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Synthesis and in vitro evaluation of 9-anilino-3,6-diaminoacridines active against a multidrug-resistant strain of the malaria parasite Plasmodium falciparum.

A series of 9-anilinoacridines have been prepared and evaluated for their activity against a multidrug-resistant K1 strain of the malaria parasite Plasmodium falciparum in erythrocyte suspensions. 3,6-Diamino substitution on the acridine ring resulted in lower mammalian cell cytotoxicity and higher antiparasitic activity than other substitution patterns, providing compounds with the highest in vitro therapeutic indices. A new synthesis of 3,6-diamino-9-anilinoacridines, via reduction of the corresponding diazides, gives much higher yields than traditional methods. Within the subset of 3,6-diamino-9-anilinoacridines, there was considerable tolerance to substitution at the 1'-anilino position. In a sharp divergence with structure-activity relationships for high mammalian cell toxicity and anticancer effects, derivatives bearing electron-withdrawing 1'-substituents (e.g., SO2-NHR and CONHR) showed the most potent antimalarial activity (IC50 values of 10-20 nM). Representative compounds were shown to be potent inhibitors of the DNA strand-passing activity of human topoisomerase II and of the DNA decatenation activity of the corresponding parasite enzyme. The 1'-SO2NH2derivative 7n completely inhibited strand passage by Jurkat topoisomerase II at 20 microM, and an increase in linear DNA (indicative of inhibition of religation) was seen at or above 1 microM. It also inhibited the decatenating activity of the parasite topoisomerase II at 6 microM and above. In contrast, the analogous compound without the 3,6-diamino substituent was inactive in both assays up to 100 microM. Overall, there was a positive relationship between the ability of the drugs to inhibit parasite growth in culture and their ability to inhibit parasite topoisomerase II activity in an isolated enzyme assay. The 1'-SO2NH2 derivative 7n showed a high IVTI (1000) and was a potent inhibitor of both P. falciparum in vitro (IC50 20 nM) and P. falciparum-derived topoisomerase II. However, the compound was inactive against Plasmodium berghei in mice; reasons may include rapid metabolic inactivation (possibly by N-acetylation) and/or poor distribution.

Aminoacridines↗

Pathways of removal of free DNA vector ends in normal and DNA-PKcs-deficient SCID mouse hepatocytes transduced with rAAV vectors.

Elucidation of the mechanisms of transformation of single-stranded (ss) recombinant adeno-associated virus (rAAV) vector genomes into a variety of stable double-stranded (ds) forms is key to a complete understanding of rAAV vector transduction in vivo. Ds monomer genome formation and cellular ds DNA break (DSB) repair pathways that remove free vector ends toxic to cells, presumably play a central role in this process. By delivering rAAV and naked ds linear DNA vectors into livers of DNA-dependent protein kinase catalytic subunit (DNA-PKcs)-deficient severe combined immunodeficiency (SCID) and wild-type mice, we demonstrate the presence of three major pathways for free ds vector end removal: (1) DNA-PKcs-dependent self-circularization, (2) DNA-PKcs-independent self-circularization, and (3) DNA-PKcs-independent concatemerization. By using the DNA-PKcs-independent pathways, mouse hepatocytes efficiently removed free ds rAAV vector ends even in the absence of DNA-PKcs. Our studies suggest a hierarchical organization of these processes; self-circularization is the preferred pathway over concatemerization, although the former has a limited capacity to remove free vector ends. These studies shed new light on the molecular mechanisms of rAAV vector transduction in vivo.

3' Untranslated Regions↗

The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling.

We determined the free energy of DNA supercoiling as a function of the concentration of magnesium and sodium chloride in solution by measuring the variance of the equilibrium distribution of DNA linking number,<(DeltaLk)2>. We found that the free energy of supercoiling changed >1.5-fold over the range of ionic conditions studied. Comparison of the experimental results with those of computer simulations showed that the ionic condition dependence of<(DeltaLk)2>is due mostly to the change in DNA effective diameter, d, a parameter characterizing the electrostatic interaction of DNA segments. To make this comparison we determined values of d under all ionic conditions studied by measuring the probability of knot formation during random cyclization of linear DNA molecules. From the topoisomer distributions we could also determine the changes in DNA helical repeat, gamma, in mixed NaCl/MgCl2 solutions. Both gamma and d exhibited a complex pattern of changes with changing ionic conditions, which can be described in terms of competition between magnesium and sodium ions for binding to DNA.

