Structure of the interaction sites of eukaryotic DNA with steroid hormone-apolipoprotein A-I complexes

A high affinity of apolipoprotein A-I for DNA and synthetic oligonucleotides was found using the affinity chromatography, affinity modification, and enzyme analysis. The competitive inhibition and Southern hybridization allowed disclosing the specificity of the interaction of the tetrahydrocortisol-apolipoprotein A-I complex (THC-ApoA-I) with high molecular weight DNA in regions contained GCC/CGG-sequences. The S1 nuclease sensitivity of the duplex CC(GCC)3 x GG(CGG)3 was found to occur under the action of THC-ApoA-I complex. The role of the interaction sites of eukaryotic DNA with steroid (THC, androsterone)-ApoA-I complexes in the initiation of the copy reaction in vitro was revealed.     

Characteristics of the interactions of cortisol-apolipoprotein A-I and tetrahydrocortisol-apolipoprotein A-I complexes with eukaryotic DNA

Primary hepatocyte culture has been used to demonstrate that the cortisol-apolipoprotein A-I complex does not affect the DNA and protein biosynthesis rates, whereas the tetrahydrocortisol-apolipoprotein A-I complex (THC-apoA-I) substantially increases the rates of ³H-thymidine and ¹⁴C-leucine incorporation into DNA and protein, respectively. Small-angle X-ray scattering data show that only THC-apoA-I effectively interacts with eukaryotic DNA, which is accompanied by local DNA melting. The (GCC)_n repeat, a component of many human and other eukaryotic genes, is the most probable region of the interaction of this complex with DNA. An oligonucleotide (duplex) of this type has been synthesized. Its interaction with THC-apoA-I yields a larger complex, which breaks up, giving rise to complementary oligonucleotide strands. They also interact with THC-apoA-I. The equilibrium kinetics of this multiphase process is described. The interaction of the cortisol-apolipoprotein A-I complex with the duplex is less specific and does not cause its breakup or the formation of complementary oligonucleotides.     

Mechanisms of interaction of tetrahydrocortisol and its complex with apolipoprotein A-I and DNA regulatory cis-elements of CC(GCC)5/GG(CGG)5 type

An IR-spectroscopy study of the mechanism of interaction between duplex CC(GCC)5/GG (CGG)5Li2 and tetrahydrocortisol or tetrahydrocortisol-apolipoprotein A-I complex revealed the formation of hydrogen bonds between the OH group of the tetrahydrocortisol A-ring and the C=0 group of cytosine or guanine. Tetrahydrocortisol forms hydrogen bonds with the PO2-group of the duplex and with the OH-group of monosaccharide. The interaction of tetrahydrocortisol and apolipoprotein A-I with the duplex occurs at the same active site, namely, with the C=O-group of bases. The order --> order structural transition takes place in the duplex under the action of tetrahydrocortisol. The order --> disorder structural transition takes place in the duplex under the action of tetrahydrocortisol-apolipoprotein A-I complex.     

Features of interaction of complexes cortisol-apolipoprotein A-I and tetrahydrocortisol-apolipoprotein A-I with eukariotic DNA

On primary culture of hepatocytes it is shown, that a complex cortisol-apolipoprotein A-I did not change rate of biosynthesis DNA and protein, whereas the complex tetrahydrocortisol-apolipoprotein A-I (THC-apoA-I) essentially raised rate of incorporation 3H-thymidine in DNA and 14C-leucine into protein. By a method of small-angle X-ray scattering it is shown, that appreciable interaction with eukariotic DNA is marked only in case of use of a complex THC-apoA-I, thus there is local fusion of DNA. The most probable region of interaction of the given complex with DNA is repetition (GCC)n the type, included in structure of many genes eukariot, including the human. It is synthesized oligonucleotid (duplex) of this type. It is shown, that at his interaction with complex THC-apoA-I there is a formation of more difficult complex, which breaks up with formation of complementary chains of oligonucleotides. The last also enter interaction with complex THC-apoA-I. It is given of kinetic this multiphasic process. Interaction of a complex cortisol-anoA-I with a duplex is less specific and does not result reduce in decay of the duplex and in formation of complementary oligonucleotides.     

