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PubMed1984

[Polymorphism of the left-handed helix (Z form) of poly(dG-dC).poly(dG-dC) induced by MgCl2, studied by infrared spectroscopy].

The existence of a left-handed double-helical DNA, called Z-DNA was proved by X-ray crystallographic analysis of the hexanucleotide d(CpGpCpGpCpG). The possible biological relevance of the Z conformation is enhanced by recent studies using immunostaining. Antibodies against Z-DNA have been raised and used to detect the Z conformation in polytene and mammal chromosomes. In this work we have studied the conditions necessary to generate the transition from the right-handed to the left-handed conformation of poly d(G-C).poly d(G-C) exposed to various concentrations of MgCl2 and various relative humidities. The infrared (IR) spectra were used to characterize the different conformations. Only below 0.5 Mg2+ ion per nucleotide we have observed the right-handed helix. Above 1 Mg2+ ion per nucleotide, the left-handed helix is always present under low and high relative humidity conditions. Furthermore, under low relative humidity and high salt content conditions we found a new IR spectrum which can be correlated with a polymorphic Z form, called here Z degree form.

DNA↗
PubMedDate not supplied

[Hydration and stability of the double helical complex poly(dA)-poly(dT)].

IR-spectrometry and thermopiezogravimetry are used to study the structure formation and the water environment of the double-helix Na-poly(dA)-poly(dT) complex in films in the 0-100% interval of the relative humidity (RH). It has been found that three different structures of the complex are formed in the 0-32, 32-76 and 88-100% intervals of RH. The calculations of resonance frequencies of out-of-ring (C-0) and in-ring (C-N) vibrations in adenine and thymine using perturbation theory show that the second and the third forms are the X-ray beta-B'- and alpha-B'-forms. Distribution of the binding energy of water molecules has been found from IRS data about water sorption and isotherms of hydration at different temperatures. The enthalpy of helix-coil transition has been found from microcalorimetry data. These results allow us to estimate the energy contribution of water molecules (about 75%) and other interactions (about 25%) in the total stabilization energy of the complex structure.

Polydeoxyribonucleotides↗
PubMed1976

Anti-viral activity against encephalomyocarditis virus and Semliki Forest virus and acute toxicity of poly I and poly C administered sequentially to mice.

Mice are protected against lethal intraperitoneal and intravenous infection by encephalomyocarditis virus and Semliki Forest virus by sequential treatment with poly I followed by either polyC or poly5-hydroxyC without production of interferon when the treatments are 4 or more hours apart and by the intraperitoneal or intravenous routes. Maximum protection occurs around 4 hours before infection and is still significant 20 hours after infection. Treatments with combinations of other homoribopolynucleotides were not found to be anti-viral. Protection by sequential polyI, polyC treatment of mice is relatively short-lived and does not 'hypo-reactivate' the protective effect of polyI:C and shows approximately half the protective effect of polyI:C. The toxicity of sequential polyI, polyC treatment is lower than that of polyI:C particularly if poly5-hydroxyC is substituted for polyC. Silica treatment of mice indicates that stationary macrophages are required for protection by polyI followed by polyC but an effect on humoral or cell mediated immune responses does not appear to be involved. The effect appears to be a synergism between the protection conferred by polyI or polyC alone.

Animals↗
PubMed2002

Anti-cancer action of 4-iodo-3-nitrobenzamide in combination with buthionine sulfoximine: inactivation of poly(ADP-ribose) polymerase and tumor glycolysis and the appearance of a poly(ADP-ribose) polymerase protease.

