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At least 433 records · Page 24Linked to original sources
PubMed1996

Enhanced peptide nucleic acid binding to supercoiled DNA: possible implications for DNA "breathing" dynamics.

The influence of DNA topology on peptide nucleic acid (PNA) binding was studied. Formation of sequence-specific PNA2/dsDNA (double-stranded DNA) complexes was monitored by a potassium permanganate probing/primer extension assay. At low ionic strengths, the binding of PNA was 2-3 times more efficient with supercoiled than with linear DNA. In the presence of 140 mM KCI, the PNA binding rate was reduced but, notably, highly dependent on template topology. Negative supercoiling (mean superhelix density, sigma approximately -0.051) increased the rate of binding by 2 orders of magnitude compared to that of relaxed DNA. The pseudo-first-order rate constant [k psi (sigma)] obeys an exponential function, k psi (sigma) = k psi (lin)e-sigma delta, where delta is a constant of 105 and k psi lin is the rate of PNA binding to linear DNA (sigma = 0). The activation energy [Ea(sigma)] was determined as approximately 93 and approximately 48 kJ mol-1 for PNA binding to linear and supercoiled DNA, respectively. The results are discussed in relation to the possible future use of PNA as an antigene agent and in the framework of DNA "breathing" dynamics.

Base Sequence↗
PubMed1989

Topological complexes between DNA and topoisomerase II and effects of polyamines.

The polyamines spermine and spermidine were found to enhance the formation of a stable noncovalent complex between mammalian topoisomerase II and DNA. This complex is not associated with DNA strand breaks and forms to a greater extent with supercoiled than with relaxed circular or with linear DNA. Polyamine-induced complex formation is associated with a stimulation of the enzymatic relaxation of DNA supercoils. In these respects, the polyamine-enhanced complex differs from the covalent cleavable complexes stabilized by DNA intercalators such as amsacrine (m-AMSA) or epipodophylotoxins such as teniposide (VM-26). In the polyamine-enhanced complex, the topoisomerase II may be a donutlike structure topologically bound to the DNA and able to migrate and dissociate from the ends of linear DNA molecules. At relatively high concentrations, spermine (1 mM) enhances topoisomerase II induced cleavage at certain sites on the SV40 genome that could have regulatory significance.

Amsacrine↗
PubMed1983

31P NMR and viscometric studies of the interaction of meso-tetra(4-N-methylpyridyl) porphine and its Ni(II) and Zn(II) derivatives with DNA.

The interactions of meso-tetra(4-N-methylpyridyl) porphine (TMPyP) and its Zn(II) and Ni(II) derivatives with DNA have been investigated by 31P NMR and viscometric titrations. TMPyP and its Ni derivative increase the viscosity of linear DNA, cause unwinding and reverse coiling of superhelical DNA, and induce a separate downfield peak in the 31P NMR spectrum of DNA. The Zn derivative slightly decreases the viscosity of linear DNA, does not unwind superhelical DNA, and does not give a downfield NMR peak. The main DNA 31P NMR signal is shifted slightly upfield on either the addition of TMPyP or the Ni compound. These results indicate that TMPyP and the Ni(II), but not the Zn(II), derivative bind to DNA by intercalation.

Animals↗
PubMed1976

A method for the deletion of restriction sites in bacterial plasmid deoxyribonucleic acid.

A general method has been developed for the deletion of restriction endonuclease sites in bacterial plasmid DNA. The procedure involves partial digestion of the covalently closed circular plasmid DNA with an appropriate restriction endonuclease under conditions which allow accumulation of unit-length linear DNA molecules, a controlled digestion of the exposed 5' ends with the lambda 5'-exonuclease, and in vivo recircularization of the resulting linear DNA in a bacterial host cell. The method has been used for the deletion of one of the two EcoRI sites in the plasmid pML2 (colE1-Km). Two of the resulting plasmids, pCR1 and pCR11, have a single EcoRI cleavage site, but retain genetic determinants specifying resistance to colicin E1 and kanamycin, and thus may be useful as vectors for the cloning and amplification of DNA in bacteria.

Coliphages↗
PubMed2006

Microdetermination of double-stranded DNA by linear sweep voltammetry with phenosafranine.

