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PubMed1990

A.U and G.C base pairs in synthetic RNAS have characteristic vacuum UV CD bands.

The vacuum UV CD spectra of GpC, CpG, GpG, poly[r(A)], poly[r(C)], poly[r(U)], poly[r(A-U)], poly[r(G).r(C)], poly[r(A).r(U)], and poly[r(A-U).r(A-U)] were measured down to at least 174 nm. These spectra, together with the published spectra of poly[r(G-C).r(G-C)], CMP, and GMP, were sufficient to estimate the CD changes upon base pairing for four double-stranded RNAs. The vacuum UV CD bands of poly[r(A)], poly[r(C)], and the dinucleotides GpC and CpG were temperature dependent, suggesting that they were due to intrastrand base stacking. The dinucleotide sequence isomers GpC and CpG had very different vacuum UV CD bands, indicating that the sequence can play a role in the vacuum UV CD of single-stranded RNA. The vacuum UV CD bands of the double-stranded (G.C)-containing RNAs, poly[r(G).r(C)] and poly[r(G-C).r(G-C)], were larger than the measured or estimated vacuum UV CD bands of their constituent single-stranded RNAs and were similar in having an exceptionally large positive band at about 185 nm and negative bands near 176 and 209 nm. These similarities were enhanced in difference-CD spectra, obtained by subtracting the CD spectra of the single strands from the CD spectra of the corresponding double strands. The (A.U)-containing double-stranded RNAs poly[r(A).r(U)] and poly[r(A-U).r(A-U)] were similar only in that their vacuum UV CD spectra had a large positive band at 177 nm. The spectrum of poly[r(A).r(U)] had a shoulder at 188 nm and a negative band at 206 nm, whereas the spectrum of poly[r(A-U).r(A-U)] had a positive band at 201 nm. On the other hand, difference spectra of both of the (A.U)-containing polymers had positive bands at about 177 and 201 nm. Thus, the difference-CD spectra revealed CD bands characteristic of A.U and G.C base pairing. (ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed1995

Comparison of base inclination of ribo-GC and deoxyribo-GC polymers, and synthesis of poly(rGrC)-poly(rGrC).

The inclination angle between the base normal and the helix axis, and the axes around which the bases incline, are measured for ribo-GC polymers in buffer by using flow linear dichroism (LD), and compared to measurements for deoxyribo-GC polymers in buffer and under dehydrating conditions. A new method is designed to synthesize poly(rGrC)-poly(rGrC), which is not available commercially, in large quantities. The LD of this RNA reveals inclination angles that are similar to the B-form DNA in buffer, although the axes are different. The CD of poly(dGdC)-poly(dGdC) under the dehydrating conditions is similar to poly(rGrC)-poly(rGrC), indicating it is in the A form, and the LD gives larger inclination angles than either the B form or the corresponding RNA. Poly(dG)-poly(dC) is in the A form in buffer. Comparison among poly(rG)-poly(rC) in buffer, and poly(dG)-poly(dC) in buffer under dehydrating conditions, reveals similar inclination angles and axes, although the LD shows that the DNA has the largest inclination angles. Except for poly(rGrC)-poly(rGrC), which has a unique reduced dichroism, all the axes for G are similar, as are the axes for C.

Circular Dichroism↗
PubMed1996

Nutritional pharmacology and malignant disease: a therapeutic modality in patients with cancer.

It is now established that certain nutrients have a significant effect on cellular metabolism and growth, tissue repair and regeneration, and modulation of host defences. So far, however, potential clinical benefits have been difficult to demonstrate. Nevertheless, the use of nutrients in combinations seems to have promise and may be associated with a reduction in infectious complications and length of hospital stay. Nutritional pharmacology in the future may be able to improve tumour response to chemotherapy and may minimize the metabolic effect of cachexia.

Animals↗
PubMed2003

Indolocarbazole glycosides in inactive conformations.