Blotting, Southern↗

In situ localized amplification and contact replication of many individual DNA molecules.

We describe a method to clone and amplify DNA by performing the polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the diffusion of the linear DNA molecules so that the amplification products remain localized near their respective templates. At the end of the reaction, a number of PCR colonies, or 'polonies', have formed, each one grown from a single template molecule. As many as 5 million clones can be amplified in parallel on a single slide. If an Acrydite modification is included at the 5' end of one of the primers, the amplified DNA will be covalently attached to the polyacrylamide matrix, allowing further enzymatic manipulations to be performed on all clones simultaneously. We describe techniques to make replicas of these polony slides, and high throughput sequencing protocols for this technology. Other applications are also discussed.

Acrylic Resins↗

An active foamy virus integrase is required for virus replication.

Foamy viruses (FVs) make use of a replication strategy which is unique among retroviruses and shows analogies to hepadnaviruses. The presence of an integrase (IN) and obligate provirus integration distinguish retroviruses from hepadnaviruses. To clarify whether a functional IN is required for FV replication, a mutant in the highly conserved DD35E motif of the active centre was analysed. This mutant was found to be able to express Gag and Pol protein precursors and cleavage products and to generate and deliver cDNA. However, this mutant was replication-deficient. The junctions of individual foamy proviruses with cellular DNA were sequenced. The findings suggest that FV integration is asymmetrical, because the proviruses started with what is believed to be the U3 end of the free linear DNA to generate the conventional TG dinucleotide, while apparently two nucleotides from the U5 end were cleaved to create the complementary CA dinucleotide. Alignment of known FV genome sequences indicated that this mechanism of integration is not restricted to the two FV isolates from which integrates were studied, but appears to be a common feature of this retrovirus subfamily. In conclusion, with respect to the necessity of a functionally active IN for virus replication FVs behave like other retroviruses; their mechanism of integration, however, is probably unique.

Animals↗

Surface-located trypsin-activated Streptococcus sanguis strain Wicky endonuclease.

A new Streptococcus sanguis strain Wicky endonuclease was isolated, purified and partially characterized. This nuclease acts preferentially on thermally denatured DNA, is not inhibited by RNA and is activated 3-5 times by trypsin. This activation is accompanied by the reduction of molecular weight of the enzyme. These features distinguish the new S, sanguis nuclease from the 3 previously described S. sanguis endonucleases. With covalently closed circular plasmid DNA, the enzyme causes first the appearance of a single stranded nick, then the second nick on the opposite DNA strand, resulting in plasmid DNA linearization. This nuclease most likely is located at the cell surface. The possible relationship of the described nuclease with ability of S. sanguis cells to take up DNA in genetic transformation is discussed.

Cell Membrane↗

Modification and restriction of T-even bacteriophages. In vitro degradation of deoxyribonucleic acid containing 5-hydroxymethylctosine.

Using the single-stranded circular DNA of bacteriophage fd as template, double-stranded circular DNA has been prepared in vitro with either 5-hydroxymethylcytosine ([hmdC]DNA) or cytosine ([dC]DNA) in the product strand. Extracts prepared from Escherichia coli cells restrictive to T-even phage containing nonglucosylated DNA degrade [hmdC]DNA to acid-soluble material in vitro, but do not degrade [dC]dna. In contrast, extracts prepared from E. coli K12 rglA- rglB-, a strain permissive to T-even phage containing nonglucosylated DNA, do not degrade [hmdC]DNA or [dC]DNA. In addition, glucosylation of the [hmdC]DNA renders it resistant to degradation by extracts from restrictive strains. The conversion of [hmdC]DNA to acid-soluble material in vitro consists of an HmCyt-specific endonucleolytic cleavage requiring the presence of the RglB gene product to form a linear molecule, followed by a non-HmCyt-specific hydrolysis of the linear DNA to acid-soluble fragments, catalyzed in part by exonuclease V. The RglB protein present in extracts of E. coli K12 rglA- rglB+ has been purified 200-fold by complementation with extracts from E. coli K12 rglA- rglB-. The purified RglB protein does not contain detectable HmCyt-specific endonuclease or exonuclease activity. In vitro endonucleolytic cleavage of [hmdC]DNA thus requires additional factors present in cell extracts.

