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PubMedDate not supplied

[Energetics of hydration of nucleic acids with various nucleotide composition].

The energetics of hydration of natural DNA of different AT/GC content and model double-helical polyribonucleotides was studied. The results obtained by a new approach, which is based on calorimetric measurements of hydration-dehydration energy of nucleic acid-water systems at different relative humidities are presented. A correlation between the dehydration energy and the nucleotide composition of native DNA was found. The energetic characteristics of systems containing deoxynucleoside monophosphates and water clusters of different dimensions were obtained by the Monte Carlo method. The results of computer simulation correlate with the experimental calorimetric data.

Calorimetry↗
PubMed1976

Polyadenylic acid content and electrophoretic behavior of in vitro released RNA's in chemical carcinogenesis.

Cytoplasmic RNA from control and thioacetamide-intoxicated rat livers was compared with regard to components separated by polyacrylamide electrophoresis and for the proportion containing polyadenylic acid segments. A further comparison was made with the RNA's released from rat liver nuclei in vitro. Exposure in vivo to thioacetamide was associated with more cytoplasmic RNA's with migrations of 9 to 16 S and with both an acute and prolonged increase in the relative quantity of polyadenylic acid-containing polyribonucleotides. Incubation of control nuclei in vitro was associated with a leakage of approximately 1 to 2% of nuclear RNA with a major migration band at 9 S. Addition of adenosine 5'-triphosphate increased the transport 20-fold, and 9 and 16 S species were transported as well as a 4 S group. Following exposure to thioacetamide, an enhanced "leakiness" released 9 S RNA. Addition of adenosine 5'-triphosphate doubled the quantity of released RNA, which consisted of 9 and 4 S species. Both leaked and adenosine 5'-triphosphate-transported RNA's contained polyadenylic acid segments in roughly 20% of the macromolecules. These studies extend the observation of less stringent control of RNA release and transport in carcinogen exposure and suggest the potential usefulness of the in vitro release system for assaying cellular regulatory phenomena.

Acetamides↗
PubMedDate not supplied

[RNA world and its evolution].

The early idea of A. N. Belozersky on the precedence of RNA in the origin of life on Earth is developed. Basing on the present knowledge of functional omnipotence of RNA, the author considers three novel mechanisms that could play a critical role in the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, discovered by A.B. Chetverin, which could result in elongation of primary short oligoribonucleotides and generation of sequence variants for subsequent selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist solid surfaces, in the absence of membranes and any other coats; (3) systematic exponential enrichment of RNA population in functionally "the best" molecules by means of alternately dissolving the colonies upon flooding and forming new ones upon drying a pool ("primordial natural SELEX").

Esterification↗
PubMed1990

[Interaction of hormone-receptor complexes of triiodothyronine with DNA and RNA].

Some parameters of triiodothyronine hormone-receptor complexes (HRC) interactions with DNA-cellulose were studied. The competition between DNA and polyribonucleotides for HRC was demonstrated. It was found that in a model system of RNA transport HRC stimulate the 3H-RNA liberation from the nuclei. The functional significance of HRC-RNA interactions is discussed.

Animals↗
PubMed1975

A novel oligoribonuclease of Escherichia coli. II. Mechanism of action.

Detailed studies of the mechanism of action of the novel oligoribonuclease of Escherichia coli described in the previous paper (1) led to the following conclusions. 1. The enzyme prefers a free 3'-hydroxyl group for its action. 2. The enzyme attacks the oligoribonucleotide substrate in a sequential manner from the 3' end producing 5'-ribonucleotides. 3. The mode of attack appears to be processive; the enzyme acts by degrading one oligoribonucleotide chain to completion before proceeding to the hydrolysis of another chain. 4. The reaction rate is inversely proportional to the chain length of the substrate; however, the enzyme has a higher affinity for longer chains. 5. The enzyme activity is markedly inhibited by secondary structure; oligoribonucleotides combined with complementary polyribonucleotides are attacked poorly below the melting temperature of the complex and efficiently above the melting temperature. 6. The enzyme is inhibited by 5'-nucleotides of adenine and guanine; those of cytosine and uracil have a much smaller effect. The enzyme is not inhibited by 3'-nucleotides. 7. Studies with dinucleoside monophosphate show highest reaction rates with pyrimidine sequences in the order: CpCgreater than UpUgreater than CpUgreater than UpC. The presence of guanine at the 3' end is strongly inhibitory, and reaction rates are CpGgreater than UpG=ApGgreater than GpG.