A novel voltammetric method for the determination of microamounts of fish sperm double-stranded (ds) DNA based on its interaction with phenosafranine (PSF) is proposed in this paper. In a pH 3.5 Britton-Robinson (B-R) buffer solution, PSF had a well-defined second-order derivative linear-sweep voltammetric reductive peak at -0.32 V (vs. SCE) on a mercury electrode. After the addition of dsDNA into the PSF solution, the reductive peak current decreased significantly without a shift of the peak potential, and no new peak appeared. The experiment results showed that a new supramolecular complex was formed after the interaction of dsDNA with PSF, which resulted in a decrease of the diffusion coefficient, and then a decrease of the reductive peak current. The interaction conditions and the electrochemical detection conditions were carefully investigated. Under the optimal conditions, the decrease of the peak current was proportional to the dsDNA concentration in the range 1.0 - 40.0 microg/mL with the linear regression equation DeltaI(p)''(nA) = 32.59C(microg/mL) - 4.03 (n = 13, gamma = 0.998) and a detection limit of 0.25 microg/mL (3 sigma). The interaction mechanism was considered based on the aggregation of the dsDNA-PSF supramolecular complex; the stoichiometry of this supramolecular complex was calculated based on voltammetric data with a binding number of 3 and a binding constant of 2.76 x 10(12). This method was successfully applied to the determination of synthetic samples and the polymerase chain reaction (PCR) product of the nopaline synthase gene (NOS) DNA from genetically modified organisms (GMOs) with satisfactory results.

Animals↗
PubMed1984

Circular Herpesvirus sylvilagus DNA in spleen cells of experimentally infected cottontail rabbits.

Cottontail rabbits (Sylvilagus floridanus) were infected with Herpesvirus sylvilagus, and spleen cells were analyzed for the presence of virus-specific, covalently closed circular, and linear DNA molecules by a simple electrophoretic technique, followed by transfer to nitrocellulose filters and hybridization with cloned viral DNA (Gardella et al., J. Virol. 50:248-254, 1984). Approximately 0.2 copies per cell of circular DNA and 0.2 copies per cell of linear DNA were detected by hybridization with a cloned viral DNA fragment. The size of the viral DNA was estimated at ca. 158 kilobase pairs. Restriction endonuclease patterns suggested structural similarities to cottontail herpesvirus DNA.

Animals↗
PubMed1990

Expression of antigens from chromosomal and linear plasmid DNA of Borrelia coriaceae.

Three recombinant plasmids containing DNA from Borrelia coriaceae, the putative agent of epizootic bovine abortion, expressed antigens in Escherichia coli that reacted with antibodies specific for B. coriaceae. Two of the recombinants each expressed a single high-molecular-weight antigen. The third recombinant expressed three smaller antigens. The DNA inserts were sized and mapped. Hybridization of the cloned inserts to pulsed-field electrophoresis samples of B. coriaceae whole-cell DNA revealed the origin of two of the inserts to be located in linear plasmids. One of these, expressing three antigens, was located in a 210-kilobase linear plasmid. A second recombinant expressed a single antigen but hybridized to at least three distinct linear plasmids. The third clone also expressed a single antigen but was demonstrated to be chromosomal in origin.

Antigens, Bacterial↗
PubMed1979

Binding of bleomycin to DNA: intercalation of the bithiazole rings.

At pH 5.5, binding of bleomycin relaxed supercoiled ColE1 DNA without breaking it. Binding of tripeptide S, a fragment of the drug containing the bithiazole rings, also relaxed and then recoiled supercoiled DNA, at pH 5.5 and at pH 8.0, where bleomycin is normally active. The unwinding angle was 12 degrees. Both compounds lengthened linear DNA by 3.1 A per molecule bound, and linear dichroism (303--315 nm) of bleomycin bound to linear DNA oriented in an electric field indicated the presence of a chromophore making an angle of 59--61 degrees with the helix axis. These results strongly suggest that bleomycin binding to DNA involves intercalation of the bithiazole rings. In 0.1 M Na Cl at pH 8, supercoiled ColE1 DNA was broken at a rate 50% greater than relaxed closed circular ColE1 DNA. Since supercoiling increases the affinity of DNA for intercalators, this result suggests that intercalative binding is involved in bleomycin-induced breakage of DNA.

