Dideoxynucleoside triphosphates inhibit a late stage of SV40 DNA replication in vitro

The role of DNA polymerases in the replication of SV40 DNA was studied using a T-antigen-dependent assay supplemented with a human KB cell extract. Inhibition of DNA polymerase alpha by addition of aphidicolin or monoclonal antibodies prevented DNA synthesis, confirming the requirement for this enzyme in replication. The replication process was unaffected by ddTTP at a concentration (5 microM) inhibitory to DNA polymerases beta and gamma, however, higher concentrations of ddTTP (200 microM) caused an apparent accumulation of relaxed circular plasmid with a concomitant decrease in DNA synthesis. An analysis of this replication intermediate indicated that it was formed during the replication reaction and that the replicative cycle was nearly complete. A kinetic study of ddTTP inhibition strongly suggested DNA polymerase epsilon (PCNA-independent DNA polymerase delta) was the target of the inhibitor and that this enzyme functions during the final stages of DNA replication.

Z-DNA as a probe for localized supercoiling in vivo

Biological processes such as transcription are expected to generate local variations in DNA supercoiling. The existence of localized supercoiling was recently demonstrated in Escherichia coli by using the supercoil-driven B-to-Z transition as a superhelicity probe. This new methodology is described and its extension to other biological systems discussed.

Quantitation of supercoiled DNA cleavage in nonradioactive DNA: application to ionizing radiation and synthetic endonuclease cleavage

Quantitation of the conversion of nonradioactive supercoiled DNA to its open circular or linear forms on ethidium-stained electrophoretic gels has been difficult because of differential binding of ethidium to supercoiled DNA vs other forms under different conditions and the nonlinear response of photographic film. We have developed methods for adding a linear DNA as an internal fluorescence standard to "normalize" the quantity of DNA loaded into each lane of a gel. Inclusion of a linear normalizing DNA in samples before partitioning for individual supercoil cleavage reactions allows the quantitation of the resultant species, is technically easy, and does not require quantitative application of the sample to the gel. If the presence of a normalizing DNA during supercoil cleavage is undesirable, the addition of a normalizing plasmid to each sample after supercoil cleavage (but before electrophoresis) or the quantitative application of samples containing test DNA alone to the gel gives similar data, but with increased variability. We use the normalizing DNA method in cleavage by a physical agent (ionizing radiation) and in a more complex situation, by a protein-based, light-dependent synthetic endonuclease. We show how the fraction of intact supercoiled DNA can be calculated from measurement of the cleaved and normalizing species only. The method also can be used in reactions involving the depletion of one DNA species, whether supercoiled or not, such as protein-DNA interactions as detected by gel retardation assays.

Active efflux of ofloxacin by a highly quinolone-resistant strain of Proteus vulgaris

A clinical isolate of Proteus vulgaris, strain 881051, highly resistant to ofloxacin (MIC for ofloxacin; 800 mg/L) possessed three types of resistance mechanisms to ofloxacin. The supercoiling activity of DNA gyrase from this strain was barely inhibited by ofloxacin, the ID50 value of ofloxacin against the enzyme was 2700 times higher than that against the enzyme from a susceptible strain, P. vulgaris 08602. In the outer membrane of this resistant strain, no porin protein of 37 kDa was detectable. In the presence of carbonylcyanide m-chloro-phenylhydrazone (CCCP), we found that the accumulation of ofloxacin in the cells of strain 881051, treated with the drug, was about 40-fold higher than that in the absence of CCCP. The CCCP-induced increase in the intracellular drug was 10 and 30 times higher than those in strain 880561 (a moderately resistant strain, MIC 50 mg/L) and 08602 (a fully sensitive strain), respectively. Simultaneous treatment of the strain 881051 with ofloxacin and CCCP resulted in bactericidal synergy. These results indicated that in addition to alterations of DNA gyrase and outer membrane proteins, the active efflux, as the third mechanism, could operate the resistance of strain 881051 to ofloxacin.