Base Sequence↗
PubMedDate not supplied

Phospholipid-nucleic acid recognition: energetics of DNA-Mg2+-phosphatidylcholine ternary complex formation and its further compaction as a gene delivery formulation.

Thermodynamic features related to the preparation and use of self-assemblies formed between multilamellar and unilamellar zwitterionic liposomes and polynucleotides with various conformation and sizes are presented. The divalent metal cation-induced adsorption, aggregation, and adhesion between single- and double-stranded polyribonucleotides and phosphatidylcholine vesicles was followed by differential adiabatic scanning microcalorimetry. Nucleic acid condensation and compaction mediated by Mg2+ was followed, with regard to interfacial interaction with unilamellar vesicles. Microcalorimetric measurements of synthetic phospholipid vesicles and poly(ribo)nucleotides and their ternary complexes with inorganic cations were used to build the thermodynamic model of their structural transitions. The increased thermal stability of the phospholipid bilayers is achieved by affecting their melting transition temperature by nucleic acid-induced electrostatic charge screening. Measurements give evidence for the stabilization of polynucleotide helices upon their association with liposomes in the presence of divalent metal cations. Such an induced aggregation of vesicles leads either to heterogeneous multilamellar DNA-lipid arrangements or to DNA-induced bilayer destabilization and lipid fusion. The further employment of these polyelectrolyte nanostructures as improved formulations in therapeutic gene delivery trials, as well as in DNA chromatography, is discussed.

Animals↗
PubMedDate not supplied

[Hybridase cleavage of RNA. V. Complementary precision of cleavage].

The efficiency of the cleavage of RNA involved in perfect as well as imperfect hybrid duplexes composed of three components: (1) homogeneous RNA's or polyribonucleotides; (2) corresponding complementary synthetic oligodeoxyribonucleotides; (3) E. coli RNase H was investigated. The predominant RNA hydrolysis was shown to take place within the perfect hybrid duplexes formed by the target RNA and the complementary oligodeoxyribonucleotide probes. RNase H was found to cleave effectively a number of imperfect hybrid duplexes containing a central base pair mismatch.

Autoradiography↗
PubMed1991

Expression of interferon-beta during the triggering phase of macrophage cytocidal activation. Evidence for an autocrine/paracrine role in the regulation of this state.

The expression of cytocidal activity is induced by the sequential interaction of macrophages with a priming stimulus, such as interferon (IFN)alpha, -beta, or -gamma, and a triggering stimulus, such as poly(I.C) or lipopolysaccharide. However, most triggering stimuli are also capable of inducing IFN expression. This suggested to us the possibility that in addition to its role in initially priming macrophages for cytocidal activity, IFN may also be expressed during the triggering stage where it may potentially contribute to the regulation of cytocidal activity. We have explored this question by (i) attempting to dissociate IFN-inducing activity from triggering activity with a variety of structurally related and charge-related polyanions; (ii) determining if macrophages express IFN during the triggering stage; and (iii) questioning if IFN produced during the triggering stage contributes to the regulation of cytocidal activation. Exposure of unprimed macrophages to a triggering concentration of poly(I.C) alone failed to induce IFN beta expression. However, exposure of IFN beta-primed cells to poly(I.C) dramatically increased the expression of IFN beta mRNA. Priming with IFN gamma was likewise found to increase the expression of IFN beta mRNA in response to a triggering concentration of polyribonucleotides. Three approaches were adopted to ascertain if the increased expression of IFN beta contributed to cytocidal activation. First, macrophages derived from strains of mice which differ in their susceptibility to IFN induction by poly(I.C) were primed with IFN beta, washed, and triggered with poly(I.C). Under these conditions, macrophages derived from stain B10.A(2R), which are hyporesponsive to poly(I.C) in terms of IFN induction, also showed a diminished capacity to express Bf, a marker of cytocidal activation. Second, exposure of IFN-primed macrophages to poly(I.C) in the presence of anti-IFN alpha/beta antibody was found to reduce substantially the synthesis of NO2/NO3, an alternative marker of macrophage cytocidal activation. Third, exposure of IFN-primed macrophages to the calcium ionophores ionomycin or A23187, which do not induce the production of IFN beta during triggering, led to an abbreviated expression of Bf compared with stimuli that induce IFN beta expression such as poly(I.C). However, the capacity to synthesize Bf in response to A23187 was partially reconstituted when macrophages were triggered with the ionophore in the continuous presence of IFN beta. Collectively, these data show that IFN beta is expressed during the triggering stage of macrophage cytocidal activation and suggest that it plays an important and previously unsuspected role in the expression of this state.