E-ras 20 tumorigenic malignant cells and CV-1 non-tumorigenic cells were treated with a drug combination of 4-iodo-3-nitrobenzamide (INO(2)BA) and buthionine sulfoximine (BSO). Growth inhibition of E-ras 20 cells by INO(2)BA was augmented 4-fold when cellular GSH content was diminished by BSO, but the growth rate of CV-1 cells was not affected by the drug combination. Analyses of the intracellular fate of the prodrug INO(2)BA revealed that in E-ras 20 cells about 50% of the intracellular reduced drug was covalently protein-bound, and this binding was dependent upon BSO, whereas in CV-1 cells BSO did not influence protein binding. Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was identified as the protein that covalently binds the reduction product of INO(2)BA, which is 4-iodo-3-nitrosobenzamide. Since only the enzymatically reduced drug INOBA bound covalently to GAPDH, the BSO-dependent covalent protein-drug association indicated an apparent nitro-reductase activity present in E-ras 20 cells, but not in CV-1 cells, explaining the selective toxicity. Covalent binding of INOBA to GAPDH inactivated this enzyme in vitro; INO(2)BA+BSO also inactivated cellular glycolysis in E-ras 20 cells because it provided the precursor to the inhibitory species: INOBA. Another event that occurred in INO(2)BA+BSO-treated E-ras 20 cells was the progressive appearance of a poly(ADP-ribose) polymerase protease. This enzyme was partially purified and characterized by the polypeptide degradation product generated from PARP I, which exhibited a 50kDa mass. This pattern of proteolysis of PARP I is consistent with a drug-induced necrotic cell killing pathway.

Antineoplastic Agents↗
PubMed2000

The analysis of the poly(ADPR) polymerase mode of action in rat testis nuclear fractions defines a specific poly(ADP-ribosyl)ation system associated with the nuclear matrix.

The poly(ADP-ribosyl)ation system, associated with different nuclear fractions of rat testis, has been analyzed for both pADPR and pADPR acceptor proteins. The DNase I sensitive and resistant chromatin contain 35% and 40%, respectively, of the total pADPR synthesized in intact nuclei incubated with [32P]NAD. Moreover, the residual 25% were estimated to be associated with the nuclear matrix. Three different classes of pADPR are present in the nuclei. The longest and branched ADPribose polymers modify proteins present in the DNase I resistant (2 M NaCl extractable) chromatin and in the nuclear matrix, whereas polymers of> 20 residues interact with the components of the DNase I sensitive chromatin and oligomers of 6 ADPribose residues are bound specifically to the acid-soluble chromosomal proteins, present in isolated nuclear matrix. The main pADPR acceptor protein in all the nuclear fractions is represented by the PARP itself (auto-modification reaction). The hetero-modification reaction occurs mostly on histone H1 and core histones, that have been found associated to DNase I sensitive and resistant chromatin, respectively. Moreover, an oligo(ADP-ribosyl)ation occurs on core histones tightly-bound to the matrix associated regions (MARs) of chromatin loops.

Animals↗
PubMed1973

Poly(inosinic acid)-poly(cytidylic acid) inhibition of DNA synthesis in synchronized HeLa cells.

Inhibition by double-stranded polyribonucleotides of DNA synthesis in synchronized HeLa cultures is dose- and time-dependent. Inhibition by poly(I.C) primarily affected late G(1) and early S phases of the cell cycle. Single-stranded polynucleotides, native calf-thymus DNA, and yeast RNA had no effect. Radioautography showed that after 2-hr exposure the synthetic polyribonucleotides were predominantly inside the nucleus. The results extend the spectrum of action of double-stranded RNA.

Autoradiography↗
PubMed1992

Conformational transitions of poly(dA-bromo5dU) and poly(dA-iodo5dU) in solution.

Extensive circular dichroism studies have been conducted with the title polynucleotides under various solution conditions. The studies provided the following information: (i) The halogen atoms in place of thymine methyl hinder the isomerization into X-DNA. (ii) The brominated but not iodinated polynucleotide isomerizes into Z-DNA in concentrated NaCl+NiCl2. The transition takes place at lower NiCl2 concentrations than with poly(dA-dT). (iii) The iodinated polynucleotide forms an unusual conformation in aqueous solution in which it is very stable. It isomerizes from this conformer into the usual B-type double helix in concentrated ethanol solutions. The isomerization is a two-state cooperative process. (iv) Both title polynucleotides undergo still another two-state cooperative transition in trifluorethanol solutions presumably into A-DNA showing a rather unusual circular dichroism spectrum.