Image analysis-based measurement of DNA supercoiling changes in transformed and nontransformed human cell lines

An image analysis system was used to visualize and measure the changes in nucleoid diameter (nuclear matrix core plus extruded DNA loops) which occur when increasing concentrations of propidium iodide are used to titrate the DNA supercoiling response. Parallel core size measurements allow estimates of the changes in apparent DNA loop size. Unlike sedimentation assays, DNA loop size estimates are not influenced by particle mass, require no prior cell labeling, and can be performed on a per cell basis. This technique was used to examine changes in DNA loop characteristics which may occur when cells are transformed or undergo changes in their proliferative state. SV40-transformation of human diploid fibroblast lines resulted in a significant increase in both the nucleoid core and average DNA loop size. Lymphoblast cell lines also had larger nucleoid dimensions than normal lymphocytes. The response of several established human tumor cell lines indicated slightly increased loop but not core sizes as compared to normal human diploid fibroblasts. Changes in proliferative state also resulted in changes in DNA loop characteristics as measured in this assay. Both quiescent fibroblasts and unstimulated lymphocytes appeared to have smaller or more condensed DNA loop structures than their proliferating counterparts. These results demonstrate the utility of this assay in detecting changes in DNA loop structure which occur in association with changes in the proliferative activity of cells in culture.

Characterization of high-level quinolone resistance in Campylobacter jejuni

High-level resistance to quinolones has previously been shown to occur in Campylobacter spp. both in vitro and in patients treated with quinolones. We have selected isolates that are resistant to quinolones by plating cells from a susceptible C. jejuni strain, UA535, on medium containing nalidixic acid at 32 micrograms/ml. Fluctuation analysis indicated that resistance occurred by mutation at a frequency of 5 x 10(-8) per cell plated. Unlike what is observed with other gram-negative organisms, the nalidixic acid-resistant mutants demonstrated high-level cross-resistance (MIC, greater than or equal to 4 micrograms/ml) to newer quinolones, including ciprofloxacin, norfloxacin, and temafloxacin, yet remained susceptible to coumermycin A1 and several other unrelated antibiotics. Mutants with an identical resistance phenotype could also be selected from UA535 with ciprofloxacin and norfloxacin at a similar frequency. To study the mechanism of quinolone resistance, DNA gyrases were purified from C. jejuni UA535 and two resistant mutants by heparin-agarose and novobiocin-Sepharose chromatography. After the respective enzyme concentrations were adjusted to equivalent units of activity in the DNA supercoiling reaction, the DNA gyrases from the resistant mutants were found to be 100-fold less susceptible than the wild-type enzyme to inhibition by quinolones. Subunit switching experiments with purified A and B subunits from the wild type and one of the quinolone-resistant mutants indicated that an alteration in the A subunit was responsible for resistance. These results show that a single-step mutation can occur in vitro in the gene encoding DNA gyrase in C. jejuni, producing clinically relevant levels of resistance to the newer quinolones.

Spontaneous quinolone resistance in Serratia marcescens due to a mutation in gyrA

Spontaneous quinolone-resistant mutants of MP050, a quinolone-susceptible clinical strain of Serratia marcescens, were isolated on nutrient agar containing 0.5 microgram of ciprofloxacin per ml. One mutant, designated MP051, was selected for further study. Quinolone MICs for MP051 were 4- to 16-fold higher than those for MP050; nonquinolone MICs were unchanged. The DNA gyrase isolated from MP051 was 24-fold less sensitive to inhibition of supercoiling by ciprofloxacin than the DNA gyrase isolated from MP050 was. Inhibition studies on reconstituted combinations of heterologous gyrase subunits showed that the decreased inhibition was dependent on the A subunit of DNA gyrase from MP051. Further evidence that this decreased inhibition was due to a gyrA mutation was provided by analysis of Escherichia coli gyrA gene expression in S. marcescens heterodiploids containing pNJR3-2, a broad-host-range gyrA gene probe. Quinolone susceptibilities of MP051 heterodiploids containing the wild-type E. coli gyrA gene decreased to those of MP050, while quinolone susceptibilities of MP050 containing the same plasmid were unchanged. These results indicate that spontaneous quinolone resistance in MP051 was due to a mutation in gyrA.

Negative supercoiling increases the sensitivity of plasmid DNA to single-strand break induction by X-rays

Negatively supercoiled topoisomers of the plasmid pIBI 30 were irradiated with 250 kV X-rays and assayed for strand scission by agarose gel electrophoresis. The survival of supercoiled molecules (Form I) decreased exponentially with increasing X-ray exposure and the dose required to reduce the fraction of DNA in Form I to 37% of its value in unirradiated controls (D37) decreased with increasing negative superhelicity. This enhanced radiation sensitivity of underwound DNA is tentatively attributed to the transient denaturation of the double helix that increases the susceptibility of individual strands to free radical attack.