Animals↗
PubMed1991

Purification and characterization of a mammalian polyadenylate polymerase involved in the 3' end processing of messenger RNA precursors.

A polyadenylate polymerase involved in the polyadenylation of pre-mRNA has been purified 6,000-fold to apparent homogeneity from extracts of calf thymus. In the last purification step, anion exchange chromatography separates the enzyme into three major peaks that are indistinguishable by other physical or functional criteria. On denaturing polyacrylamide gels, the two predominant forms of poly(A) polymerase have molecular weights of 57,000 and 60,000. In solution, the enzyme is a monomer. It polymerizes exclusively ATP. The reaction is distributive and proceeds linearly without any lag phase. The requirement for a primer can be satisfied by any of a number of polyribonucleotides. A significantly higher activity in the presence of Mn2+ as opposed to Mg2+ is due to a hundredfold higher affinity for the primer terminus. In the presence of mg2+ and of a specificity factor partially purified from HeLa cells, the enzyme specifically polyadenylates an RNA that ends at the natural adenovirus L3 polyadenylation site. This reaction depends on the AAUAAA polyadenylation signal.

Animals↗
PubMed1979

[Synthesis of spin-labeled rubomycin and a study of its interaction with DNA].

Hydrochloride of 14-(I-oxyl-2,2,6,6-tetramethylpiperidyl-4)-acetoxyrubomycin (spin-labeled rubomycin or SL-rubomycin) was prepared by interaction of hydrochloride of 14-bromrubomycin with potassium salt of I-oxyl-2,2,6,6-tetramethylpiperidyl-4-acetic acid. Its interaction with DNA and synthetic poly A and poly U polyribonucleotides was studied. The character of the EPR spectra was indicative of DNA binding with SL-rubomycin and forming a system with a high level of regularity similar to that of liquid crystals. The results of the study of the EPR spectra correlated with the model of rubomycin intercalation between the pairs of DNA bases and were indicative of water surrounding of the nitroxyl group of SL-rubomycin bound with DNA.

DNA↗
PubMed1975

The effects of polyamines on a residue-specific human plasma ribonuclease.

A ribonuclease, purified some 2700-fold from human plasma, exhibited a strong predilection for the hydrolysis of internucleotide bonds containing cytidylic acid. Analysis of [3'-32P]- and [5'-32P]phosphoryl-terminal fragments obtained after enzymic digestion of rabbit liver and yeast RNA indicated that the nucleotide found at the 3' terminus of the fragments was invariably cytidylic acid. The nucleotide at the 5' terminus varied between cytidylic and uridylic acids in a ratio of 9:1. When characterized by DEAE-cellulose chromatography, approximately 70 per cent of the digest consisted of oligonucleotides from 4 to 8 nucleotides in length. Enzyme activity, when measured in low ionic strength buffer, could be increased severalfold above control levels by the addition of either of the polyamines, spermidine or spermine. These substances also restored nucleolytic activity to preparations inhibited by such ordered synthetic polyribonucleotides as polyguanylic acid. Estimations of the molecular weight of the enzyme, both by Sephadex gel filtration and sucrose density centrifugation, indicate that the weight may vary, depending on the presence or absence of certain cations. Of the cations examined, spermidine and spermine appear to have the greatest effect, causing an alteration in molecular weight from greater than 150,000 to approximately 32,000.

Calcium↗
PubMed1975

A deoxyribonucleic acid ligase from nuclei of rat liver. Purification and properties.

A DNA ligase has been extensively purified from nuclei of rat livers. The ligase seals single strand nicks in DNA with any of the four usual bases on either the 3 or 5 sides. It requires ATP and a divalent cation (Mg-2plus or Mn-2plus) for activity. At low Mg-2plus concentrations the activity is greatly stimulated by a variety of monovalent cations. Relatively small excesses of either monovalent or divalent cation above the amounts which give maximal activity lead to inhibition of activity. Poly(G) and poly(I) inhibit ligase activity; several other polyribonucleotides are not inhibitory. Low concentrations of inorganic pyrophosphate are inhibitory. The molecular weight of the ligase is estimated from gel filtration to be about 10 times 10-4.

Adenosine Triphosphate↗
PubMed1975

Characterization of a polyriboadenylate polymerase from vaccinia virions.