Indolocarbazole glycosides related to rebeccamycin represent a promising category of antitumor agents targeting DNA and topoisomerase I. These drugs prefer to adopt a closed conformation with an intramolecular hydrogen bond between the indole NH group and the pyranose oxygen atom. Three pairs of indolocarbazole monoglycosides bearing an NH or an N-methyl indole moiety were synthesized and their biological properties investigated at the molecular and cellular level. Replacing the indole NH proton with a methyl group reduces DNA interaction and abolishes activity against DNA topoisomerase I. Surface plasmon resonance studies performed with a pair of water-soluble indolocarbazole glycosides and two hairpin oligonucleotides containing an [AT]4 or a [CG]4 sequence indicate that both the NH and the N-methyl derivative maintain a relatively high affinity for DNA (Keq = 2 - 6 x 10(5) M(-1)) but the incorporation of the methyl group restricts access to the DNA. The number of ligand binding sites (n) on the oligonucleotides is about twice as high for the NH compound compared to its N-methyl analogue. Modeling and 1H NMR studies demonstrate that addition of the N-methyl group drives a radical change in conformation in which the orientation of the aglycone relative to the beta-glucoside is reversed. The loss of the closed conformation by the N-methyl derivatives perturbs thir ability to access DNA binding sites and prevents the drug from inhibiting topoisomerase I. As a consequence, the NH compounds exhibit potent cytotoxicity against CEM leukemia cells with an IC50 value in the 1 microM range, whereas the N-methyl analogues are 10 to 100 times less cytotoxic. These studies offer circumstantial evidence supporting the importance of the closed conformation in the interaction of indolocarbazole glycosides with their molecular targets, DNA and topoisomerase I.

Anti-Bacterial Agents↗
PubMed1982

Comparative kinetics of poly(6-thioinosinic acid) and 6-mercaptopurine treated L1210 cells.

Poly(6-thioinosinic acid), poly(s6I), a synthetic polynucleotide shown to inhibit L1210 ascites growth in vivo, was compared with 6-mercaptopurine (6-MP) for their effects on cellular kinetics of L1210 cells in vitro. These kinetic perturbations were monitored by changes in growth rates, cell volumes and cell-cycle distributions. At equimolar exposure doses (based on molar concentration of purine bases), 0.1 mM poly(s6I) was more effective than 6-MP in reducing growth rate and total cell number. A 20-fold increase in the 6-MP exposure dose (to 2 mM) was required to reduce total cell number similar to 0.1 mM poly(s6I). Concomitant determination of Coulter volume distributions of treated cell populations indicated 0.1 mM poly(s6I) increased the mean population volume more than either concentration of 6-MP. Cell-cycle distributions obtained by flow cytometry showed that, simultaneously with the increase in mean population volume, poly(s6I) exposure caused a decrease of cells in G1 and S and a pronounced accumulation of cells in G2. Treatment with 6-MP caused similar cell-cycle redistributions but always less than for poly(s6I). Flow sorting of these redistributed populations indicated the increase in mean population volume during treatment with 0.1 mM poly(s6I) was almost equally due to an increased percentage of G2 cells and to an increased volume of cells with the G2 DNA content. However, with 0.1 mM 6-MP, increased volume of G2 cells was predominant. Although poly(s6I) was synthesized in an attempt to develop more effective delivery forms of biologically active compounds like 6-MP and it has close structural similarities to 6-MP, its mechanism of action is unknown.

Animals↗
PubMed1980

A ribonucleic acid-specific antibody produced during autoimmune disease: evidence for nucleotide sequence specificity.

A hybridoma secreting RNA-binding autoantibody has been produced by fusion of spleen cells from autoimmune NZB/NZWF1 mice with drug-resistant IgG2b-producing myeloma cells from BALB/c mice. Studies on the specificity of the purified monoclonal autoantibody revealed: (a) absolute specificity for ribopolynucleotides as compared with deoxyribopolynucleotides; (b) specificity for single-stranded RNA as compared with double-stranded RNA; (c) high affinity for the random copolymer poly(G, C); and (d) preference for the random heteropolymer poly(G, C, U). These studies were complemented by stoichiometric measurements of the antibody-RNA complex and computer analysis of the abundance of various di-, tri- and tetranucleotide sequences in native RNA. Taken together, these data suggest that the antigenic determinant recognized by the monoclonal autoantibody is largely composed of a trinucleotide sequence of single-stranded RNA containing, G, C and U residues.

Animals↗
PubMed1978

Natural cell-mediated cytotoxicity in rats. III. Effects of immunopharmacologic treatments on natural reactivity and on reactivity augmented by polyinosinic-polycytidylic acid.