Circular Dichroism↗
PubMed2005

Regulation of poly(ADP-ribose) metabolism by poly(ADP-ribose) glycohydrolase: where and when?

Poly(ADP-ribose) glycohydrolase (PARG) is a catabolic enzyme that cleaves ADP-ribose polymers formed by members of the PARP family of enzymes. Despite its discovery and subsequent partial purification in the 1970s and the cloning of its single gene in the late 1990s, little is known about the role of PARG in cell function. Because of its low abundance within cells and its extreme sensitivity to proteases, PARG has been difficult to study. The existence of several PARG isoforms with different subcellular localizations is still debated today after more than 30 years of intensive research. In this article, we want to summarize and discuss the current knowledge related to PARG, its different forms and subcellular distribution. We also examine the possible biological roles of PARG in modulating chromatin structure, transcription, DNA repair and apoptosis.

Animals↗
PubMed1984

Synthesis and protective effects of poly-8-bromoriboadenylic acid: poly ribouridylic acid hybrid against Wesselsbron virus in chick embryos.

Poly-8-bromoriboadenylic acid was synthesized by the bromination of adenosine-5'-monophosphate to yield 8-bromoadenosine-5'-monophosphate which on conversion to the 5'-diphosphate form was polymerized by polynucleotide phosphorylase (PNPase). The polymer formed a 1:1 hybrid with polyribouridylic acid and the hybrid was found to protect chick embryos against Wesselsbron virus (H10964).

Animals↗
PubMed2003

Ssu72 protein mediates both poly(A)-coupled and poly(A)-independent termination of RNA polymerase II transcription.

Termination of transcription by RNA polymerase II (Pol II) is a poorly understood yet essential step in eukaryotic gene expression. Termination of pre-mRNA synthesis is coupled to recognition of RNA signals that direct cleavage and polyadenylation of the nascent transcript. Termination of nonpolyadenylated transcripts made by Pol II in the yeast Saccharomyces cerevisiae, including the small nuclear and small nucleolar RNAs, requires distinct RNA elements recognized by the Nrd1 protein and other factors. We have used genetic selection to characterize the terminator of the SNR13 snoRNA gene, revealing a bipartite structure consisting of an upstream element closely matching a Nrd1-binding sequence and a downstream element similar to a cleavage/polyadenylation signal. Genome-wide selection for factors influencing recogniton of the SNR13 terminator yielded mutations in the gene coding for the essential Pol II-binding protein Ssu72. Ssu72 has recently been found to associate with the pre-mRNA cleavage/polyadenylation machinery, and we find that an ssu72 mutation that disrupts Nrd1-dependent termination also results in deficient poly(A)-dependent termination. These findings extend the parallels between the two termination pathways and suggest that they share a common mechanism to signal Pol II termination.

3' Flanking Region↗
PubMed1996

The activation of murine macrophages and natural killer cells by the partially thiolated double stranded RNA poly(I)-mercapto poly(C).

Partially thiolated analogs of the biological response modifier poly I.poly C (pI.pC) were synthesized. Each of these analogs (pI.MPC) contained a partially thiolated polycytidylate (MPC) strand containing either 1.2%, 4.6%, or 17% 5-mercaptocytosine (%SH) randomly introduced throughout the polynucleotide. The ability of these double stranded RNAs (dsRNAs) to activate murine peritoneal macrophages in vitro and augment natural killer (NK) cell activity in mice following intraperitoneal (i.p.) administration was determined. Macrophages were treated in vitro for 24 hours with pI.pC, or pI.MPC, washed, and then overlayed with exponentially growing L1210 leukemia cells at an effector to target (E:T) ratio of 25:1. The cytostatic effect of the macrophages on the L1210 cells was determined by 3H.thymidine pulse labelling. The rank order of potency for macrophage activation was determined to be: pI.pC>pI.MPC(1.2% SH)>pI.MPC(4.6% SH)pI.MPC(17% SH). Twenty hours following i.p. administration of 5 mg/kg of each pI.MPC analog, splenic NK cell activity was assessed in a standard 51Cr release assay using the murine tumor target cell line YAC- 1. The rank order of potency observed for NK cell activation was determined to be; pI.pCpI MPC(1.2% SH)>pI.MPC(4.6% SH)>pI.MPC(17% SH). These dsRNAs activated NK cells in a dose dependent manner. The efficacy and time course for NK cell activation following i.p. administration of pI.MPC (1.2% SH) at a dose of 10 mg/kg was directly compared to an equivalent 10 mg/kg i.p. dose of pI.pC. NK cell activation took place within three hours following treatment with pI-pC whereas the onset of NK cell activation by pI.MPC (1.2%) occurred between 8 and 20 hours post treatment. NK cell activity steadily declined from 24 to 50 hours post treatment at which time the NK activity in both treatment groups was similar. There was a significant correlation between the immunostimulatory potency of these dsRNAs and their experimentally determined melting temperatures (r2 = 0.88) and percent hyperchromicity upon thermal denaturation (r2 = 0.99). At the lower %SH, pI.MPC retains most of the immunostimulatory activities of p1.pC and may serve as a useful and potent biological response modifier.