A poly(A) polymerase with a molecular weight of approximately 80,000 containing 51,000 and 35,000 molecular weight subunits, was purified by affinity chromatography from vaccinia virus cores. The enzyme had a pH optimum of about 8.6, was dependent on divalent cations, and had considerably more activity with Mn-2+ than Mg-2+. At equimolar concentrations, other ribonucleoside triphosphates inhibited poly(A) polymerase activity by less than 10%; NaCl was extremely inhibitory at concentrations above 0.1 M. Under standard assay conditions, poly(A) polymerase activity was stimulated more than 10-fold by poly(C), but to small extent or not at all by other homopolyribonucleotides or natural RNA species unless they were first subjected to partial hydrolysis and alkaline phosphatase treatment. The ineffectiveness of most long polyribonucleotides was attributed to enzyme binding to internal regions. Short poly- or oligoribonucleotides prepared from natural or synthetic RNAs, except poly(G), exhibited similar priming abilities, and isotope transfer experiments indicated the covalent attachment of poly(A) to cytidylate, uridylate, and inosinate residues. Experiments with a series of uridylate oligomers indicated that the minimum effective primer length was four to six nucleotides. Partially digested DNA and short poly- and oligodeoxyribonucleotides of dT, dC, and dI, but not of dA and dG, also acted as effective primers for the poly(A) polymerase.

Adenine Nucleotides↗
PubMed1975

Binding of [3H]benzo(a)pyrene to natural and synthetic nucleic acids in a subcellular microsomal system.

Several carcinogens are bound covalently to cellular nucleic acids. This is also the case with polycyclic hydrocarbon carcinogens, but their precise mechanism of in vivo activation to reactive forms and the structure(s) of the nucleic acid adducts are not known. This study demonstrates that in the presence of rat liver microsomes and reduced nicotinamide adenine dinucleotide phosphate there is covalent attachment of tritiated benzo(a)pyrene (BP) to transfer RNA, DNA, certain synthetic polyribonucleotides, and an RNA species endogenous to the microsomal fraction. Evidence has been obtained that the binding occurs mainly to guanine and, to a lesser extent, adenine residues and is not simple an artifact of tritium exchange. The microsomal-mediated binding of [3H]BP to nucleic acids requires reduced nicotinamide adenine dinucleotide phosphate and in inhibited by 7,8-benzoflavone, glutathione, and magnesium. It is enhanced somewhat by the addition of styrene oxide, cyclohexene oxide, and trichloropropylene oxide. These results provide the first evidence that: (a) the microsome-mediated binding of [3H]BP to nucleic acids is not just due to tritium exchange; (b) a derivative of the hydrocarbon is covalently bound to the nucleic acid, and not simply intercalated; (c) there is a preferential binding to guanine residues; and (d) in addition to binding to exogenous nucleic acids, [3H]BP is bound to an RNA species present in the microsomes. Our data are consistent with but do not prove that nucleic acid binding of this polycyclic hydrocarbon proceeds via an epoxide intermediate.

9,10-Dimethyl-1,2-benzanthracene↗
PubMed1985

Phase I trials of poly(I,C) complexes in advanced cancer.

We have performed Phase I trials of two synthetic double-stranded polyribonucleotide complexes--poly(I,C)-LC, a complex of polyinosinic-polycytidylic acid with poly-L-lysine and carboxymethylcellulose, and poly(I,C)-L, which lacks carboxymethylcellulose--in patients with advanced cancer. With poly(I,C)-LC, several treatment schedules were investigated in an attempt to decrease toxicity and maximize interferon (IFN) induction. The best tolerated was an alternate-day schedule, with gradual dose escalation. Daily short infusions and continuous (24-h) infusions were tolerated less well. Maximum tolerated doses varied over a several hundredfold dose range. Toxicity consisted of fever, rigors, hypotension, and blood count depression. Two patients treated with poly(I,C)-L developed systemic allergic reactions, and antibodies to poly(I,C)-L and its components were detected in the serum of some patients treated with both compounds. IFN-alpha was induced in most patients at serum levels similar to those achieved after intramuscular administration of human IFN-alpha. Of 32 patients, one with renal cell carcinoma showed partial tumor regression. Poly(I,C) complexes are effective IFN inducers in humans, but their toxicity limits their use in cancer patients.

Adult↗
PubMed1986

1,1,2-Trichloroethane: evidence of genotoxicity from short-term tests.

