3) With 2000 mg/L of available chlorine of NaDCC solution, within a contact time of 20 minutes, or 4000 mg/L, 5 minutes, the reductions of bacteriophage f2 might achieve the "disinfection" level. CONCLUSION: The order of resistance of the above three bacteriophages to NaDCC from greatest to smallest is as follows: bacteriophage f2 > bacteriophage T4 > bacteriophage Phichi 174D.

[A comparative study on the resistance of bacteriophage T4, phiXM174D, and f2 to glutaraldehyde in laboratory].

OBJECTIVE: To identify the best indicative bacteriophage in disinfection tests through comparing the resistance of bacteriophage T4, phiX174D, and f2 to glutaraldehyde. METHODS: The virucidal activities of glutaraldehyde against bacteriophage T4, phiX174D, and f2 were assessed with suspension tests along with neutralizer tests. The double-agar-layer plaque technique was used to detect the bacteriophage T4, phiX174D, and f2. RESULTS: (1)In a condition of 3000 mg/L of glutaraldehyde and 20 minutes of contact or 6000 mg/L of glutaraldehyde and 5 minutes of contact, "disinfection" level for bacteriophage T4 was achieved, with the log10 inactivation value (LIV) or log10o reduction value (LRV) (=log10No-log10Nt) > or = 4. 00 log10. (2) In a condition of 2500 mg/L of glutaraldehyde and 20 minutes of contact or 5000 mg/L of glutaraldehyde and 5 minutes of contact, the LIV for bacteriophage phiX174D reached "disinfection" level; (3) In a condition of 4000 mg/L of glutaraldehyde and 40 minutes of contact or 8000 mg/L of glutaraldehyde and 10 minutes of contact, the LIV for bacteriophage f2 reached "disinfection" level. CONCLUSION: Bacteriophage f2 and bacteriophage phiX174D has the strongest and weakest resistance to glutaraldehyde respectively.

Role of metals in free radical generation and genotoxicity induced by airborne particulate matter (PM2.5) from Pune (India).

In the present study, metal-facilitated free radical generation in particulate matter (PM) and its association with deoxyribonucleic acid (DNA) damage were studied. The examined data showed that the concentration of fine PM in Pune exhibited seasonal variations. Inductively coupled plasma-atomic emission spectrometry (ICP-AES) was used to examine the metal composition, which showed the presence of metals such as Cu, Zn, Mn, Fe, Co, Cr, Pb, Cd, and Ni. Fe metal was present in the highest concentrations in both the seasons, followed by Zn. The scanning electron microscopy-energy-dispersive spectrometer (SEM-EDS) results also demonstrated that the fine PM particles deposited in summer samples were less than those of winter samples, suggesting that the PM load in winter was higher as compared to that in summer. Elemental mapping of these particles substantiates deposition of metals as Fe, Zn, etc. on particles. The electron paramagnetic species (EPR) technique was utilized for free radical detection, and plasmid DNA assay was utilized to study the genotoxicity of ambient fine PM. Obtained g values show the presence of radicals in PM samples of Pune. PM contains the C-centered radical with a vicinal oxygen atom (g = 2.003). In addition to this, the g value for Fe was also observed. Therefore, we intend that the radicals related with fine PM comprise metal-mediated radicals and produce DNA damage. The plasmid DNA assay results indicated that the TM50 values (toxic mass of PM causing 50 % of plasmid DNA damage) of PM exhibited seasonal variations with higher TM50 values for summer and lower TM50 values during winter.

DNA damage induced by ascorbate in the presence of Cu2+.

DNA damage induced by ascorbate in the presence of Cu2+ was investigated by use of bacteriophage phi X174 double-stranded supercoiled DNA and linear restriction fragments as substrates. Single-strand cleavage was induced when supercoiled DNA was incubated with 5 microM-10 mM ascorbate and 50 microM Cu2+ at 37 degrees C for 10 min. The induced DNA damage was analyzed by sequencing of fragments singly labeled at their 5'- or 3'-end. DNA was cleaved directly and almost uniformly at every nucleotide by ascorbate and Cu2+. Piperidine treatment after the reaction showed that ascorbate and Cu2+ induced another kind of DNA damage different from the direct cleavage. The damage proceeded to DNA cleavage by piperidine treatment and was sequence-specific rather than random. These results indicate that ascorbate induces two classes of DNA damage in the presence of Cu2+, one being direct strand cleavage, probably via damage to the DNA backbone, and the other being a base modification labile to alkali treatment. These two classes of DNA damage were inhibited by potassium iodide, catalase and metal chelaters, suggesting the involvement of radicals generated from ascorbate hydroperoxide.

Terminations of DNA synthesis on 'proflavine and light'-treated phi X174 single-stranded DNA.

Bacteriophage phi X174 single-stranded DNA molecules were primed with five different restriction fragments and irradiated with visible light in the presence of proflavine. This photodamaged DNA was used as template for the in vitro complementary chain synthesis by E. coli DNA polymerase I (Klenow fragment). Chain terminations were observed by polyacrylamide gel electrophoresis of the synthesized products and localized by comparison with standard sequencing performed simultaneously on the untreated template. 90% of the chain terminations occurred one nucleotide before a guanine residue in the template strand. More than 80% of the sequenced guanine residues were blocking lesions demonstrating the absence of 'hot-spots' for the photodamaging effect of proflavine. At a defined position, the chain termination frequency increased linearly with the irradiation time and was directly influenced by the proflavine concentration present. An important part of lesions resulted from the action of singlet oxygen produced by excited proflavine as shown by the effect that both NaN3 and 2H2O exerted on the reaction. The induced blocking lesions must be important in vivo since no complete replicative forms could be extracted from cell infected with bacteriophages inactivated by 'proflavine and light' treatment.

Eclipse kinetics as a probe of quaternary structure in bacteriophage phi X174.

The extracellular form of bacteriophage phi X174 consists of single-stranded DNA within an icosahedral capsid, which has short spikes at each of its vertices. Each spike is composed of gene G and H proteins, while the capsid itself consists of gene F protein. Since several molecules of gene H protein are injected into the cell along with the DNA, specific protein--protein and DNA--protein interactions must be broken when the genome exits and leaves an intact capsid structure at the receptor site. To demonstrate this we examined the eclipse (DNA ejection) reaction with two types of phi X174 mutants. The first contains missense mutations in a capsid or spike protein gene, and the second involves insertions or deletions in non-coding regions of the DNA. Using an improved procedure, the eclipse rate in vivo of the eclipse mutants Fcs70 has been redetermined over a larger temperature range than in previous studies. The three- to fivefold decrease in rate between 37 degrees C and 25 degrees C is due to an increase in both the enthalpy and entropy of activation when compared to the wild-type values of these kinetic parameters. This missence mutation also confers an increase in virus stability in 2 to 3 M-urea. In contrast to this, inserting 163 bases into the length of DNA packaged within the phi X174 capsid does not lead to a detectable change in eclipse rate over the same temperature range. yet this insertion into the J--F intercistronic region imparts a significant decrease in virus stability in urea. These results suggest that a specific set of non-covalent interactions is involved in phi X174 DNA ejection. This is supported by the small (50%), but significant, increase in eclipse rate that occurs when 27 bases are deleted from the J--F intercistronic region. The latter effect must be base-sequence-specific since no change in rate is observed when only seven of the 27 bases are deleted. Thus, the kinetics of the phi X174 eclipse reaction can be used as a sensitive probe of quaternary structure by correlating the change in reaction rate with alterations in amino acid and base sequences in the structural components of the virus.