5-Methylcytosine↗

Gel electrophoresis measurement of counterion condensation on DNA.

We used agarose gel electrophoresis to measure the effective charge neutralization of DNA by counterions of different structure and valence, including Na+, Mg2+, Co(NH3)3+6, and spermidine3+, which competed for binding with an excess of Tris acetate buffer. Linear DNA molecules ranged in size from 1 to 5 kilobases, and supercoiled plasmid pUC18 was also measured. In all cases, the results were in good agreement with theoretical predictions from counterion condensation theory for two-counterion mixtures.

Cations, Divalent↗

Release of telomeric DNA from chromosomes in immortal human cells lacking telomerase activity.

Some immortal human cell lines lack telomerase activity. These cell lines were found to contain small dispersed DNA hybridizing to TTAGGG repeats. Such DNA was located in their cytoplasm and nuclei. Normal human fibroblasts or telomerase-positive cell lines did not contain such DNA. Upon cloning and sequencing, it was shown to consist of TTAGGG repeats. When electrophoresed on neutral and alkaline agarose gels, it behaved as double-stranded and linear DNA. These results suggest that telomeric DNA is released from chromosomes in association with maintenance of telomeres in telomerase-negative cell lines.

Cell Line↗

Paired DNA three-way junctions as scaffolds for assembling integrase complexes.

Early steps of retroviral replication involve reverse transcription of the viral RNA genome and integration of the resulting cDNA copy into a chromosome of the host cell. The initial DNA breaking and joining steps of integration are carried out by the virus-encoded integrase enzyme. Integrases bind specifically to the ends of the unintegrated viral cDNA but nonspecifically to target DNA. Conventional assays in vitro reveal primarily the nonspecific DNA binding mode, complicating studies of integrase--DNA complexes. Here, we report an investigation of unconventional DNA structures useful for positioning integrase at predetermined sites. We find that paired DNA three-way junctions can be used to mimic branched DNAs normally formed as reaction intermediates. The three-way junctions differ from authentic intermediates in the connectivity of the DNAs, which, in contrast to the authentic intermediate, allow formation of stable DNA structures under physiological conditions. Assays in vitro showed that integrase can direct hydrolysis at sequences resembling the viral cDNA ends within the three-way junction, but not on junctions with mutant sequences. Changing the spacing between the paired three-way junctions disrupted the cleavage pattern, emphasizing the importance of the correct DNA scaffold. DNase I footprinting studies revealed protection of specific bases at the terminus of the LTR in the three-way junction complex, but not on control linear DNA, specifying the locations of tight interactions between integrase and DNA. Paired DNA three-way junctions are attractive reagents for structural studies of integrase-DNA complexes.

Avian Sarcoma Viruses↗

Differences in the cleavage of DNA by bleomycin under light (300-350 nm) and dark conditions.

Incubation of supercoiled plasmid DNA (both pBR 322 and pPLC-28) with increasing concentrations of bleomycin in the presence and absence of light (300-350 nm) showed extensive conversion of supercoiled to linear DNA which occurred at much lower levels of bleomycin (BLM) in the light than in the dark. Preliminary results indicate that superoxide dismutase (SOD) may offer DNA more protection against bleomycin in the dark than in the light conditions.

Bleomycin↗

A new method for rapidly generating gene-targeting vectors by engineering BACs through homologous recombination in bacteria.

Generating knockout mice is still an expensive and highly time-consuming process. Target construct generation, the first labor-intensive step in this process, requires the manipulation of large fragments of DNA and numerous, and often cumbersome, cloning steps. Here we show the development of a rapid approach for generating targeting constructs that capitalizes on efficient homologous recombination between linear DNA fragments and circular plasmids in Escherichia coli ("recombineering"), the availability of bacterial artificial chromosomes (BACs), and the accessibility of the sequence of the mouse genome. Employing recombineering, we demonstrate with only 1-2 template plasmids, short homologies (40-50bp) between donor and target DNA, and one subcloning step that we can efficiently manipulate BACs in situ to generate a complicated targeting vector. This procedure avoids the need to construct or screen genomic libraries and permits the generation of most standard, conditional, or knock-in targeting vectors, often within two weeks.