Bleomycin↗
PubMed1981

Homologous pairing in genetic recombination. The pairing reaction catalyzed by Escherichia coli recA protein.

Purified recA protein, which is essential for genetic recombination of Escherichia coli, catalyzed ATP-dependent homologous pairing of double-stranded DNA and single-stranded fragments to form D-loops. When the double-stranded DNA was nicked circular DNA (form II) or linear DNA (form III), the reaction proceeded nearly linearly during 30 min of incubation at 37 degrees C. When the double-stranded DNA was superhelical (form I), anomalous kinetics was observed. This anomaly was suppressed by the addition of spermidine without affecting the final yield of D-loops. The formation of D-loops required stoichiometric amounts of recA protein, which were proportional to the concentration of single-stranded DNA but which were not affected by the concentration of double-stranded DNA. With form II or III DNA as the recipient for the formation of D-loops, the rate of the reaction was greatest when there was one monomer of recA protein/2-3 nucleotide residues of single-stranded DNA; larger amounts of single-stranded DNA inhibited the reaction. The formation of D-loops was half inhibited by 30 mM NaCl and by 0.6 mM ADP, one of the products of the reaction. The thermal stability of D-loops made by recA protein was the same as that of D-loops made by annealing. In addition to pairing linear single strands with duplex DNA, recA protein made joint molecules from single-stranded circular DNA and homologous form II or III DNA. According to these and previous observations (Cunningham, R. P., DasGupta, C., Shibata, T., and Radding, C. M. (1980) Cell 20, 223-235), rcA protein will stably pair two molecules of DNA if one of them is single-stranded or partially single-stranded and if either molecule has a free end.

Bacterial Proteins↗
PubMed1983

Correlation of enzyme-induced cleavage sites on negatively superhelical DNA between prokaryotic topoisomerase I and S1 nuclease.

Negatively superhelical pNS1 DNA with a molecular weight of 2.55 MDa (4 kbp) was found to contain 13 specific, unbasepaired sites that are sensitive to a single-strand-specific S1 nuclease cleavage. The S1-cleavage occurred once at these sites. In the absence of added Mg2+, the topoisomerase I purified from Haemophilus gallinarum formed a complex with the superhelical pNS1 DNA which has a hidden strand cleavage. Extensive proteinase K digestion of the complex led to cleavage of the DNA chain. Then the proteinase K-cleaved product was digested with S1, which can cut the opposite strand at the preexisting strand cleavage to generate unit-length linear DNA. Restriction endonuclease analysis of the linear DNA shows that the topoisomerase-induced cleavage occurred once at ten specific sites on the DNA. The topoisomerase caused mainly single-strand cleavage at these sites, but infrequently also caused double-strand cleavage at the same sites. Of interest is the fact that these sites considerably coincide with the S1-cleavable, unbasepaired sites.

Bacillus subtilis↗
PubMed1992

Bacteriophage lambda DNA fragments replicate in the Paramecium macronucleus: absence of active copy number control.

We show that bacteriophage lambda DNA fragments microinjected into the macronucleus of the ciliated protozoan Paramecium can replicate as unit-length linear molecules. These linear DNA molecules are substrates for the addition of Paramecium telomeres by an endogenous telomerase. The linear DNA pieces can exist at copy numbers much higher than that of typical endogenous macronuclear chromosomes. We show that the copy number of injected DNA many fissions after microinjection reflects that of the original input copy number, suggesting that active control of copy number does not occur. Instead, the results suggest that injected DNA is replicated once per cell division.

Animals↗
PubMed2000

The use of oligonucleotide directed cleavage of DNA and homologous recombination in the production of large recombinant adenoviral vectors.