Effect of tetrahydrocortisol-apolipoprotein A-I complex on RNA polymerase interaction with eukaryotic DNA and the rate of protein biosynthesis in hepatocytes

A mechanism of activation of protein biosynthesis in hepatocytes was proposed as effected by the conditioned medium of nonparenchymal liver cells incubated in the presence of high density lypoproteins, cortisol, and lypopolysaccharides. It was found that the increase in the biosynthesis rate was associated with the formation of the tetrahydrocortisol-apolipoprotein A-I (THC-apoA-I) complex in macrophages, which display 5 alpha- and 5 beta-reductase activity and are constituents of nonparenchymal liver hepatocytes. Using the small-angle X-ray scattering technique, it was shown that the THC-apoA-I-eukaryotic DNA interaction may break hydrogen bonds between pairs of complementary nucleic bases and cause the formation of single-stranded DNA fragments capable of binding to DNA-dependent RNA polymerase. The interaction is highly cooperative and has a saturating mode, up to six enzyme molecules being bound per DNA molecule.     

Tetrahydrocortisol-apolipoprotein A-I complex specifically interacts with eukaryotic DNA and GCC elements of genes

Tetrahydrocortisol stimulates DNA and protein biosynthesis in hepatocytes only when it enters the complex with apolipoprotein A-I. Tetrahydrocortisol–apolipoprotein A-I (THC–apoA-I) complex specifically interacts with eukaryotic DNA isolated from rat liver. In the process of interaction, rupture of hydrogen bonds between the pairs of nitrous bases occurs with the formation of single-stranded DNA structures. In such state DNA forms complexes with DNA-dependent RNA-polymerase. The most probable site of binding the tetrahydrocortisol–apolipoprotein A-I complex with DNA is the sequence of CC(GCC)_n type entering the structure of many genes, among them the structure of human apolipoprotein A-I gene. Oligonucleotide of this type has been synthesized. Association constant (K_ass) of it with tetrahydrocortisol–apolipoprotein A-I complex was shown to be 1.66×10⁶ M⁻¹. Substitution of tetrahydrocortisol for cortisol in the complex results in a considerable decrease of K_ass. It was assumed that in the GC-pairs of the given sequence tetrahydrocortisol itself participates in the formation of hydrogen bonds with cytosine, favoring their rupture with complementary base—guanine.     

Heliomycin suppression of RNA synthesis in a cell-free system]

Heliomycin inhibited in vitro the RNA-polymerase reaction catalyzed by the preparation of DNA-dependent RNA-polymerase from E. coli. The blocking effect increased with a rise in the antibiotic concentration. The inhibitory effect of heliomycin decreased, when the amount of RNA-polymerase in the system increased. Yet, it did not depend on the content of DNA and the nature of the DNA preparation. Preincubation of RNA-polymerase with DNA resulting in formation of the enzyme-matrix complex did not prevent blocking RNA synthesis by heliomycin. Suppression of the RNA-polymerase reaction did not depend on the time of the antibiotic addition to the polymerizing system. Heliomycin had a significant activity not only with respect to the bacterial RNA-polymerase, but also in the system containing the enzyme isolated from the cells of Crithidia oncopelti.     

Specific modification of DNA at E. coli RNA-polymerase binding sites

Specific modification of promoter regions of DNA has been studied. Plasmid pK56B1 DNA has been used as a model to test RNA-polymerase binding with DNA under various conditions. RNA-polymerase is shown to form specific complexes with DNA which are stable in solutions with a moderate ionic strength (0.1-0.2 M NaCl), under pH 5-8 in the presence of 0.5 M O-methylhydroxylamine of O-delta-aminooxybutylhydroxylamine. Escherichia coli JM103 cells have been transfected with DNAs treated with 0.5 M O-methylhydroxylamine at 37 degrees C, pH 5.2. The inactivation effects of the mutagen on single-stranded DNA of bacteriophage M13 m p1, double-stranded form of this bacteriophage (replicative form-RF) and on the complex of RNA-polymerase with RF DNA have been compared. The obtained data confirmed the specificity of reagent action with DNA sites binding with the enzyme. Selectivity of promoters modification has been confirmed also by the analysis of M13 m p1 DNA mutations induced in lacZ' gene by delta-aminooxybutylhydroxylamine effect on the DNA complex with DNA-polymerase.     