Treatment of rats with high doses of hydrocortisone, X-irradiation, or cyclophosphamide had a suppressive effect on natural cytotoxicity in vivo. However, when rats were given poly I:C after any of these agents, the levels of NK activity were similar to those in normal rats which had been given poly I:C alone. To explain these findings, we have postulated that a population of pre-NK cells, resistant to hydrocortisone, cyclophosphamide and X-irradiation was induced by poly I:C to become cytotoxic NK cells. Treatment of rats with silica, in doses that had no effect on proliferative responses of host lymphocytes to Con A in vitro, sharply diminished NK activity. With this agent, the boosting effect of poly I:C, although still detectable, was diminished. Since there is little if any indication that NK cells are phagocytic, these data suggest that phagocytes may play a role in maintaining high levels of NK activity in vivo and, further, may be involved in the mechanism by which natural cytotoxicity is boosted by poly I:C. Adult thymectomized rats had easily detectable levels of natural reactivity and the response to poly I:C was unimpaired, indicating a lack of thymic dependence for boosting as well as for spontaneous levels of NK activity.

Animals↗
PubMed1987

The first step in the functional inactivation of the Escherichia coli polynucleotide phosphorylase messenger is a ribonuclease III processing at the 5' end.

The transcripts covering pnp, the gene encoding polynucleotide phosphorylase, are processed by ribonuclease III. In this study, it is shown that the steady state level of the pnp mRNA increased 11-fold in a ribonuclease III-deficient strain. The synthesis rate of this messenger is only slightly affected in the mutant strain whereas the half-life, which is 1.5 min in the wild type, is considerably increased to more than 40 min. Moreover, polynucleotide phosphorylase is 10-fold over-expressed in the mutant strain, which shows that unprocessed pnp mRNA is functional. The position of the ribonuclease III-sensitive site suggests that the sequence involved in the stabilization of the pnp mRNA is located at the 5' end of the message and that the RNase III processing triggers the decay of the transcripts downstream. A similar function for ribonuclease III in the processing of the messenger for the beta beta' subunits of RNA polymerase is proposed.

Endoribonucleases↗
PubMed1992

E.coli polynucleotide phosphorylase expression is autoregulated through an RNase III-dependent mechanism.

It has been previously shown that the pnp messenger RNAs are cleaved by RNase III at the 5' end and that these cleavages induce a rapid decay of these messengers. A translational fusion between pnp and lacZ was introduced into the chromosome of a delta lac strain to study the expression of pnp. In the presence of increased cellular concentrations of polynucleotide phosphorylase, the level of the hybrid beta-galactosidase is repressed, whereas the synthesis rate of the corresponding message is not significantly affected. In the absence of pnp, the level of the hybrid protein increases strongly. Thus, polynucleotide phosphorylase is post-transcriptionally autocontrolled. However, autocontrol is totally abolished in strains where the RNase III site on the pnp message has been deleted or in strains devoid of RNase III. These results suggest that polynucleotide phosphorylase requires RNase III cleavages to autoregulate the translation of its message. Other mutations in the ribosome binding site region support the hypothesis that this 3' to 5' processive enzyme could recognize a specific repressor binding site at the 5' end of pnp mRNA. Implications of these results on the mechanism of regulation and on messenger degradation are discussed.

Base Sequence↗
PubMed1994

Structure of influenza virus RNP. I. Influenza virus nucleoprotein melts secondary structure in panhandle RNA and exposes the bases to the solvent.

The influenza virus genome consists of eight segments of negative-sense RNA, i.e. the viral (v) RNA forms the template for the mRNA. Each segment is encapsidated by the viral nucleoprotein to form a ribonucleoprotein (RNP) particle and each RNP carries its own polymerase complex. We studied the interaction of purified nucleoprotein with RNA in vitro, by using a variety of enzymatic and chemical probes for RNA conformation. Our results suggest that the nucleoprotein binds to the vRNA backbone without apparent sequence specificity, exposing the bases to the outside and melting all secondary structure. In this way, the viral polymerase may transcribe the RNA without the need for dissociating the nucleoprotein and without being stopped by RNA secondary structure, and the viral RNPs are ready to start transcription as soon as they enter the host cell.

Base Composition↗
PubMed1994

Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant.

The Escherichia coli rpsO gene gives rise to different mRNA species resulting either from termination of transcription or from processing of primary transcripts by RNase E and RNase III. The main degradation pathway of these transcripts involves a rate-limiting RNase E cleavage downstream of the structural gene which removes the 3' terminal stem-loop structure of the transcription terminator. This structure protects the message from the attack of 3'-5' exonucleases and its removal results in very rapid degradation of the transcript by polynucleotide phosphorylase and RNase II. Polynucleotide phosphorylase is also able to degrade slowly the mRNA harboring the 3' terminal hairpin of the terminator. In contrast, RNase II appears to protect the rpsO mRNA species which retains the 3' hairpin structure. Rapid degradation of the rpsO mRNA is observed after inactivation of RNase II even in a strain deficient for RNase E and polynucleotide phosphorylase. The enzyme(s) involved in this degradation pathway is not known. We detected an unstable elongated rpsO mRNA presumably resulting from the addition of nucleotides at the 3' end of the transcript.