Animals↗
PubMed1997

Characterization of antibodies specific for the caspase cleavage site on poly(ADP-ribose) polymerase: specific detection of apoptotic fragments and mapping of the necrotic fragments of poly(ADP-ribose) polymerase.

Intracellular cysteine proteases are important mediators of apoptosis. Indeed, some nuclear proteins and enzymes are cleaved during apoptosis, in particular poly(ADP-ribose) polymerase (PARP), which is activated by DNA strand interruptions and is involved in DNA repair. PARP is cleaved into two fragments of 29 and 85 kDa (apparent molecular mass) in human promyelomonocytic leukemia cells, HL-60, treated with etoposide to induce apoptosis. These cells possess protease activities, caspases, that share many features with the ICE/CED-3 family. The cleavage occurs between Asp-214 and Gly-215, a site that is conserved in human, bovine, and chicken PARP. This cleavage has been shown to be an early marker of apoptosis. To monitor apoptosis, to understand the role of PARP cleavage by caspases, and to study the role of the two fragments in DNA repair, members of our laboratory have developed two polyclonal antipeptide antibodies directed against the two human PARP sequences: [196-214] for LP96-22 and [215-228] for LP96-24. Moreover, these antibodies will be useful to map the necrotic cleavage of PARP, which generates fragments different from those obtained during apoptosis, and thus to discriminate between apoptotic and necrotic cell death.

Amino Acid Sequence↗
PubMed1996

In vivo biocompatibility study of ABA triblock copolymers consisting of poly(L-lactic-co-glycolic acid) A blocks attached to central poly(oxyethylene) B blocks.

Films of three ABA-block copolymers composed of lactic-co-glycolic acid A blocks and poly(oxyethylene) (PEO) B blocks and one random lactic-co-glycolic acid copolymer (PLG) were studied to investigate the influence of different polymer compositions and molecular weights on the tissue reaction, appearance of toxic degradation products, and swelling behavior in the cage implant system in rats. The inflammatory tissue reaction was followed over a 21-day implantation period by monitoring the leukocyte concentration, the extracellular acid, and alkaline phosphatase activities in a quantitative manner. Size and density of adherent macrophages and foreign body giant cells on the film surfaces were determined. The ABA and PLG implants caused only a minimal inflammatory reaction, as characterized by a low concentration of leukocytes during the implantation period when compared to empty cage controls. The content of PEO had an influence on the density of the adherent cells on the surface of the polymer film. An increase in PEO content and molecular weight decreased the cellular density during the implantation period. As demonstrated by scanning electron microscopy, no degradation was observed for all polymers during the implantation period. Our results demonstrate that the ABA block copolymers and PLG copolymer, are equally well tolerated in the cage implant test system.

Alkaline Phosphatase↗
PubMed1998

Insight into externally bound 5,10,15,20-tetrakis(2-N-methylpyridyl) porphyrinatopalladium(II), PdP(2), with B-form DNA duplexes poly(G-c)2, poly(A-t)2, and CT DNA by using combined MCD, CD, and optical data.