Interaction of Ag+ ions with DNA and its monomers

Differential UV spectra of DNA and its monomers that were induced by Ag+ ions were measured, and the effect of ions on the parameters of the helix-coil transition was studied. The data obtained confirm the existence of "strong" and "weak" modes of binding of Ag+ to DNA. The earlier proposed proton transfer from N1G to N3C, which is determined by the interaction of Ag+ with N7G (a "strong" complex), follows immediately from the shape of the differential UV spectra. The positive cooperativity of the binding of Ag+ to DNA upon the formation of a "weak" complex is due to the cooperativity of the transition of DNA to a new double-helical conformation. A model of this conformation is proposed which suggests the formation of Hougsteen GC and AT pairs.     

Anthracycline antibiotic, beromycin. The formation of complexes with DNA and the suppresion of nucleic acid biosynthesis]

Beromycin, an antitumor anthracycline antibiotic formed in vitro complexes with native and denaturated DNA and ribosomal RNA. Beromycin had a comparatively low constant of DNA binding and to a less extent increased the melting temperature and viscosity of DNA than the other anthracycline antibiotics. A peculiar property of beromycin was very slow binding with DNA, the complex formation was completed in 60 minutes. Beromycin had a selective inhibitory effect on synthesis of nucleic acids in bacterial and tumor cells. Beromycin inhibited synthesis of RNA in the DNA-dependent RNA-polymerase reaction when both the native and denaturated DNA were used as the template. A lower biological activity of beromycin as compared to the other anthracycline antibiotics, such as rubomycin or carminomycin may be explained by lower affinity of this antibiotic to DNA.     

The DNA-dependent RNA-polymerase of Thermotoga maritima; characterisation of the enzyme and the DNA-sequence of the genes for the large subunits.

An improved purification procedure for Thermotoga maritima RNA-polymerase holoenzyme was developed. The enzyme is highly active with poly dAT or T7 phage DNA as template. DNA gyrase was found to be a side product of this RNA-polymerase purification. The genes for the large subunits beta and beta' of RNA-polymerase were cloned and sequenced. The phylogenetic position of T.maritima within the bacterial domain was determined by various methods. It is the lowest bacterial offspring but slightly higher than the chloroplasts.     

Effect of etimizol on the RNA synthesizing activity of brain cell nuclei during the learning process in rats

A study was made of the effect of the central nervous system stimulant ethymizol on RNA-polymerase activity of cell nuclei of the rat cerebral cortex and hippocampus during learning with different reinforcements. Ethymizol stimulated the incorporation of 3H-UTP in the TCA-insoluble fraction of hippocampal nuclei during training of the animals in the avoidance response to the light in a Y-shaped mize and training in the reaction of spontaneous alternation of food reinforcements in a complex mize, and decreased the ratio brain cortex/hippocampus RNA-polymerase activity. The data obtained are discussed from the standpoint that the action of ethymizol is consequent on the activation of the genome of nervous cells.     

The Escherichia coli PriA Helicase-Double-Stranded DNA Complex: Location of the Strong DNA-Binding Subsite on the Helicase Domain of the Protein and the Affinity Control by the Two Nucleotide-Binding Sites of the Enzyme

The Escherichia coli PriA helicase complex with the double-stranded DNA (dsDNA), the location of the strong DNA-binding subsite, and the effect of the nucleotide cofactors, bound to the strong and weak nucleotide-binding site of the enzyme on the dsDNA affinity, have been analyzed using the fluorescence titration, analytical ultracentrifugation, and photo-cross-linking techniques. The total site size of the PriA-dsDNA complex is only 5 ± 1 bp, that is, dramatically lower than 20 ± 3 nucleotides occluded in the enzyme-single-stranded DNA (ssDNA) complex. The helicase associates with the dsDNA using its strong ssDNA-binding subsite in an orientation very different from the complex with the ssDNA. The strong DNA-binding subsite of the enzyme is located on the helicase domain of the PriA protein. The dsDNA intrinsic affinity is considerably higher than the ssDNA affinity and the binding process is accompanied by a significant positive cooperativity. Association of cofactors with strong and weak nucleotide-binding sites of the protein profoundly affects the intrinsic affinity and the cooperativity, without affecting the stoichiometry. ATP analog binding to either site diminishes the intrinsic affinity but preserves the cooperativity. ADP binding to the strong site leads to a dramatic increase of the cooperativity and only slightly affects the affinity, while saturation of both sites with ADP strongly increases the affinity and eliminates the cooperativity. Thus, the coordinated action of both nucleotide-binding sites on the PriA-dsDNA interactions depends on the structure of the phosphate group. The significance of these results for the enzyme activities in recognizing primosome assembly sites or the ssDNA gaps is discussed.     