Animals↗

Repair of the plasmid pBR322 damaged by gamma-irradiation or by restriction endonucleases using different recombination-proficient E. coli strains.

The plasmid pBR322 was treated with BamHI, PvuII and gamma-irradiation to generate double-strand breaks (dsb) containing differently structured ends. Transformation efficiencies, mutation frequencies and clone analyses of enzymatically damaged DNA are compared with the corresponding results from radiolytically damaged DNA. In E. coli K-12 SFX, the yield of transformants produced by the action of BamHI, PvuII and gamma-irradiation (30 Gy) is 4.3%, 0.14%, and 0.10%, respectively. The survival of open circular DNA (ocDNA) produced by 30 Gy is 1.3%. The transformation efficiencies show only a slight dependence on SOS induction and on the RecA protein. Mutation frequencies to tetracycline sensitivity (tets) per surviving plasmid are 2.6% (BamHI), 11.8% (PvuII) and 0.2% (gamma-irradiated DNA with 30 Gy containing approximately 50% ocDNA and 50% linearized (lin) DNA). The mutation frequency is low at all radiation doses studied (1-50 Gy). Only 15% of the DNA of the tets mutants from gamma-irradiated plasmids contained deletions whereas with enzymatically damaged DNA, 30-50% (BamHI) or 90% (PvuII) contained deletions. In all cases, the deletions comprised 500-1700 base pairs (bp). After SOS induction of the host cells, the mutation frequency of gamma-irradiated plasmids increased by a factor of 4, whereas that of the enzymatically damaged plasmids did not change. For the repair of the enzymatically linearized DNA 2 recombinational pathways are discussed which lead to deletant (pathway I) and non-deletant transformants (pathway II). In addition, BamHI-linearized plasmids may be repaired by enzyme-induced or spontaneous circular alignment followed by ligation. The high percentage of deletions of the tets mutations for PvuII-linearized DNA with blunt ends is explained by the illegitimate or site-specific recombination pathway I (see text). The lower percentage of deletions of the tets mutations with BamHI-linearized DNA with short cohesive ends (4 bp) is proposed to be due to a greater contribution of pathway II and/or by circular alignment followed by ligation. The very small yield and the low percentage of deletant mutations of tets mutants from radiolytically damaged DNA is proposed to be due to the large overlapping ends (16-100 bp) of the linDNA which easily leads to circular alignment followed by excision repair. The repair of radiolytically produced ocDNA is predominantly due to excision repair. In agreement with this interpretation is the observation that SOS induction of the host increases the mutation incidence of radiolytically damaged DNA but not of enzymatically damaged DNA.

DNA Repair↗

DNA gel electrophoresis: effect of field intensity and agarose concentration on band inversion.

We study the effect of electric field intensity and agarose gel concentration on the anomalous electrophoretic mobility recently predicted by the biased reptation model and experimentally observed for linear DNA fragments electrophoresed in continuous electric fields. We show that high fields and low agarose concentrations eliminate the physical mechanism responsible for anomalous DNA mobility and band inversion, in good agreement with theory, thus restoring the monotonic mobility-size relationship necessary for unambiguous interpretation of the results of DNA gel electrophoresis.

DNA↗

Improvement on genetic transformation in the nematode-trapping fungus Arthrobotrys oligospora and its quantification on dung samples.

An improved DNA-mediated transformation system for nematode-trapping fungus Arthrobotrys oligospora based on hygromycin B resistance was developed. The transformation frequency varied between 34 and 175 transformants per microg linearized DNA and 93% of the transformants were stable for drug resistance when tested 100 randomly selected transformants. More than 2000 transformants were obtained by transformation of the fungus with pBChygro in the presence of HindIII and among them, one, YMF1.00110, which lost its ability of forming predacious structure, was isolated. Southern analysis showed that the plasmid DNA had integrated into the genome of all tested transformants (including YMF 1.00110) except one. The transformant tagged with hph gene could be re-isolated and quantified from dung samples based on the resistance of hygromycin B. All the results suggested that the method of restriction enzyme mediated integration (REMI) should facilitate not only the insertional mutagenesis for tagging and analysis genes of interest but also the ecological investigation of tagged fungi in a given environment.

Animals↗

Simultaneous analysis of the bidirectional African cassava mosaic virus promoter activity using two different luciferase genes.