The Soret (B0) region of free and externally DNA-bound 5,10,15,20-tetrakis(2-N-methylpyridyl) porphyrinatopalladium(II), PdP(2), was investigated by electronic magnetic circular dichroism (MCD), natural circular dichroism (CD), and optical (UV-visible) absorption spectroscopies. We conclude that four-coordinate, "thick" PdP(2) binds to the exterior of each of poly(A-T)2 and calf thymus DNA (CT DNA) by two distinctly different AT-specific minor and major groove modes, with site 5'TA3' being favored for both modes. The minor groove mode involves an edge-on orientation of PdP(2), for which porphyrin electric dipole transition moments (edtms) mu x (most perturbed direction of the bound porphyrin) and mu y (least perturbed direction) have approximate orientation angles of alpha/beta/beta' = approximately 90 degrees/0 degree/0 degree and approximately 45 degrees/0 degree/90 degrees, respectively. Major groove binding is by a face-on mode, which results in the porphyrin plane being approximately parallel to the helix axis, such that mu x (most perturbed direction) and mu y (least perturbed direction) have approximate orientation angles of alpha/beta/beta' = approximately 45 degrees/180 degrees/90 degrees and approximately 45 degrees/180 degrees/270 degrees, respectively. The Soret MCD and optical band alterations upon binding (i.e., sign retention of the tetragonal, genuine MCD (+) A-term on becoming the (+) pseudo-A-term of similar amplitude and small DNA-induced optical red (delta lambda) and hypochromic (H) shifts) are all consistent with exterior binding perturbations of the porphyrin's p pi MOs (1a1u 3a2u 4eg) by the A and T bases of each polymer being weaker than caused by intercalation. Furthermore, that the (+) A-term of PdP(2) retains the (+) sign upon binding informs that the 4eg splitting, or delta LUMO, is less than the energy separation magnitude of 1a1u-3a2u, or delta HOMO. For the third system, PdP(2)/poly (G-C)2, the B0 CD spectrum has two extremely weak (+) and (-) CD bands at higher and lower energy, respectively, indicating that weak outside binding (wob) interactions are taking place between the cationic porphyrin and the electron-rich phosphate backbone of this rigid polymer. The composite of our CD, MCD, and optical data are suggestive of a face-on mode at the GC major groove. Band parameter extraction is performed on the Soret CD and MCD bands of each of the three bound systems, and it is determined that (1) very little spatial rotation of molecular charge is induced during CD excitation and (2) the excited state angular momentum, 'Lj', changes very little upon binding of PdP(2) to each duplex. These findings are also consistent with each PdP(2)/B-DNA interaction not being very strong.

Base Pairing↗
PubMed2000

Study of phase behavior of poly(ethylene glycol)-polysorbate 80 and poly(ethylene glycol)-polysorbate 80-water mixtures.

Mixtures of poly(ethylene glycols) (PEGs) with polysorbate 80 are often used to dissolve poorly water-soluble drugs in dosage forms, where polysorbate 80 helps either in enhancing dispersion or in inhibiting precipitation of drugs once the solution is mixed with water. Binary phase diagrams of polysorbate 80 with several low molecular weight PEGs and a ternary phase diagram of polysorbate 80 with PEG 400 and water are presented. Two phases were observed in the binary mixtures when the concentration of PEG 200, PEG 300, PEG 400, or PEG 600 was >55%(w/w). The miscibility of the binary mixtures increases with an increase in temperature; the upper consolute temperatures of PEG 200-polysorbate 80, PEG 300-polysorbate 80, PEG 400-polysorbate 80, and PEG 600-polysorbate 80 mixtures were 100, 85, 75, and 40 degrees C, respectively. The upper consolute temperature of PEG 1000-polysorbate 80 could not be determined because the melting temperature of the mixtures is approximately 40 degrees C and the consolute temperature appeared to be less than this temperature. The decrease in upper consolute temperature with an increase in PEG molecular weight indicated a greater miscibility of the two components. In the ternary system, phase separation of polysorbate 80 was observed when the concentration of PEG 400 was >50-60 % (w/w), possibly because of the high exclusion volume of PEG 400.