The genetic manipulation of large plasmid DNA often requires the fortuitous presence of convenient restriction enzyme sites. For large plasmids, such as those containing full length recombinant adenovirus, it is desirable to direct the cloning or sequence alterations without having to depend on such convenient restriction sites. We report a general and efficient method to modify or clone large covalently closed circular DNA molecules at any predetermined sequence. This procedure involves two main steps. First, supercoiled DNA is hybridized to a short pre-selected synthetic oligonucleotide to form a D-loop. This hybrid is then linearized in vitro at that target site by digestion with S1 nuclease. Second, D-loop/S1 linearized DNA is transformed into E. coli with a second linear DNA fragment carrying a foreign gene flanked by sequences homologous to the target site. In vivo recombination results in the desired recombinant construct. We demonstrate the use of this method by cloning the SV40 origin of replication into the E3 transcription unit of human adenovirus type 5.

Adenoviruses, Human↗
PubMed1993

Cloning, production and characterisation of wild type and mutant forms of the R.EcoK endonucleases.

The hsdR, hsdM and hsdS genes coding for R.EcoK restriction endonuclease, both with and without a temperature sensitive mutation (ts-1) in the hsdS gene, were cloned in pBR322 plasmid and introduced into E.coli C3-6. The presence of the hsdSts-1 mutation has no effect on the R-M phenotype of this construct in bacteria grown at 42 degrees C. However, DNA sequencing indicates that the mutation is still present on the pBR322-hsdts-1 operon. The putative temperature-sensitive endonuclease was purified from bacteria carrying this plasmid and the ability to cleave and methylate plasmid DNA was investigated. The mutant endonuclease was found to show temperature-sensitivity for restriction. Modification was dramatically reduced at both the permissive and non-permissive temperatures. The wild type enzyme was found to cleave circular DNA in a manner which strongly suggests that only one endonuclease molecule is required per cleavage event. Circular and linear DNA appear to be cleaved using different mechanisms, and cleavage of linear DNA may require a second endonuclease molecule. The subunit composition of the purified endonucleases was investigated and compared to the level of subunit production in minicells. There is no evidence that HsdR is prevented from assembling with HsdM and HsdSts-1 to produce the mutant endonuclease. The data also suggests that the level of HsdR subunit may be limiting within the cell. We suggest that an excess of HsdM and HsdS may produce the methylase in vivo and that assembly of the endonuclease may be dependent upon the prior production of this methylase.

Cloning, Molecular↗
PubMed1982

In vitro replication of bacteriophage phi 29 DNA.

We have been studying the mechanisms of linear DNA replication by using Bacillus bacteriophage phi 29 as a model system. To isolate and characterize the proteins required for phi 29 DNA replication, we have developed a cell-free replication system. A cell-free extract prepared from phi 29-infected Bacillus subtilis catalyzes the semiconservative replication of phi 29 DNA, but only if exogenous phi 29 DNA-protein complex is used as the template. This template consists of linear duplex DNA with a 30,000-dalton terminal protein attached covalently to both 5' ends. Replication starts nonsimultaneously at or near both ends of the template. The extract also catalyzes the specific binding between dATP and the phi 29 terminal protein. Thus, the in vitro system closely mimics the in vivo replication of phi 29 DNA. This system should allow characterization of the phi 29 DNA replication machinery.

Bacillus subtilis↗
PubMed1975

Circular DNA and rolling circles in nucleolar rDNA from mitotic nuclei of Physarum polycephalum.

1. About 15% of nucleolar DNA (1.712 g/cm3) from Physarum polycephalum displaying maximum hybridization to ribosomal RNA, is composed of circular DNA of 3.9 +/- 0.2 mum contour length or multiples thereof. 2. A portion of these circular molecules (25%) contained linear DNA pieces longer than circumference length. In a small fraction of circular DNA linear pieces, shorter than the unit length, were observed. 3. Most nucleolar DNA, [3H]thymidine-labeled or hybridizable to ribosomal RNA was separable from chromosomal DNA during G2 phase, mitosis and S phase of the cell cycle. 4. Ribosomal DNA content was not amplified during the cell cycle, was unchanged during exponential or stationary growth phase and amounted to about 0.11 -- 0.21% of nuclear DNA in diploid and hexaploid strains of Physarum or 100--200 ribosomal genes per diploid genome.

Cell Division↗
PubMed2003

Avian retrovirus integrase-enhanced transgene integration into mammalian cell DNA in vivo.

