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At least 685 records · Page 38Linked to original sources
PubMed2006

Requirements for Bacillus subtilis bacteriophage phi29 DNA ejection.

Phage phi29 infects Bacillus subtilis and ejects its linear DNA with a right to left polarity in a two-step, "push-pull" mechanism. In the first step 65% of the DNA is pushed inside the cell, presumably by the pressure built inside the capsid. In the second step, the remaining DNA is pulled by a hypothetical motor that comprises at least viral protein p17, encoded by the right early operon, in an energy-dependent process. We have further studied phi29 DNA ejection by using energy poisons and DNA replication and transcription inhibitors. The first step is passive, as it does not require an external energy source. The second step is transcription-independent and is completely abolished by novobiocin, suggesting a requirement for negatively supercoiled DNA. Viral DNA pulling also requires an electrochemical proton gradient, as the process is highly impaired by specific energy poisons such as gramicidin and CCCP (carbonyl cyanide m-chlorophenylhydrazone). The fact that azide has no effect in the absence of p17 suggests that this protein is essential for energy transduction.

Bacillus Phages↗
PubMed2004

Distinct properties of the two putative "globular domains" of the yeast linker histone, Hho1p.

The putative linker histone in Saccharomyces cerevisiae, Hho1p, has two regions of sequence (GI and GII) that are homologous to the single globular domains of linker histones H1 and H5 in higher eukaryotes. However, the two Hho1p "domains" differ with respect to the conservation of basic residues corresponding to the two putative DNA-binding sites (sites I and II) on opposite faces of the H5 globular domain. We find that GI can protect chromatosome-length DNA, like the globular domains of H1 and H5 (GH1 and GH5), but GII does not protect. However, GII, like GH1 and GH5, binds preferentially (and with higher affinity than GI) to four-way DNA junctions in the presence of excess linear DNA competitor, and binds more tightly than GI to linker-histone-depleted chromatin. Surprisingly, in 10 mM sodium phosphate (pH 7.0), GII is largely unfolded, whereas GI, like GH1 and GH5, is structured, with a high alpha-helical content. However, in the presence of high concentrations of large tetrahedral anions (phosphate, sulphate, perchlorate) GII is also folded; the anions presumably mimic DNA in screening the positive charge. This raises the possibility that chromatin-bound Hho1p may be bifunctional, with two folded nucleosome-binding domains.

Amino Acid Sequence↗
PubMed2002

Biolistic transformation of Trichoderma reesei using the Bio-Rad seven barrels Hepta Adaptor system.

Effective biolistic transformation of intact conidia from the filamentous fungus Trichoderma reesei was achieved using the Bio-Rad Hepta Adaptor system with seven barrels for particle launch. Transformation frequencies of up to 39 colonies per microg of circular DNA and 37 colonies per microg of linear DNA were obtained at an optimal target distance of 3 cm and a helium pressure of 1350 psi. These values are about 3.5- to 6-fold higher than transformant yields reported earlier for T. reesei using the hygromycin phosphotransferase (hph) gene conferring resistance to the antibiotic hygromycin B as a selectable marker in combination with the PDS-1000/He single barrel system. High mitotic stability of the transformants (98-100%) was demonstrated. The Hepta Adaptor device allowing bombardment of seven lots of conidia in a single plate offers clear advantage in terms of transformant numbers over the single barrel system where target cells are restricted to the center of the plate.

Cellulase↗
PubMed1983

Do planar alkaloids from Strychnos usambarensis intercalate into the DNA helix?

The mode of binding of melinonine F and normelinonine F to DNA has been investigated through physico-chemical methods which proved most valuable in the study of dye-DNA interactions, namely absorption spectrophotometry, circular and linear dichroism, fluorescence polarization, viscosity increase of linear DNA and circular DNA unwinding. The spectroscopic properties resembled those observed with planar heterocyclic compounds intercalating between the DNA base pairs: bathochromic shift and hypochromism in the ligand absorption bands; presence of a strong binding process with an association constant of the order of 10(6)M-1 and a number of binding sites of 0.1 to 0.15; appearance of extrinsic optical activity in the ligand absorption bands with a dependence on the binding ratio typical for an excitonic origin; negative reduced electric dichrosim of the ligand chromophore of the same order of magnitude as that of the DNA heterocyclic bases. However the increase of the length of sonicated DNA determined from viscosity changes was much smaller than for most intercalating compounds and no unwinding of PM2 circular DNA was detected.