Topoisomerase II-mediated DNA damage of episomes in tumor-bearing mice

Observations of cells in culture have demonstrated that, for many antitumor agents, topoisomerase II-mediated DNA damage relates to cytotoxicity. However, there is no evidence in tumor-bearing animals to suggest that such agents induce topoisomerase II-mediated damage of DNA in solid tumors or that such damage reflects inhibition of tumor growth. To address this question, a mouse fibroblast cell line neoplastically transformed by an episomal element containing the v-Ha-ras and bovine papillomavirus genes was utilized to measure topoisomerase II-induced DNA damage and growth inhibition of solid tumors derived from this line. Using the topoisomerase II inhibitor amsacrine, the episomal element was found to be a sensitive indicator of topoisomerase II-mediated damage in vivo. The DNA breaks induced by single i.v. injections of amsacrine were protein linked and occurred preferentially in episomal regulatory regions. A strong correlation between suppression of tumor growth and topoisomerase II-mediated damage of the episome was demonstrated.

The human ETS-2 gene promoter: molecular dissection and nuclease hypersensitivity

The human ETS-2 gene is a homolog of the v-ets oncogene of the E26 virus, coding for a 56 kilodalton nuclear protein. Herein we characterize the ETS-2 gene promoter, using a series of deletion constructs. Analysis of the nucleotide sequences from -3600 bp to +141 bp reveal that the region -159 bp to +141 bp is absolutely essential for maximum promoter activity. This region includes half of the lengthy polypyrimidine (CT) tract of the ETS-2 promoter, one Sp1 binding site and the GC element proximal to the initiation site. This CT tract is able to increase in an orientation independent manner, the transcription from alpha-globin promoter. Several S1 hypersensitive sites are found to be located in this promoter region, using chromatin and supercoiled DNA, in close proximity with cis regulatory elements. Our results indicate that an unusually long (approximately 250 bp) CT tract is necessary for ETS-2 transcription and this tract can also serve as a transcription activator using a heterologous promoter.

DNA linking potential generated by gyrase

Whether or not DNA gyrase can supercoil DNA so that alternative structures will arise in it is the major question of this work. We have shown gyrase to produce in pAO3 DNA a superhelix density sufficient for cruciform formation. However, the transition does not take place because of too slow kinetics. A change of ionic conditions in favour of more intense DNA supercoiling by gyrase shifts the midpoint of the equilibrium transition to the cruciform structure toward more supercoiled topoisomers. The width of the equilibrium transition to the cruciform as a function of linking number has been revealed to be an order of magnitude larger in buffers containing magnesium and spermidine than in buffers with monovalent cations only. We ascribe this effect to the influence that the counter ions surrounding the DNA molecule have on its elasticity, the coefficient of elasticity being dependent on superhelix density sigma. Thus, the free energy of supercoiling (a) depends on the ionic conditions and (b) is not a quadratic function of sigma in the physiological range of parameters. We propose a description of DNA as a system of links that can be either closed or open; we also introduce a new concept of the DNA linking potential akin to the chemical and electric potentials. The linking potential is a suitable parameter for describing the equilibrium distribution of links in heterogeneous DNA, the coexistence of various DNA structures, the equilibrium input and output of DNA links by enzymes, and the nonequilibrium movement of links along DNA chains. Within the framework of this approach DNA gyrase is considered as the source of the DNA linking potential.

