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At least 793 records · Page 44Linked to original sources
PubMed1983

DNA structure, and hemagglutination properties of bovine adenovirus type 2 strains which bypass species specificity.

Bovine adenovirus type 2 (Ad bos 2) strains were examined which had been isolated during natural outbreaks among calves, and lambs in Hungary [Belák, S., Pálfi, V.: Arch. ges. Virusforsch. 46,366-369 (1974)]. Differences were detected in hemagglutination properties, and in the restriction site maps of the DNA, which seem to be sufficient to group isolates of Ad bos 2 into two subtypes (subspecies). Some of the strains, recovered from cattle including prototype strain No. 19 are suggested to be separated as subtype A. These viruses hemagglutinate bovine red blood cells, and the physical map of the DNA is similar to, or identical with that of the prototype strain. Virus strains tentatively grouped into subtype B are pathogenic for both cattle, and sheep under natural conditions. Members of subtype B hemagglutinate only rat erythrocytes, and characteristic differences may be detected with BamHI, EcoRI, KpnI, and SalI restriction endonucleases in comparison to the physical maps of the DNA of prototype virus. The genome size of all isolates tested was measured to be of Mr 19.5 to 20.0 X 10(6), similar to Ad ovi 1, 4, and Ad bos 4, and 6. All isolates of subtype B characteristics were shown to encapsidate heterogeneous genome populations which could be distinguished from those of subtype A by the presence of specific restriction endonuclease cleavage fragments with molar ratios of less than 1.0.

Adenoviridae↗
PubMed2005

Fractal nature of chromatin organization in interphase chicken erythrocyte nuclei: DNA structure exhibits biphasic fractal properties.

Arrangement of chromatin in intact chicken erythrocyte nuclei was investigated by small angle neutron scattering. The scattering spectra have revealed that on the scales between 15 nm and 1.5 microm the interior of the nucleus exhibited properties of a mass fractal. The fractal dimension of the protein component of cell nucleus held constant at approximately 2.5, while the DNA organization was biphasic, with the fractal dimension slightly higher than 2 on the scales smaller than 300 nm and approaching 3 on the larger scales.

Animals↗
PubMed2002

Substrate specificity of RusA resolvase reveals the DNA structures targeted by RuvAB and RecG in vivo.

RusA endonuclease cleaves Holliday junctions by introducing paired strand incisions 5' to CC dinucleotides. Coordinated catalysis is achieved when both subunits of the homodimer interact simultaneously with cleavage sites located symmetrically. This requirement confers Holliday junction specificity. Uncoupled catalysis occurs when binding interactions are disturbed. Genetic studies indicate that uncoupling occurs rarely in vivo, and DNA cleavage is therefore restricted to Holliday junctions. We exploited the specificity of RusA to identify the DNA substrates targeted by the RuvAB and RecG branch-migration proteins in vivo. We present evidence that replication restart in UV-irradiated cells relies on the processing of stalled replication forks by RecG helicase and of Holliday junctions by the RuvABC resolvasome, and that RuvAB alone may not promote repair.

Bacterial Proteins↗
PubMed1991

Polymorphism in N-2-acetylaminofluorene induced DNA structure as revealed by DNase I footprinting.

In this paper, we have constructed double stranded helices (60-mers) containing a single N-2-acetylaminofluorene (-AAF) adduct covalently bound to one of the three guanine residues of the Narl site (G1G2CG3CC). This sequence was identified as a strong frameshift mutation hot spot for many carcinogens that bind to the C8 position of guanine. Using DNase I as a probe for DNA conformation we show i) that the average size of the helix deformation extends over 3 to 5 base pairs in both directions from the adduct site, and ii) that there is a strong polymorphism in the adduct induced DNA conformation. The present study supports the idea that adducts induce specific sequence dependent local conformational changes in DNA that are differentially recognized and processed by the enzymatic machineries that lead to repair or mutagenesis.

2-Acetylaminofluorene↗
PubMed2006

Specific interactions with intra- and intermolecular G-quadruplex DNA structures by hydrosoluble coronene derivatives: a new class of telomerase inhibitors.

In developing G-quadruplex interactive telomerase inhibitors two main features have to be taken into account: the hydrophobic interactions with the G-quartet plane and the electrostatic interactions with the negatively charged phosphates of the four grooves. In this paper, we report the synthesis of four hydrosoluble coronene derivatives, which are characterized by a large hydrophobic aromatic core and four orthogonal hydrophilic side chains. We have studied their ability to induce both inter- and intramolecular G-quadruplex structures and found a significant selectivity of all the coronene derivatives for the intramolecular G-quadruplex. The efficiency in inhibiting human telomerase has been evaluated in a cell-free system and the experimental results correlate with the relative affinities of these compounds for the G-quadruplex monomeric structure, as derived by molecular modelling simulations. Thus, the coronene derivatives can be considered as a new class of telomerase inhibitors, although further investigations are surely necessary to fully exploit their features.