Alkaloids↗
PubMed1985

Hierarchy of binding sites for chromosomal proteins HMG 1 and 2 in supercoiled deoxyribonucleic acid.

The interaction of chromosomal proteins HMG 1 and 2 with various DNA structures has been examined with plasmid pPst-0.9, which contains DNA sequences that can form the Z-DNA conformation and palindromic sequences that can form cruciform structures. Direct binding and competition experiments with 32P-labeled plasmid indicated that proteins HMG 1 and 2 preferentially bind to supercoiled form I DNA as compared to double-stranded linear DNA. The preferential binding to form I is due to the presence of single-stranded regions in this DNA. The binding of HMG 1 and 2 to the form I plasmid results in inhibition of S1 nuclease digestion in a selective manner. The B-Z junction is preferentially protected as compared to the cruciform, which in turn is more protected than other minor S1-sensitive structures present in pPst-0.9. Our results indicate that the binding of HMG 1 and 2 proteins to DNA is not random in that HMG 1 and 2 can distinguish between various S1 nuclease sensitive sites in the plasmid. The existence of a hierarchy of DNA binding sites for these proteins suggests that they can selectively affect the structure of distinct regions in the genome.

Actins↗
PubMed2006

Adsorption of DNA into mesoporous silica.

In these experiments, double-stranded, linear DNA sequences were adsorbed into the pores of spherically shaped acid-prepared mesoporous silica (APMS). The lengths of the sequences were either 760 base pairs or 2000 base pairs. DNA adsorption into the interior of the mesoporous material was confirmed using confocal microscopy of sequences containing fluorescently labeled DNA molecules. Additional characterization with N(2) physisorption and powder X-ray diffraction supported this finding. The extent of adsorption was measured at various concentrations using UV-visible spectrophotometry to establish adsorption isotherms. APMS alone adsorbed a negligible amount of DNA; however, exchanging divalent cations such as Mg(2+) and Ca(2+) into the pores of APMS prior to DNA uptake was found to cause a significant amount of DNA to be adsorbed. Using Na(+) caused a lower amount of DNA to be adsorbed. DNA adsorption was also dependent on the pore diameter of APMS. Adsorption increased upon expansion of the pore size of the metal ion-exchanged material from 34 to 54 A; however, no additional uptake was measured by further increasing the pore size to 100 A. The amount of DNA adsorbed could also be significantly increased by using (aminopropyl)triethoxysilane to covalently link ammonium ions to the surface. Postsynthetic modification of the silica surface with aminopropyl groups increased the maximum DNA adsorption to 15.7 microg/mg silica, for materials with pore diameters of 100 A, which is 2 to 3 times more adsorbed DNA than for metal ion-exchanged material. This indicated that DNA binds more strongly in the presence of the ammonium group compared to the metal counterions. Finally, calculation and comparison of Freundlich and Langmuir constants for these adsorption processes indicate that intermolecular interactions between the DNA molecules within the pores are significant when the effective pore diameter is small, including materials with larger pores that were modified with organosilane.

Adsorption↗
PubMed2005

Multicomponent cationic lipid-DNA complex formation: role of lipid mixing.

Multicomponent cationic lipid-DNA complexes (lipoplexes) were prepared by adding linear DNA to mixed lipid dispersions containing two populations of binary cationic liposomes and characterized by means of small angle X-ray scattering (SAXS). Four kinds of cationic liposomes were used. The first binary lipid mixture was made of the cationic lipid (3'[N-(N',N'-dimethylaminoethane)-carbamoyl]cholesterol (DC-Chol) and the neutral helper lipid dioleoylphosphocholine (DOPC) (DC-Chol/DOPC liposomes), the second one of the cationic 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) and the neutral dioleoylphosphatidylethanolamine (DOPE) (DOTAP/DOPE liposomes), the third one of DC-Chol and DOPE (DC-Chol/DOPE liposomes), and the fourth one of DOTAP and DOPC (DOTAP/DOPC liposomes). Upon DNA-induced fusion of liposomes, large lipid mixing at the molecular level occurs. As a result, highly organized mixed lipoplexes spontaneously form with membrane properties intermediate between those of starting liposomes. By varying the composition of lipid dispersions, different DNA packing density regimes can also be achieved. Furthermore, occurring lipid mixing was found to induce hexagonal to lamellar phase transition in DOTAP/DOPE membranes. Molecular mechanisms underlying experimental findings are discussed.