Properties of the rat liver DNA-dependent RNA-polymerase stored at -25 degrees C in the presence of glycerol or polyethyleneglycol-400

The effect of slow freezing (1-2 degrees C/min) was studied as applied to the template activity of DNA in the RNA-polymerase reaction. It was found out that the activity of each RNA-polymerase form decreases after 24-hour storage by freezing at -25 degrees C in the presence of glycol or polyethylene glycol-400. The study of the enzyme in the glycerol concentration gradient showed sedimentation constant changes.     

Photocleavage of DNA and photofootprinting of E. coli RNA polymerase bound to promoter DNA by azido-9-acridinylamines.

The long-wavelength ultraviolet (lambda approximately 420 nm) radiation induced reaction between 6-azido-2-methoxy-9-acridinylamines and supercoiled plasmid DNA results in single strand scissions and formation of covalent adducts (ratio approximately 1:10). By treating azidoacridine-photomodified DNA with piperidine at 90 degrees C, additional strand scissions are observed in a complex sequence dependent manner with an overall preference for T greater than or equal to G greater than C much greater than A. The resulting DNA fragments migrate as 5'-phosphates in polyacrylamide gels. Photofootprinting of the binding site of RNA-polymerase on promoter DNA is demonstrated with an azido-9-acridinylamino-octamethylene-9-aminoacridine. Similar experiments using 9-amino-6-azido-2-methoxyacridine indicate that this reagent recognizes changes in the DNA conformation induced by RNA polymerase binding, in relation to open complex formation.     

Role of the functional groups of the sibiromycin molecule in DNA binding]

Biological activity of 2 derivatives of sibiromycin, an antibiotic close by its chemical structure to antramycin and their capacity for formation of complexes with DNA was studied. Anhydrosibiromycin like sibiromycin formed a complex with DNA. The antibiotic increased the DNA melting point but to a less extent than sibiromycin. Anhydrosibiromycin had a low activity in the system of DNA-dependent RNA-polymerase. The low biological activity of anhydrosibiromycin must be due to instability of the antibiotic complex with DNA. Methyl ether of sibiromycin by the phenol hydroxyl, the other derivative of sibiromycin had no biological activity and did not interact with DNA. On the basis of experimental data it was suggested that definite functional groups of the sibiromycin participated in DNA binding.     

Effect of vitamin E on transcription in isolated nuclei and rat liver chromatin in normal status and in E-hypovitaminosis]

The effect of alpha-tocopherol on the RNA-polymerase activity in isolated rat nuclei and chromatin from normal and E-deficient rats and the possible role of tocopherol-binding proteins in this process were studied. Some differences in the RNA-polymerase activities of the nuclei were found; however, in vitro added alpha-tocopherol had no effect on the level of the label incorporation into RNA. No effect of alpha-tocopherol on this process was observed after addition of cytosol either. Analysis of chromatins from normal and E-deficient rats revealed no differences in their RNA-polymerase activities. In vitro added alpha-tocopherol increased the RNA-polymerase activity of normal (but not of vitamin E-deficient) rats. Some differences in the RNA-polymerase activities were noted after addition to the incubation medium of the Triton X-100-solubilized nuclear fraction specifically binding alpha-tocopherol. This effect was enhanced in the presence of exogenous alpha-tocopherol. The susceptibility of chromatin from normal and E-deficient rats to DNAse I hydrolysis was also found to be different. It was concluded that vitamin E can influence the RNA-polymerase activity of the nuclei and chromatin as well as the chromatin structure and that alpha-tocopherol-binding proteins are necessary for the vitamin E effect on the RNA-polymerase activity to be manifested.