Mechanism of action of lomefloxacin

The inhibition of supercoiling activity of reconstituted Escherichia coli DNA gyrase by lomefloxacin, ciprofloxacin, and norfloxacin was determined. The concentrations of quinolones needed to inhibit DNA synthesis in Escherichia coli, Enterobacter cloacae, Serratia marcescens, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Staphylococcus aureus were also measured. The kinetics of uptake of [14C]lomefloxacin and unlabeled lomefloxacin into whole cells of E. coli KL-16 and S. aureus NCTC 8532 and the induction of RecA in E. coli GC2241 were assayed. All strains had wild-type susceptibilities to quinolones. The concentration of quinolones needed to inhibit DNA synthesis by 50% correlated with the MIC for members of the family Enterobacteriaceae and P. aeruginosa. The concentration of quinolones needed to inhibit DNA synthesis by 50% for late-logarithmic-phase S. aureus also correlated with the MIC, unlike the data from early-logarithmic-phase cultures. E. coli and S. aureus showed a similar pattern of uptake kinetics of [14C]lomefloxacin and unlabeled lomefloxacin, indicating that the difference in the susceptibilities of the two species is probably due to different target site affinities. Essentially, lomefloxacin was less active than ciprofloxacin and ofloxacin and had activity similar to those of norfloxacin and enoxacin.

Rapid high-performance liquid chromatography of nucleic acids with polystyrene-based micropellicular anion exchangers

Nucleic acids were separated by ion-exchange chromatography on 30 x 4.6 and 100 x 4.6 mm columns packed with a micropellicular anion exchanger made of 3-microns rigid polystyrene-based non-porous microspheres with a covalently bound hydrophilic layer and DEAE functional groups at the surface. The stationary phase particles showed negligible swelling in methanol according to permeability measurements with water and methanol. Nucleic acids and their fragments including synthetic single-stranded oligonucleotides, linear, nicked and supercoiled DNAs as well as DNA restriction fragments were separated in less than 5 min, a time scale that is much smaller than that of conventional high-performance liquid chromatographic analysis for such samples. When only buffer and sodium chloride were used in the eluent for the separation of double-stranded DNA restriction fragments pGEM-3Z/Taq I, electrophoretic analysis of the effluent revealed the presence of smaller fragments in the bands of the larger ones. Upon addition of ethylenediaminetetraacetic (EDTA) salt to the eluent, however, such contamination by shorter fragments was no longer observed. In the absence of EDTA, magnesium chloride in the eluent at a concentration of 1 mM precluded the separation of the restriction fragments under otherwise identical chromatographic conditions.

A simplified biochemistry for DNA sequencing

A simplified method of DNA sequencing by dideoxy chain termination is developed that approaches a single-step protocol. Utilizing the sequencing advantages contributed by a thermophilic polymerase and a guanine analog, stable sequencing reaction concentrates have been obtained that readily perform the entire sequencing reaction simply by adding prepared DNA to each of the four reaction concentrates required by this method. The mechanics and dynamics of these reactions have been investigated and the capacity of these reactions to withstand normal user variation is demonstrated. This study focuses on one form of this simplified method embodied in the FASTaq DNA sequencing kit.

Determination of the DNA conformation of the simian virus 40 (SV40) enhancer in SV40 minichromosomes

The simian virus 40 (SV40) enhancer contains three 8-bp purine-pyrimidine alternating sequences which are known to adopt the left-handed Z-DNA conformation in vitro. In this paper, we have undertaken the determination of the DNA conformation adopted by these Z-motifs in the SV40 minichromosome. We have analyzed the presence of Z-DNA through the change in linkage which should accompany formation of this left-handed conformation. Our results indicate that, regardless of the precise moment of the viral lytic cycle at which minichromosomes are harvested and the condition of the transfected DNA, either relaxed or negatively supercoiled, none of the three Z motifs of the SV40 enhancer exist to a significant extent as Z-DNA in SV40 minichromosomes. The SV40 enhancer adopts predominantly a right-handed B-DNA conformation in vivo.

Correlation between the DNA supercoiling and the initiation of transcription by Escherichia coli RNA polymerase in vitro: role of the sequences upstream of the promoter region

Binding of Escherichia coli RNA polymerase and the abortive initiation of transcription at the A2 promoter of bacteriophage T7, separately cloned in pBR322, was found to be strongly dependent on the degree of supercoiling of the plasmid. Supercoiling does not seem to play any role in the initiation of transcription at the T7A1 promoter under identical conditions. Plasmid containing T7A2 promoter was found to be less amenable to S1 nuclease in comparison to that having T7A1. Sequence comparison reveals a high G/C content upstream to the -35 region of T7A2 which by extra duplex stability probably renders the initiation of transcription more dependent on the state of supercoiling of the template.