Base Sequence↗
PubMed1989

Transformed cells overexpress a cytosolic nucleic acid binding protein.

A protein blotting technique was used to identify a 57,000 dalton cytosolic nucleic-acid-binding protein found in neoplastically transformed cell lines. Specifically, greater amounts of this protein were found in Kirsten Murine Sarcoma Virus-, Simian Virus 40-, and methylcholanthrene-transformed Balb 3T3 cells than in comparable untransformed cells. An analogous protein was identified in other transformed mammalian cells. Increased levels of the DNA binding protein in sarcoma virus transformants were shown to be dependent on the continued maintenance of the transformed phenotype. The properties of this protein are compared to those of other previously reported nucleic acid binding proteins.

Animals↗
PubMed2003

Failure to generate atheroprotective apolipoprotein AI phenotypes using synthetic RNA/DNA oligonucleotides (chimeraplasts).

BACKGROUND: Elevated plasma high-density lipoprotein (HDL), and its major constituent apolipoprotein AI (apoAI), are cardioprotective. Paradoxically, two natural variants of apoAI, termed apoAI(Milano) and apoAI(Paris), are associated with low HDL, but nevertheless provide remarkable protection against heart disease for heterozygous carriers and may even lead to longevity. Both variants arise from point mutations and have Arg(173) and Arg(151) to Cys substitutions, respectively, which allow disulphide-linked dimers to form. Potentially, synthetic RNA/DNA oligonucleotides (chimeraplasts) can permanently correct single point mutations in genomic DNA. Here, we use a variation of such targeted gene repair technology, 'gain-of-function chimeraplasty', and attempt to enhance the biological activity of apoAI by altering a single genomic base to generate the atheroprotective phenotypes, apoAI(Milano) and apoAI(Paris). METHODS: We targeted two cultured cell lines that secrete human apoAI, hepatoblastoma HepG2 cells and recombinant CHO-AI cells, using standard 68-mer chimeraplasts with polyethyleneimine (PEI) as carrier and then systematically varied several experimental conditions. As a positive control we targeted the dysfunctional APOE2 gene, which we have previously converted to wild-type APOE3. RESULTS: Conversion of wild-type apoAI to apoAI(Milano) proved refractory, with limited correction in CHO-AI cells only. However, a successful conversion to apoAI(Paris) was achieved, as demonstrated by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis and direct genomic sequencing. Unexpectedly, attempts with a new batch of 68-mer chimeraplast to enhance conversion, by using different delivery vehicles, including chemically modified PEI, failed to show a base change; nor could conversion be detected with an 80-mer or a 52-76-mer series. In contrast, when a co-culture of CHO-E2 and CHO-AI cells was co-targeted, a clear conversion of apoE2 to apoE3 was seen, whereas no apoAI(Paris) could be detected. When the individual chimeraplasts were analysed by denaturing electrophoresis only the active apoE2-to-E3 chimeraplast gave a sharp band. CONCLUSIONS: Our findings suggest that different batches of chimeraplasts have variable characteristics and that their quality may be a key factor for efficient targeting and/or base conversion. We conclude that, although an evolving technology with enormous potential, chimeraplast-directed gene repair remains problematical.

Animals↗
PubMed1976

RNA tumor virus-like activities in human solid tissues: endogenous RNA:DNA polymerase activities in the prostate.