Cations↗
PubMed1997

New insight on the role of extrachromosomal retroviral DNA.

During infection with different retroviruses, high levels of unintegrated extrachromosomal DNA accumulate in infected cells. While extrachromosomal linear DNA is the immediate precursor of the integrated provirus, the function, if any, of extrachromosomal circular DNA has been unclear. Several groups have attempted to address the possible function, activity, and importance of this unintegrated DNA during the life cycle of retroviruses and the course of retroviral-associated diseases. This review summarizes recent work in this field and tries to analyze some aspects of extrachromosomal forms of retroviral DNA and their possible application as a molecular biological tool.

Animals↗
PubMed2002

ParE toxin encoded by the broad-host-range plasmid RK2 is an inhibitor of Escherichia coli gyrase.

Broad-host-range plasmid RK2 encodes a post-segregational killing system, parDE, which contributes to the stable maintenance of this plasmid in Escherichia coli and many distantly related bacteria. The ParE protein is a toxin that inhibits cell growth, causes cell filamentation and eventually cell death. The ParD protein is a specific ParE antitoxin. In this work, the in vitro activities of these two proteins were examined. The ParE protein was found to inhibit DNA synthesis using an E. coli oriC supercoiled template and a replication-proficient E. coli extract. Moreover, ParE inhibited the early stages of both chromosomal and plasmid DNA replication, as measured by the DnaB helicase- and gyrase-dependent formation of FI*, a highly unwound form of supercoiled DNA. The presence of ParD prevented these inhibitory activities of ParE. We also observed that the addition of ParE to supercoiled DNA plus gyrase alone resulted in the formation of a cleavable gyrase-DNA complex that was converted to a linear DNA form upon addition of sodium dodecyl sulphate (SDS). Adding ParD before or after the addition of ParE prevented the formation of this cleavable complex. These results demonstrate that the target of ParE toxin activity in vitro is E. coli gyrase.

Adenosine Triphosphate↗
PubMed2000

DNA integrity and transgene expression after passage through the NOGA needle catheter used for therapeutic myocardial angiogenesis.

BACKGROUND: The NOGA (Biosense Webster, Markham, ON, Canada) injection catheter is an innovative navigational device that provides an ideal platform for intra-myocardial injection material. However, injection through a long (1.91 m), narrow (27G) nitinol needle could result in deterioration in the integrity and functionality of DNA. METHODS: To test this possibility, DNA in plasmid form (pcDNA3.1) containing the Lac Z transgene (250 micro l) was passed through the NOGA needle using a hand-held 1 cc syringe at a gentle hand injection pressure (43 +/- 3 PSI, 3.0 +/- 0.2 kg/cm(2)) or at maximal manual pressure (90 +/- 6 PSI, 6.3 +/- 0.4 kg/cm(2)), either once or 20 times. This DNA, compared to DNA not passed through the NOGA needle (control), was then used to transfect primary cultures of rat skin fibroblasts (FB) from Fisher 344 rats and the cells were subsequently stained for beta galactosidase (betagal). RESULTS: Transfection efficiency was significantly reduced by passing the DNA through the needle at both 43 +/- 3 PSI (78 +/- 4% of control, n = 10, P < 0.05 versus control) and 90 +/- 6 PSI (66 +/- 4 % of control, n = 10, P < 0.01 versus control, P < 0.02 versus 43 +/- 3 PSI). Passage of the DNA through the NOGA needle 20 times resulted in a transfection efficiency of only 5 +/- 1% of control (n = 20, P < 0.1 x 10(-11) versus control). Capillary Electrophoresis revealed that the reduction in transfection efficiency was due to a conformational change in the DNA from predominantly supercoiled to nicked and linearized DNA. Transfection efficiency as compared with control decreased as the concentration of the DNA solution which was passed through the needle was increased from 0.3 micro g/ micro l to 2.4 micro g/ micro l. Recovery experiments confirmed that the reduction in transfection efficiency was not due to loss of DNA by binding to the NOGA needle. CONCLUSION: These results suggest that DNA is susceptible to shear forces when injected through the NOGA needle even at nominal clinical injection pressures, suggesting that careful and controlled injections will be required to achieve optimal gene integrity and expression.