Dramatic increase in negative superhelicity of plasmid DNA in the forespore compartment of sporulating cells of Bacillus subtilis

Plasmid pUB110, isolated from vegetative cells of Bacillus subtilis, has an average of 34 negative supertwists (tau av = -34). This value falls to -30 early in sporulation, and the plasmid in the mother cell compartment maintains a tau av of -30. However, the plasmid within the developing forespore becomes much more negatively supercoiled, reaching a tau av of -47 in the dormant spore. This increased negative supercoiling in the forespore plasmid takes place in parallel with the synthesis of small, acid-soluble spore proteins, alpha and beta; and the plasmid from spores lacking small, acid-soluble proteins alpha and beta has a tau av of -40. The large increase in negative supercoiling of spore plasmid was also observed with Bacillus megaterium and in B. subtilis containing a plasmid with an origin different from that of pUB110. During spore germination plasmid pUB110 rapidly relaxed back to the tau av value characteristic of vegetative cells. It is possible that the observed changes in forespore plasmid topology are involved in modulating gene expression, DNA photochemistry, or both of these parameters in this compartment.

[Study of the properties of condensed forms of the complexes of linear and supercoiled DNA with mitoxantrone and bisantrene]

The effect of anthrachinone and anthracene derivatives on linear and circular superstranded molecules of DNA in conditions of their condensation was studied. It was shown that the compounds formed strong intercalation complexes with the molecules of the linear and circular superstranded DNA when the DNA molecules were in the condensed condition. The optical properties of the disperse liquid crystal phases formed of the complexes of the investigated compounds with the molecules of linear double-chain DNA differed. Moreover, the optical properties of the condensed phases formed of the complexes of the compounds with the molecules of linear and circular superstranded DNA also differed. The causes of the differences are discussed.

Bidirectional sequencing of supercoiled plasmid DNA

In this paper we show that restriction DNA fragments can prime DNA synthesis of a homologous supercoiled plasmid DNA. Using the dideoxyribonucleotide chain terminator method, newly synthesized truncated chains can be detached from the primers by restriction enzyme digestion. Therefore, by choosing DNA fragments flanked by two different restriction enzymes sites, nucleotide sequence information can be simultaneously obtained on both regions of the DNA surrounding the restriction fragment. The advantage of this sequencing approach over current methods is that no prior knowledge of the primary sequence is needed to find the nucleotide sequence of a given DNA fragment. Thus, synthetic primers are not required and internal sequences of a given clone can be easily accessed without the need of fragmenting the original construct. The method has been used with rapid plasmid preparations, thus considerable time and effort can be saved in the gathering of nucleotide sequence information.

Detection of supercoiled hepatitis B virus DNA and related forms by means of molecular hybridization to an oligonucleotide probe

A novel assay for supercoiled and other fully double-stranded forms of hepatitis B virus (HBV) DNA in blood is presented that utilizes molecular hybridisation to a radiophosphorous-labeled oligonucleotide probe. The probe [5'-d(ACGTGCAGAGGTGAAGCGA)] is complementary to the S(+)-strand sequence furthest downstream, at the end of the gap. We examined blood specimens from 137 healthy HBsAg-positive individuals, applying the probe to dots representing 2-3.5 ml serum or plasma. We found that supercoiled HBV is present in many HBV DNA-positive blood specimens albeit in small quantities. Of the 104 specimens that were positive for HBV DNA of any form, 53 annealed to the probe. Serial specimens from the same subject taken over a period of months showed that the proportion of supercoil to other HBV DNA forms was variable. The presence of supercoil HBV DNA was not closely correlated with the level of serum HBV DNA polymerase. The supercoil is an HBV DNA form that can persist in the liver in the presence or absence of other replicative intermediates. This assay may enable further characterization of the status of HBV infection.