Several human prostatic tissues have been examined for possible particles and associated DNA polymerizing activity generally associated with the C-type RNA tumor virus family. Partially purified tissue extracts, when centrifuged to equilibrium in sucrose gradients, yield fractions which contain actinomycin D resistant, endogenous DNA polymerase activity; this activity bands at a density of 1.15-1.18 gm/cm3. Further analysis of the endogenous products by sucrose gradient sedimentation suggested the presence of high molecular weight RNA:DNA hybrids generally felt to be indicative of a faithful copy of a lengthy stretch of viral specific RNA. However, most of the DNA products synthesized in these endogenous reactions sedimented in much lower molecular weight regions of these sucrose gradients. Clearly, the relative distributions of "high" and "low" molecular weight products could critically depend on the nuclease content of the subcellular fraction under study, and the prostate may be relatively enriched in nucleases. Further, oligo (dT) stimulated the endogenous DNA polymerase activity contained in these extracts, and omission of one of the DNA precursor nucleotides depressed it. Thus, it seems unlikely that terminal transferase activity, rather than genuine DNA polymerization, was being measured primarily. Because of the spectrum of molecular weight classes formed by these DNA:RNA hybrids, as well as their apparent presence in normal prostatic tissue, we find it difficult to ascribe their presence with certainty either to the presence of typical C-type RNA viruses or to the exclusive behavior of the neoplastic prostatic tissue. Thus, our studies lend support to the growing evidence for functions similar to those of C-type RNA viruses being relatively widespread in human tissues without the apparent necessity for a possible etiologic role in neoplastic production (Strand and August, 1974; Sherr et al., 1974). At the same time, our current studies emphasize the need for caution in drawing conclusions from results utilizing probes generally felt quite useful in scoring for presence of virus in lower animals at least in the human prostate.

Centrifugation, Density Gradient↗
PubMed1993

Polyethenoadenosine phosphate as a fluorogenic substrate for barnase.

Polyethenoadenosine phosphate is rapidly hydrolyzed by barnase with an accompanying large increase in fluorescence. At pH 8, 0.2 M ammonium acetate, the initial rate of fluorescence increase is proportional to barnase concentration and thus provides an excellent quantitative assay for its activity. The preparation and use of this substrate in the barnase assay is presented in detail.

Bacterial Proteins↗
PubMed1999

Photometric assay for polynucleotide phosphorylase.

Polynucleotide phosphorylase (PNPase) is a prokaryotic enzyme that catalyzes phosphorolysis of polynucleotides with release of NDPs. It is also believed to play a key role in turnover of prokaryotic transcripts, thus regulating gene expression. At the moment, only radioisotopic methods are available for assaying PNPase in crude extracts; these involve incubating [32P]phosphate and poly(A) in the presence of the enzyme, separating [32P]phosphate from [32P]ADP, and quantifying ADP by scintillation counting. Photometric assay using pyruvate kinase and lactate dehydrogenase as auxiliary enzymes is not feasible in crude extracts because of endogenous ATPase activities, which regenerate ADP from the ATP released by pyruvate kinase. Here, we present a simple photometric assay that uses a cyclic detection system which, due to the sequential action of pyruvate kinase and hexokinase, results in an exponential increase of ADP and glucose 6-phosphate. Glucose 6-phosphate is then revealed by a glucose-6-phosphate dehydrogenase reaction. Based on the theoretical model, a linear increase in absorbance is predicted as a function of the square of the reaction time, with a slope proportional to PNPase activity. Experimental data confirmed the theoretical predictions and showed that the assay was quantitative and unquestionably specific. We also devised a simple procedure for determining absolute enzyme activities (expressed in micromoles of product formed per minute) using exact amounts of pure PNPase as internal standards.

Adenosine Diphosphate↗
PubMed1994

Identification of a second poly(A) polymerase in Escherichia coli.

A second poly(A) polymerase (PAP II) has been identified in Escherichia coli using a strain carrying a deletion of pcnB (the structural gene for PAP I; Cao and Sarkar, 1992b) and pnp-7 (a null mutation in the structural gene for polynucleotide phosphorylase). While PAP I has a M(r) of 53,000, PAP II is a smaller protein with a native M(r)-35,000. PAP II differs from PAP I in preferring poly(A) over tRNA primers and being more thermolabile. The presence of multiple poly(A) polymerases in E. coli raises interesting questions regarding the role of polyadenylation in mRNA synthesis and decay.

Bacterial Proteins↗
PubMed1994

Short, terminally phosphorylated oligoriboguanylic acids effectively inhibit cytopathicity caused by human immunodeficiency virus.

Various synthetic ribonucleic acids were evaluated for inhibition of HIV-induced cytopathicity of cultured cells; only poly and oligoguanylic acids, but not other homopolymers, showed potent inhibitory activity. Phosphorylation of either the 5'- or 3'-end of oligoribonucleotides converted short inactive oligomers, such as dimers to effective anti-HIV agents. The efficacy of the 3'-phosphorylated phosphorothioate trimer of guanylic acid was comparable to that of other longer oligonucleotides so far reported. Phosphorothioate oligoriboguanylic acids were superior to the corresponding oligodeoxyguanylic acids in their capacity to prevent HIV cytopathicity.

Antiviral Agents↗