Journal Article↗
PubMed2002

The Drosophila nuclear lamina protein YA binds to DNA and histone H2B with four domains.

Dramatic changes occur in nuclear organization and function during the critical developmental transition from meiosis to mitosis. The Drosophila nuclear lamina protein YA binds to chromatin and is uniquely required for this transition. In this study, we dissected YA's binding to chromatin. We found that YA can bind to chromatin directly and specifically. It binds to DNA but not RNA, with a preference for double-stranded DNA (linear or supercoiled) over single-stranded DNA. It also binds to histone H2B. YA's binding to DNA and histone H2B is mediated by four domains distributed along the length of the YA molecule. A model for YA function at the end of Drosophila female meiosis is proposed.

Animals↗
PubMed1999

DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes.

Type I restriction enzymes bind to a specific DNA sequence and subsequently translocate DNA past the complex to reach a non-specific cleavage site. We have examined several potential blocks to DNA translocation, such as positive supercoiling or a Holliday junction, for their ability to trigger DNA cleavage by type I restriction enzymes. Introduction of positive supercoiling into plasmid DNA did not have a significant effect on the rate of DNA cleavage by EcoAI endonuclease nor on the enzyme's ability to select cleavage sites randomly throughout the DNA molecule. Thus, positive supercoiling does not prevent DNA translocation. EcoR124II endonuclease cleaved DNA at Holliday junctions present on both linear and negatively supercoiled substrates. The latter substrate was cleaved by a single enzyme molecule at two sites, one on either side of the junction, consistent with a bi-directional translocation model. Linear DNA molecules with two recognition sites for endonucleases from different type I families were cut between the sites when both enzymes were added simultaneously but not when a single enzyme was added. We propose that type I restriction enzymes can track along a DNA substrate irrespective of its topology and cleave DNA at any barrier that is able to halt the translocation process.

DNA, Bacterial↗
PubMed1989

Unusual promoter-independent transcription reactions with bacteriophage RNA polymerases.

Efficient transcription reactions of DNA-dependent RNA polymerases require the presence of a specific promoter sequence. This report shows that in the absence of their cognate promoter, two bacteriophage RNA polymerases are capable of performing unusual transcription reactions: (i) the DNA template serves also as a primer for RNA synthesis and this leads to hybrid DNA/RNA molecules, (ii) if the DNA template forms a hairpin structure, the linear DNA can be transcribed via the 'rolling circle' mechanism.

Biological Evolution↗
PubMed2006

Tapping diversity lost in transformations--in vitro amplification of ligation reactions.

Molecular evolution is a powerful means of engineering proteins. It usually requires the generation of a large recombinant DNA library of variants for cloning into a phage or plasmid vector, and the transformation of a host organism for expression and screening of the variant proteins. However, library size is often limited by the low yields of circular DNA and the poor transformation efficiencies of linear DNA. Here we have overcome this limitation by amplification of recombinant circular DNA molecules directly from ligation reactions. The amplification by bacteriophage Phi29 polymerase increased the number of transformants; thus from a nanogram-scale ligation of DNA fragments comprising two sub-libraries of variant antibody domains, we succeeded in amplifying a highly diverse and large combinatorial phage antibody library (>10(9) transformants in Escherichia coli and 10(5)-fold more transformants than without amplification). From the amplified library, but not from the smaller un-amplified library, we could isolate several antibody fragments against a target antigen. It appears that amplification of ligations with Phi29 polymerase can help recover clones and molecular diversity otherwise lost in the transformation step. A further feature of the method is the option of using PCR-amplified vectors for ligations.

Bacillus Phages↗
PubMed1983

In vivo catenation and decatenation of DNA.