Dosage Forms↗
PubMed1992

Helix formation in poly (N epsilon,N epsilon,N epsilon-trimethyl-L-lysine) and poly (L-lysine): dependence on concentration and molecular weight.

Helix formation in (Lys)n.HClO4 and poly(N epsilon,N epsilon,N epsilon-trimethyl-L-lysine).HClO4 +AD(LysMe3)n.HClO4+BD is dependent on peptide concentration and on molecular weight. For (LysMe3)n.HClO4 of degree of polymerization (DP) 2510 the midpoint of the coil-to-helix transition is 2 mM and for DP of 190 it is 5 mM. For (Lys)n.HClO4 the peptide concentration for half-helix is 30-60 times as high, and is only weakly dependent, if at all, on molecular weight. Helix formation is an intermolecular process. The use of methylated (Lys)n as the perchlorate permits study of the intermolecular coil-helix transition at low concentration, instead of the high concentration (ca. 1-2 M) required for (Lys)n.HBr. At constant peptide concentration helix content increases with added NaClO4. The higher the peptide concentration, the less NaClO4 is needed to induce helix.

Methylation↗
PubMed2005

Adsorption of poly(ethylene glycol)-modified ribonuclease A to a poly(lactide-co-glycolide) surface.

Protein adsorption is a source of variability in the release profiles of therapeutic proteins from biodegradable microspheres. We employ optical reflectometry and total internal reflection fluorescence to explore the extent and kinetics of ribonuclease A (RNase A) adsorption to spin-cast films of poly(lactide-co-glycolide) (PLG) and, in particular, to determine how covalent grafting of polyethylene glycol (PEG) to RNase A affects adsorption. Adsorption kinetics on PLG surfaces are surface-limited for RNase A but transport-limited for unconjugated PEG homopolymers and for PEG-modified RNase A, indicating that PEG anchors the conjugates to the surface during the transport-limited regime. PEG modification of RNase A decreases the total number of adsorbed molecules per unit area but increases the areal surface coverage because the grafted PEG chains exclude additional surface area. Total internal reflection fluorescence-based exchange measurements show that there is no exchange between adsorbed and solution-phase protein molecules. This indicates an unusually tenacious adsorption. Streaming current measurements indicate that the zeta potential of the PLG surface becomes increasingly negative as the film is exposed to water for several weeks, as expected. Aging of the PLG surface results in increased adsorption of unmodified RNase A but decreased adsorption of unconjugated PEG homopolymers and of PEG-RNase A conjugates, relative to the extent of adsorption on freshly prepared PLG surfaces. Adsorption results correlate well with an increase in the rate, total extent and preservation of bioactivity of RNase A released from PLG microspheres for the PEG-modified version of RNase A.

Adsorption↗
PubMed2004

Ultraviolet sealing and poly(dimethylacrylamide) modification for poly(dimethylsiloxane)/glass microchips.

Simple sealing methods for poly(dimethylsiloxane) (PDMS)/glass-based capillary electrophoresis (CE) microchips by UV irradiation are described. Further, we examined the possibility to modify the inner surface of separation channels, using polymethylacrylamide (PDMA) as a dynamic coating reagent. The surface properties of native PDMS, UV-irradiated PDMS, and PDMA-coated PDMS were systematically studied by atomic force microscopy (AFM), infrared absorption by attenuated total reflection infrared (ATR-IR) spectroscopy, and contact angle measurement. We found that PDMA forms a stable coating on PDMS and glass surfaces, eliminating the nonhomogeneous electroosmotic flow (EOF) in channels on PDMS/glass microchips, and improving the hydrophilicity of PDMS surfaces. Mixtures of flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), and fluorescein were separated in 35 s using PDMA-coated PDMS/glass microchips. A high efficiency of theoretical plates with at least 1365 (105 000 N/m) and a good reproducibility with relative standard deviations (RSD) below 4% in five successive separations were achieved.

Acrylamides↗