At 22 hr after ip injection into adult male Wistar rats, 1,1,2-trichloroethane was covalently bound to DNA, RNA and proteins of the liver, kidney, lung and stomach, as has been found with various weakly carcinogenic halo compounds. The extent of interaction of 1,1,2-trichloroethane with mouse liver DNA was much higher than that with rat liver DNA. This result provides evidence of a correlation between adducts formation and species susceptibility to hepatocarcinogenesis (only the mouse is sensitive to the oncogenic effect of this compound). Interaction with DNA mediated by murine liver microsomes occurred in vitro. No particular differences between the two species were found. In vitro binding was enhanced (approximately 5-fold) by pretreatment in vivo with phenobarbitone but was suppressed by addition of 2-diethylamino-ethyl-2,2-diphenylvalerate X HCl in vitro. Cytochrome P-450 was, therefore, involved in the interaction process. Glutathione suppressed the microsome-mediated interaction, acting as a "scavenger" of reactive intermediate(s). Murine lung microsomes were less effective bioactivators than liver microsomes for the interaction with DNA and microsomal RNA, but not microsomal protein. Kidney and stomach microsomes were ineffective, as were cytosolic fractions from all of the assayed organs of the two species. The extent of in vitro interaction of 1,1,2-trichloroethane with synthetic polyribonucleotides was of the same order of magnitude as that with DNA. The results represent further clear evidence for genotoxicity of 1,1,2-trichloroethane.

Animals↗
PubMed1987

Interactions of retroviral structural proteins with single-stranded nucleic acids.

We have studied the interactions of single-stranded polyribonucleotides with murine leukemia virus structural proteins p10, p10' (a p10 variant), and Pr65gag, as well as Rous sarcoma virus (RSV) pp12 (a p10 analog). Two quantitative assays have been used to monitor protein-RNA association: the fluorescence enhancement of polyethenoadenylic acid) poly(epsilon A) upon binding protein, and tryptophan fluorescence quenching upon binding to poly(U). With each assay p10 was shown to bind stoichiometrically to single-stranded RNA, covering a length of nucleic acid chain (occluded site size, n) of about 6 residues. RSV pp12 was also shown to bind to poly(epsilon A), with n = 5 +/- 1. Addition of NaCl to fully titrated MuLV p10-nucleic acid mixtures effected nearly complete restoration of poly(epsilon A) or MuLV p10 fluorescence. Under conditions of 0.06 M NaCl, p10 bound noncooperatively to poly(epsilon A) with an intrinsic association constant, K = 2.3 X 10(6) M-1. K and n determined in this study were shown to relate to Kapp determined by other methods, by the approximation Kapp approximately NK, where N is the number of binding sites along the polynucleotide chain ((nucleotides/chain)/n). Chemical modifications of the p10 cysteine residues did not alter the affinity for poly(epsilon A). The affinity of Pr65gag for poly(epsilon A) appears to be higher than that of p10.

Animals↗
PubMed1987

Influence of phosphatidylserine on endogeneous RNA synthesis in isolated rat liver nuclei.

The possible involvement of anionic phospholipids in the transcriptional process was studied in isolated rat liver nuclei synthesizing RNA in the presence of phosphatidylserine, which was employed in the form of multillamellar liposomes as a means of delivering the lipid to the nuclei in aqueous medium. The divalent ion requirement for RNA synthesis and the properties of the incubation mixture were not significantly modified by the phospholipid, which increased the rate and the extent of the incorporation of 3H-UMP without changing the endogeneous degradation pattern of the product or affecting the activity of a particular RNA polymerase, as indicated by the sensitivity to amanitin. The thin layer chromatography analysis of the alkaline hydrolysates of the RNA showed that the stimulation involved an increase of the total polyribonucleotide elongation rate. The size of the product was essentially unchanged in the presence of phosphatidylserine, as demonstrated by the qualitative overlapping of the sedimentation profiles of control and lipid treated samples in formamide-sucrose gradients. The release of the H1 fraction from intact nuclei occurring with phosphatidylserine indicated that the DNA template availability was increased by a partial removal of the restrictions imposed by histones, as suggested also by the comparison with heparin and Sarkosyl. These evidences, together with the data accumulated on the occurrence of lipids in chromatin and nuclear matrix, and on their changes related to cell growth, differentiation and malignant transformation, allow a better definition of the role that phospholipids might play in regulating the DNA template availability in the cell.

Amanitins↗