Systems for introducing DNA genes-of-interest into mammalian cellular genomes have ranged from the use of different physical techniques to viruses including retroviruses. We have developed a microinjection method for an efficient and permanent integration of a DNA transgene into the cell genome by use of the retrovirus integrase. A 3.0-kb linear DNA fragment containing an internal herpes simplex virus thymidine kinase gene (tk) with flanking avian retrovirus U5 and U3 terminal attachment sites (U5-pgk/tk-U3) recognized by the integrase was constructed. The other donor, a 3.3-kb linear DNA fragment containing the same gene (pgk/tk) flanked by ApaL1 restriction sites not recognized by integrase, was also produced. After assembly of integrase-transgene complexes on ice, the complexes were microinjected into the nucleus of human fibroblast cells (143Btk) containing a defective thymidine kinase. The number of hypoxanthine/aminopterin/thymidine (HAT)-resistant colonies produced upon microinjection of either naked DNA or the independently assembled integrase-transgene complexes were determined. Our data suggests that enhanced integration of U5-pgk/tk-U3 required the DNA attachment sites and co-delivery of integrase. The data was consistent with a direct role for both of these elements in producing an approximate 4-fold increase in the number of HAT-resistant colonies observed over microinjection of just naked U5-pgk/tk-U3 (P < 0.0001).

Animals↗
PubMed1990

Expression of a foreign KmR gene in linear killer DNA plasmids in yeast.

The killer plasmids of the yeast Kluyveromyces lactis, pGKL1 and 2 (k1 and k2 for short), are linear double-stranded DNAs. The expression of genes of these plasmids is thought to depend on their own transcription system. Cloning the plasmid genes in conventional circular vectors is therefore not suitable for transcriptional studies, because such vectors use the host nuclear transcription system. In vitro modification of the linear plasmid genomes in order to introduce transcription reporter genes has been difficult because the structure of the plasmids, with covalently bound terminal proteins, does not allow their manipulation in vitro and amplification in Escherichia coli. We introduced the kanamycin/G418 resistance gene, KmR, into the k1 plasmid in vivo, by transforming the yeast with the linearized KmR gene bordered with short k1 sequences (part of the region encoding the toxin) to allow homologous recombination with the resident k1. In the linear recombinants obtained, however, the KmR was not expressed, while it was expressed if carried on circularized plasmids. By replacing the native promoter of KmR by the ORF1 promoter from k1, the KmR gene could be expressed in linear recombinants and conferred on the host a high level of resistance to the drug. All the linear recombinant plasmids were extremely stable under nonselective conditions. As a rare event, the integration of KmR produced a palindromic rearrangement of the k1 plasmid.

DNA, Fungal↗
PubMed1994

Phosphorylation of the C-terminal domain of yeast topoisomerase II by casein kinase II affects DNA-protein interaction.

Eukaryotic DNA topoisomerase II is an abundant nuclear enzyme that is essential for cell proliferation. This homodimeric enzyme catalyzes the cleavage and re-ligation of double-stranded DNA required to separate replicated sister chromatids. Both biochemical and genetic studies show that its catalytic activity is required for chromosome condensation and segregation, and that its decatenation activity can be stimulated by a variety of protein kinases in vitro. In budding yeast, topoisomerase II is most highly phosphorylated in metaphase, and casein kinase II (CKII) was shown to be the major kinase modifying topoisomerase II. We have investigated the effects of phosphorylation of yeast topoisomerase II by CKII in vitro, by means of gel-retardation and filter binding assays. The phosphorylation of the C terminus of topoisomerase II by CKII appears to increase the stability of the complex formed with linear DNA fragments, while dephosphorylation has the opposite effect. Rephosphorylation of phosphatase-treated topoisomerase II by chicken casein kinase II restores a stable protein-DNA complex using a linear DNA fragment. The enhanced stability of the topoisomerase II-DNA complex is also observed with relaxed circular DNA, but not with supercoiled minicircles, in agreement with published results using topoisomerase II from Drosophila. Limited proteolysis and probing with domain-specific antibodies shows that, with the exception of a weakly modified residue between amino acid residues 660 and 1250, all residues modified by casein kinase II are in the last 180 amino acid residues of yeast topoisomerase II.

Binding Sites↗