The SV40 nucleosome-free region is detected throughout the virus life cycle

The structures of SV40 intracellular chromatin complexes and of extracellular virus particles were examined by photolabeling with a radioactive psoralen derivative in order to determine the fate of the exposed origin region during the virus life cycle. We have previously shown that the origin region of intracellular SV40 chromatin is preferentially accessible to psoralen derivatives in vivo, whereas psoralen adducts are uniformly distributed when purified virus particles are photoreacted. We demonstrate here that when virion is photoreacted prior to a freeze-thaw cycle, the exposed regulatory region detected in intracellular nucleoprotein complexes is also found in mature virus particles. In contrast, if the virion is frozen and thawed prior to the photoreaction, the origin is not preferentially exposed to photoaddition. Virus particles that have not been subjected to a freeze-thaw cycle were found to exhibit preferential labeling in the origin region whether they were irradiated intracellularly, in culture medium, or following purification. Banding the virus in CsCl had no significant effect on the relative accessibility of the origin region to psorealen. Our findings indicate that the open regulatory region found on intracellular SV40 chromatin persists throughout the virus life cycle.

Fluorometric methods employing low concentrations of ethidium bromide for DNA topoisomerase and endonuclease assays

DNA topoisomerase activity can be rapidly assayed by measuring the change in ethidium bromide fluorescence intensity after treatment of closed duplex DNA with enzyme. The sensitivity of the fluorometric assay has been enhanced 3-fold by a 10-fold reduction in ethidium bromide concentration to 0.1 microgram/ml. The results of the fluorometric assays are in close agreement with agarose gel electrophoretic analyses of reacted DNA. A sensitive fluorometric method using 0.1 microgram/ml ethidium bromide has also been developed to determine the fraction of nicked and linear DNAs in a mixture containing closed duplex DNA by measuring the fluorescence intensities of ethidium-DNA complexes at pH 7.0 and pH 12.0. These methods make possible very rapid and sensitive measurements of DNA topoisomerase and endonuclease activities.

Characterization of the plasmids of Moraxella bovis

Restriction endonuclease digestions were performed on plasmids purified from Moraxella bovis isolates GRS, Newport, and IBH64. It was determined from single and double digestions of plasmid DNA that GRS and Newport isolates carried 3 large plasmids having molecular sizes of 43.8, 41.3, and 32.8 kilobases (kb). Digestion of the 3 large plasmids and restriction endonucleases Hae III, HindIII, Nde I, and Ava I strongly indicated that these isolates shared structurally identical large plasmids. Timed single digestions with Ava I revealed that the IBH64 isolate carried 2 large plasmids having molecular sizes of 45 and 32.8 kb. The 32.8-kb plasmid was the only large plasmid that appeared to be shared by all 3 M bovis isolates. Two isolates, Newport and IBH64, carried small plasmids in addition to the large plasmids. Restriction maps were constructed for the 43.8-, 41.3-, and 32.8-kb plasmids.

Pulse time and agarose concentration affect the electrophoretic mobility of cccDNA during PFGE and FIGE [corrected]

Circular DNAs have been shown to migrate in an unusual manner during field inversion gel electrophoresis (FIGE) and orthogonal field alternating gel electrophoresis (OFAGE). We studied the effect of varying pulse time and agarose concentration on the electrophoretic mobility of supercoiled (ccc) DNAs ranging from 2 kbp to 16 kbp during FIGE and contoured homogeneous electric fields (CHEF). Both supercoiled and linear molecules display a minimum mobility as a function of pulse time in a CHEF apparatus. Linear and cccDNAs of the same size are differently affected by pulse time. Pulse-time dependence was observed for cccDNAs in both systems. Pulse-time dependence in FIGE is very small at a 1.0% agarose concentration, but is pronounced in 0.8% or 1.2% gels.

Pulsed-field gel electrophoresis of circular DNA

Mobility of supercoiled (form I) and nicked circular (form II) plasmid DNAs was determined on two major forms of pulsed-field electrophoresis, CHEF and OFAGE. Plasmids with molecular lengths ranging from 2.30 to 17.8 kilobase pairs (kb) were used with Saccharomyces cerevisiae chromosomes as standards. Agarose gel concentrations were varied from 0.3 to 2.0 percent, with higher percentage gels resolving forms I and II of smaller plasmids. The pulsing range of 3.7 to 240 seconds resulted in quite variable Saccharomyces chromosomal mobilities on both 0.5 and 1.0 percent gels, while both form I and II of all plasmid DNAs showed relatively constant mobilities with some increase at the shortest pulse times. Using a 30 second pulse time and gel concentrations of at least 1.0 percent, the usual order of migration of plasmid forms for a 17.8 kb plasmid could be changed. We interpret this result as an increase in the relative mobility of form II in our pulsed-field gel conditions.