We have noted previously that when circular, but not linear, DNA or chromatin was injected into Xenopus laevis oocytes, much of it went through an intermediate form in which it did not readily enter an agarose gel; after a few hours, it reappeared as monomer DNA that had acquired its full complement of nucleosomes (T. J. Miller and J. E. Mertz, Mol. Cell. Biol. 2:1581-1593, 1982). We determined, using electron microscopy and a variety of biochemical techniques, the structure of this aggregated material. Most of it was oligomeric and multimeric catenanes of the injected sample. In addition, injection of DNA that had been catenated in vitro with DNA gyrase resulted in the conversion of most of it back to monomer circles. These findings demonstrate directly that both catenation and decatenation of DNA occur in vivo under physiological conditions. Whether these reactions play a crucial role in nucleosome formation, as well as in DNA replication and recombination, remains to be determined.

Animals↗
PubMed2001

Systemic circulation of poly(L-lysine)/DNA vectors is influenced by polycation molecular weight and type of DNA: differential circulation in mice and rats and the implications for human gene therapy.

Effective gene therapy for diseases of the circulation requires vectors capable of systemic delivery. The molecular weight of poly(L-lysine) (pLL) has a significant effect on the circulation of pLL/DNA complexes in mice, with pLL(211)/DNA complexes displaying up to 20 times greater levels in the blood after 30 minutes compared with pLL(20)/DNA. It is shown that pLL(20)/DNA complexes fix mouse complement C3 in vitro, independent of immunoglobulin binding; are less soluble in the blood in vivo; bind erythrocytes; are rapidly removed by the liver, where they associate predominantly with Kupffer cells; and result in a rapid increase in hepatic leukocytes expressing high levels of complement receptor 3 (CR3). The circulation properties of these complexes are also dependent on the type of DNA used, with circular plasmid DNA complexes exhibiting increased circulation compared with linear DNA. PLL(211)/DNA complexes bind erythrocytes and associate with Kupffer cells but, in contrast, do not fix mouse complement in vitro and are unaffected by the type of DNA used. In rats, both types of complexes produce hematuria and are rapidly removed from the circulation. Correlation of in vivo and in vitro results suggests that the solubility of complexes in physiological saline and species-matched complement fixation and erythrocyte lysis may correlate with systemic circulation. Analysis using human blood in vitro shows no hemolysis, but both types of complexes fix complement and bind IgG, suggesting that pLL/DNA complexes may be rapidly cleared from the human circulation.

Animals↗
PubMed1990

Transfection by DNA-nuclear protein HMG1 complexes: raising of efficiency and role of DNA topology.

We have developed a novel and efficient transfection method based on the introduction of foreign DNA into mammalian cells in form of complexes of vector DNA with the nuclear protein HMG1. In this study, it is shown that a stabilization of the complexes against dilution dissociation by addition of soluble CaCl2 or by excessive HMG1 enhances the transfection efficiency. Furthermore, there are no differences in the transfection abilities between the 3 topological DNA forms, viz., supercoiled, open relaxed and linear DNA, if delivered to cells as HMG1-DNA complexes. It is further shown that transfection-inactive complexes of the core histones with foreign DNA can be activated in transfection by the addition of HMG1.

Animals↗
PubMed1989

Activation of the vaccinia virus nicking-joining enzyme by trypsinization.

The vaccinia virus nicking-joining (NJ) enzyme has been purified to homogeneity from a preparation of virus cores. The virus-specific DNA-dependent enzyme, which does not require ATP, is a single polypeptide of Mr 50,000 and possesses both endonuclease and ligase activities. The principal end product of the enzyme activity, following incubation with closed circular DNA of sufficient linking deficiency, is a linear DNA in which one of the termini has become cross-linked by the in vitro formation of a hairpin. The ability of the NJ enzyme to cross-link DNA is significantly enhanced by in vitro proteolysis. The enzymatic properties of the proteolytic digestion product, a 44-kDa polypeptide, differ in several other ways from the intact NJ enzyme. In particular, the specific activity is enhanced and the ionic strength optimum is shifted toward higher salt concentrations. It is suggested that the purified 50-kDa species is a pronuclease that is activated by proteolytic processing.

Chromatography, Affinity↗