Cell-Free System↗
PubMed1989

5-azacytidine-induced alterations in the GH12C1 cells: effects on cellular morphology, chromosome structure, DNA and protein synthesis.

Growth hormone-producing rat pituitary tumor cells (GH12C1) were cultivated in the presence of 5-azacytidine (5-AC). After cessation of treatment the cells were allowed to recover in normal cell culture medium prior to subcultivation. Within hours after the subcultivation the cells underwent several morphological alterations, later followed by changes in growth pattern: (1) cell shape was irreversibly changed from round or spindle shape to different clones of fibroblast-like cells; (2) some of these clones later formed foci; and (3) an extensive generation of multinucleated cells was seen. The demethylation was maximal approximately one week after the first subcultivation in the absence of 5-AC. Severe alterations of the chromosome structure were seen after the first subcultivation. During the following weeks the 5-AC-treated cells showed impaired chromosome condensation, and homogeneous staining with quinacrine mustard. During this period the DNA synthesis is doubled when compared to control cell DNA synthesis. The core histone synthesis increases in parallel with the DNA synthesis, but the majority of nuclear proteins, including the linker histones, remain at the control level. This results in a ratio of linker histone to core histone synthesis at approximately half the control cell level. The altered ratio of synthesis slowly decreased to control levels during a period of five weeks of continuous cultivation in the absence of the drug, and the under-condensed chromosomes could no longer be seen. The induced novel phenotypes with their pleiomorphic appearances were conserved. The growth hormone synthesis remained constant during all phases of the experiment and prolactin synthesis was not induced.

Animals↗
PubMed1998

Submillimolar levels of calcium regulates DNA structure at the dinucleotide repeat (TG/AC)n.

Submillimolar levels of calcium, similar to the physiological total (bound + free) intranuclear concentration (0.01-1 mM), induced a conformational change within d(TG/AC)n, one of the frequent dinucleotide repeats of the mammalian genome. This change is calcium-specific, because no other tested cation induced it and it was detected as a concentration-dependent transition from B- to a non-B-DNA conformation expanding from 3' end toward the 5' of the repeat. Genomic footprinting of various rat brain regions revealed the existence of similar non-B-DNA conformation within a d(TG/AC)28 repeat of the endogenous enkephalin gene only in enkephalin-expressing caudate nucleus and not in the nonexpressing thalamus. Binding assays demonstrated that DNA could bind calcium and can compete with calmodulin for calcium.

Animals↗
PubMedDate not supplied

[Mechanism of the radiation damage to the secondary structure of DNA].

The authors describe the mechanism of radiation-induced damage of a secondary DNA structure suggesting that a double-helical brim conformation adjacent to a local defect in the secondary structure, and the thermoactivated threshold process of a "confluence" of the defects are present in the irradiated DNA. It is supposed that the major type of the radiation damage to the spatial DNA structure is a triple helix repaired with the aid of the specific endonuclease.

DNA↗
PubMed2004

Activation of transcription initiation from a stable RNA promoter by a Fis protein-mediated DNA structural transmission mechanism.

The leuV operon of Escherichia coli encodes three of the four genes for the tRNA1Leu isoacceptors. Transcription from this and other stable RNA promoters is known to be affected by a cis-acting UP element and by Fis protein interactions with the carboxyl-terminal domain of the alpha-subunits of RNA polymerase. In this report, we suggest that transcription from the leuV promoter also is activated by a Fis-mediated, DNA supercoiling-dependent mechanism similar to the IHF-mediated mechanism described previously for the ilvP(G) promoter (S. D. Sheridan et al., 1998, J Biol Chem 273: 21298-21308). We present evidence that Fis binding results in the translocation of superhelical energy from the promoter-distal portion of a supercoiling-induced DNA duplex destabilized (SIDD) region to the promoter-proximal portion of the leuV promoter that is unwound within the open complex. A mutant Fis protein, which is defective in contacting the carboxyl-terminal domain of the alpha-subunits of RNA polymerase, remains competent for stimulating open complex formation, suggesting that this DNA supercoiling-dependent component of Fis-mediated activation occurs in the absence of specific protein interactions between Fis and RNA polymerase. Fis-mediated translocation of superhelical energy from upstream binding sites to the promoter region may be a general feature of Fis-mediated activation of transcription at stable RNA promoters, which often contain A+T-rich upstream sequences.

Base Sequence↗
PubMed1982

[Early changes in template DNA structure following glucocorticoid injection].

The structure of chromatin is changed at early stages of glucocorticoid hormone interaction with rat hepatocytes. These changes consist in: a) increase of actidine orange binding in rate liver nuclei after injection of the hormone; b) decrease of the number of sites in chromatin which are sensitive to nuclease S1; c) inhibition of the nuclei capacity for DNA synthesis in the presence of E. coli DNA polymerase and d) increase of molecular weight of DNA fragments. The data obtained suggest that at early stages of hormonal induction part of template DNA ruptures is reconstituted, which can result in an increase of DNA molecular weights and changes in chromatin superstructure and the template properties of the protein.