The expression of geminivirus genes is controlled by bidirectional promoters which are located in the large intergenic region of the circular DNA genomes and specifically regulated by virus encoded proteins. In order to study the simultaneous regulation of both orientations of the DNA A and DNA B promoters of African cassava mosaic virus (ACMV), they were cloned between two different luciferase genes with the firefly luciferase gene in complementary-sense and the Renilla luciferase gene in virion-sense orientation. The regulation of the ACMV promoters by proteins encoded by the complete DNA A, as well as by the individually expressed transactivator (TrAP) or replication-associated (Rep) proteins was assessed in tobacco and cassava protoplasts using dual luciferase assays. In addition, the regulation of the DNA A promoter integrated into tobacco genome was also assessed. The results show that TrAP activates virion-sense expression strongly both in cassava and tobacco protoplasts, but not in transgenic tobacco plants. In contrast to this, DNA A encoded proteins activate virion-sense expression both in protoplasts and in transgenic plants. At the same time they reduce the expression of the complementary-sense Rep gene on DNA A but activate the expression of the complementary-sense movement protein (MPB) gene on DNA B. The degree of MBP activation is higher in cassava than in tobacco protoplasts, indicating that the plant host also influences the promoter strength. Transient transformation experiments using linearized DNA indicate that the different regulation of the ACMV DNA A promoter in protoplasts and transgenic plants could be due to different DNA curvature in free plasmids and in genes integrated in plant genomic DNA.

Geminiviridae↗

Bacteriophage fd gene-2 protein. Processing of phage fd viral strands replicated by phage T7 enzymes.

Bacteriophage T7 gene 4 protein and DNA polymerase of the phage were used to study the viral strand synthesis of bacteriophage fd in vitro. Cleavage of supercoiled phage fd replicative form (RF) by fd gene 2 protein produced a nick at a specific site in the viral strand. The cleaved double-stranded DNA was unwound by T7 gene 4 protein and T7 DNA polymerase and the 3' end of the nicked strand simultaneously extended according to the rolling circle mechanism. After a complete round of DNA synthesis fd gene 2 protein cleaved the viral strand presumably at the same site, where the endonuclease cuts fd RF I, and subsequently sealed the single-stranded linear DNA into a circle. The reaction products were analyzed by velocity sedimentation, gel electrophoresis and electron microscopy. Most of the single-stranded DNA synthesized was circular. No host proteins were required for the formation of the single-stranded circles. Strand switching of the T7 DNA polymerase indicated by double-stranded tails of the rolling circle structures reduced the yield of viral single-stranded circles in this enzyme system.

DNA Replication↗

Characterization of the DNA of a Nonoccluded Baculovirus, Hz-1V.

The DNA of the nonoccluded baculovirus (Hz-1V) obtained from the IMC-Hz-1 cell line was characterized by physicochemical and restriction endonuclease techniques. Hz-1V DNA isolated from purified virus had buoyant densities of 1.58 and 1.54 g/ml in CsCl-ethidium bromide density gradients, which corresponded to supercoiled and to relaxed circular and linear DNA, respectively. Neutral CsCl equilibrium centrifugation indicated that the Hz-1V DNA had a buoyant density of 1.7024 g/ml, which corresponded to a guanine-plus-cytosine (G+C) content of 43%. Thermal denaturation indicated a high G+C domain(s) in the Hz-1V genomic DNA. The domain(s), which included about 11% of the total genomic DNA, exhibited a T(m) of 97 degrees C. The remaining portion (89%) of the DNA had a T(m) of 86.5 degrees C. The T(m)s corresponded to G+C contents of 42 and 67%, respectively. The mean genetic complexity of Hz-1V DNA determined by DNA reassociation kinetic analysis was found to be 152 x 10(6). A possible rapidly reassociating component comprising approximately 13% of the genome was observed. The mean molecular weights from restriction endonuclease digests were 159 x 10(6) for both HindIII and EcoRI. Genomic heterogeneity was found in both the wild-type Hz-1V stock and in two plaque isolates. Of 12 single-plaque isolates, 3 basic restriction endonuclease DNA fragment patterns were observed. The molecular size estimates from electron microscopic contour lengths of uncloned viral DNA ranged from 70 to 158 megadaltons, and the mode was the 130- to 140-megadalton class.

Journal Article↗