Animals↗
PubMed2002

Determination of DNA structure in solution: enzymatic deuteration of the ribose 2' carbon.

An enzymatic solution to the problem of obtaining 13C/15N-labeled nucleotides that are deuterated uniquely at the H2' ' position within the ribose ring is presented. Selective deuteration occurs with an overall yield of >80%. The deuteron at the H2' ' position allows measurement of the scalar and residual dipolar couplings for the bond vectors attached to the C2' carbon of each ribose sugar. These data allow the accurate determination of sugar conformation. Interesting DNA double helices of 2-3 turns are now within the reach of solution NMR spectroscopy. As an example, these labeled nucleotides are incorporated uniquely at positions 6-14 in a 20-bp DNA sequence containing the adenovirus major late promoter.

Carbon Isotopes↗
PubMed1998

[Molecular genetic analysis of DNA structure of pFra plasmids in plague pathogen of varying biovar].

Data on comparative molecular genetic analysis of pFra plasmids from plague bacillus belonging to either two biovars (antiqua and orientalis) are presented. It was established that during evolution these replicons were rearranged, which resulted in the differences between pFra plasmids of plague bacillus of antiqua biovar (Yersinia pestis 231 and Y. pestis 358/12) and that of orientalis biovar (Y. pestis A1122 and Y. pestis EV). These included inversions of two plasmid DNA regions and size differences of 3 kb.

Evolution, Molecular↗
PubMed1988

Conformational effects of histones H1 on DNA structure. Comparative study between H1-1, H1(0), H5 and sperm holothuria phi 0.

Interactions of mammalian histones, H1-1 and H1(0), phi 0 from holothuria sperm and H5 with poly(dA-dT), poly(dG-dC) and poly(dG-me5dC) were measured by a nitrocellulose filter binding assay and circular dichroism. All of the proteins bound to every one of the polymers, but differed in the extent of binding, which depended on the polynucleotide/protein ratios and ionic strength. The order of retention of all polymers was phi 0 greater than H1-1 greater than H1(0). The binding of H1(0) to poly(dG-me5dC) was remarkably sensitive to ionic strength. The proteins caused changes in the spectral features of the polynucleotides, but differed in the type and extent of the change. Complexes prepared with H1-1 and H1(0) with all polymers showed a strongly negative psi spectrum. Complexes of poly(dA-dT) and phi 0, at a protein/polynucleotide ratio of 0.4, displayed a distinctive spectrum, giving the appearance of a Z-like DNA spectrum, at low ionic strength. At higher ionic strength the complexes showed a psi spectrum. Complexes of poly(dG-me5dC) in the Z or B conformation with phi 0 showed spectral features characteristic of a mixture of a Z-like and a psi spectrum. In contrast, H5 reduced the Z-DNA spectral features in the presence of Mg, and produced an inversion of the B spectrum up to a polynucleotide/protein ratio of 0.24. These findings demonstrate the ability of different proteins to produce changes in the conformation of DNA. This may reflect the ability of chromatin to undergo differential condensation, depending on both the base composition of DNA and the type of H1 histone bound to it.

Animals↗
PubMed1987

Circular intensity differential scattering and chromatin-DNA structure. A combined theoretical approach.

Circular intensity differential scattering (CIDS) has been proven a powerful method in determining the higher-order structure of large biopolymers, such as chromatin. Theoretical predictions of the expected differential light scattering of circularly polarized light have previously been made for chromatin, either within the Born approximation, treating nucleosomes as noninteracting, oblate ellipsoids, or within a multiple dipole approximation, treating nucleosomes as interacting spheres. In order to conduct a meaningful interpretation of the CIDS signal in terms of given geometric parameters of the chiral structure, we have in this paper combined the two approaches considering the mutual interactions of ellipsoidal nucleosomes. In the process we have also found a confirmation for the validity of the Born approximation itself.

Chromatin↗
PubMed2006

Double cohesion in structural DNA nanotechnology.

Double cohesion has proved to be a useful tool to assemble robust 2D arrays of large tiles. Here we present a variety of examples showing the utility of this approach. We apply this principle to the 3 types of 2D lattice sections of arrays whose individual tiles are inherently 3 dimensional, because they contain three vectors that span 3-space. This application includes motifs which are based on the tensegrity triangle, the six-helix bundle motif and on three skewed triple crossover molecules. All of these designs have the potential to form 3 dimensional structures if all three directions of propagation are allowed. If one direction is blunted, 2D arrays form, and all 3 combinations are presented here. In addition, a large parallelogram array that was not attainable previously using single duplex cohesion was also constructed using double cohesion. For comparison, arrays which use another type of double cohesion, double paranemic (PX) cohesion are also presented. Double cohesion of sticky ends proved to be the more effective tool to assemble large motifs into arrays.

DNA↗