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PubMed1998

Nucleic acid vibrational circular dichroism, absorption, and linear dichroism spectra. II. A DeVoe theory approach.

The DeVoe polarizability theory is used to calculate vibrational circular dichroism (VCD) and infrared (IR) absorption spectra of four polyribonucleotides: poly(rA) x poly(rU), poly(rU) x poly(rA) x poly(rU), poly(rG) x poly(rC), and poly(rC+) x poly(rI) x poly(rC). This is the first report on the use of the DeVoe theory to calculate VCD, oriented VCD, IR absorption, and IR linear dichroism (LD) spectra of double- and triple-stranded polyribonucleotides. Results are reported for DeVoe theory calculations--within the base-stretching 1750-1550 cm(-1) spectral region--on several proposed multistranded polyribonucleotide geometries. The calculated spectra obtained from these proposed geometries are compared with previously reported measured and calculated VCD and IR spectral results. Base-base hydrogen-bonding effects on the frequencies and magnitudes of the base carbonyl stretching modes are explicitly considered. The good agreements found between calculated and measured spectra are proposed to be further evidence of the usefulness of the DeVoe theory in drawing three-dimensional structural conclusions from measured polyribonucleotide VCD and IR spectra.

Circular Dichroism↗
PubMed1989

RNA-induced transformation of the estrogen receptor detected by a monoclonal antibody which recognizes the activated receptor.

The effect of RNA and polyribonucleotides on the estrogen receptor from fetal guinea pig uterus was studied through the analysis of the sedimentation properties of this receptor and its interaction with the monoclonal antibody D547. Different exogenous RNAs (calf thymus RNA, yeast RNA and rabbit liver transfer RNA) were able to induce a transformation of the 9S native receptor to 4.5-7S sedimenting forms in low salt sucrose density gradients, as activating factors such as temperature and time do. This transformation was prevented by 20mM sodium molybdate. Moreover, the RNA treated receptor was partially recognized by the monoclonal antibody D547. This antibody, as was demonstrated previously, selectively reacts with the activated form of this receptor. When different homo-polyribonucleotides were tested, the effect depended on their composition. In contrast, DNA did not affect either the sedimentation properties of the receptor or its reaction with the antibody. These observations suggest that RNA induces a dissociation of the 9S receptor and that at least one of the resulting forms is the activated receptor. However, RNA and polyribonucleotides inhibited the receptor binding to DNA-cellulose apparently by competing with DNA. The data suggest a role of RNA in estrogen receptor activation.

Animals↗
PubMed1978

Enzymatic conversion of 5'-phosphate-terminated RNA to 5'-di- and triphosphate-terminated RNA.

We have isolated from vaccinia virus cores an enzyme, 5'-phosphate-polyribonucleotide kinase, that in the presence of ATP and Mg2+ catalyzes the conversion of 5'-phosphate and 5'-diphosphate termini of RNA to the 5'-triphosphate species. With the exception of dATP, other nucleoside triphosphates were inactive as phosphate donors; activity with dATP was 10% of that observed with ATP. The purified enzyme did not phosphorylate 5'-hydroxyl- or 5'-monophosphate-terminated polydeoxyribonucleotides, although a variety of 5'- monophosphate-terminated RNA chains were active as phosphate acceptors. By using a coupled system of 5'-phosphate-polyribonucleotide kinase and guanylyltransferase in the presence of ATP, GTP, Mg2+, and S-adenosylmethionine, capping of 5'-P-, 5'-PP-, and 5'-PPP-RNA was demonstrated; in the absence of 5'-phosphate-polyribonucleotide kinase only 5'-PPP-RNA was capped by guanylyltransferase.

Adenosine Triphosphate↗
PubMed1999

RNAs in the sera of Persian Gulf War veterans have segments homologous to chromosome 22q11.2.

Reverse transcriptase PCR (RT-PCR) was used for polyribonucleotide assays with sera from deployed Persian Gulf War veterans with the Gulf War Syndrome and a cohort of nonmilitary controls. Sera from veterans contained polyribonucleotides (amplicons) that were obtained by RT-PCR and that ranged in size from 200 to ca. 2,000 bp. Sera from controls did not contain amplicons larger than 450 bp. DNA sequences were derived from two amplicons unique to veterans. These amplicons, which were 414 and 759 nucleotides, were unrelated to each other or to any sequence in gene bank databases. The amplicons contained short segments that were homologous to regions of chromosome 22q11.2, an antigen-responsive hot spot for genetic rearrangements. Many of these short amplicon segments occurred near, between, or in chromosome 22q11.2 Alu sequences. These results suggest that genetic alterations in the 22q11.2 region, possibly induced by exposures to environmental genotoxins during the Persian Gulf War, may have played a role in the pathogenesis of the Gulf War Syndrome. However, the data did not exclude the possibility that other chromosomes also may have been involved. Nonetheless, the detection of polyribonucleotides such as those reported here may have application to the laboratory diagnosis of chronic diseases that have a multifactorial etiology.

Adult↗
PubMed1994

Human pancreatic-type and nonpancreatic-type ribonucleases: a direct side-by-side comparison of their catalytic properties.

The catalytic properties and substrate preference of several highly purified human ribonucleases from different organs and body fluids have been examined in detail using various low-molecular-weight compounds and single- or double-stranded polyribonucleotides as substrates. All single-stranded polyribonucleotides were degraded by nonpancreatic-type (npt) RNases at a slower rate than by pancreatic-type (pt) enzymes: ptRNases were 20 times more active on RNA and poly(U) substrates and more than 6000 times more active on poly(C). Pancreatic-type RNases degraded poly(C) faster than RNA, showing a strong preference for poly(C) over poly(U) with the following activity ratios: RNA/poly(C), 0.44; RNA/poly(U), 12; poly(C)/poly(U), 27. In contrast, nptRNases cleaved RNA more rapidly than synthetic homopolymers, preferring poly(U) over poly(C) with the following ratios: RNA/poly(C), 130; RNA/poly(U), 10; poly(C)/poly(U), 0.08. Human ptRNases degraded poly(A) and double-stranded polyribonucleotides about 100 and 400 times faster, respectively, than bovine RNase A. However, no measurable activity could be detected on these substrates with nptRNases. The activities of ptRNases on dinucleoside phosphates (CpN and UpN) or uridine and cytidine 2',3'-cyclic phosphates were similar to those of bovine RNase A; nptRNases, instead, cleaved only CpA and UpA at an appreciable rate. The effects of pH, ionic strength, and divalent cations on the activity of these ribonucleases were also investigated using yeast RNA as a substrate.

Catalysis↗
PubMed2002

Structural and thermodynamic features of complexes formed by DNA and synthetic polynucleotides with dodecylamine and dodecyltrimethylammonium bromide.

Complex formation of native and denatured DNA, single-stranded polyribonucleotides poly(A) and poly(U), as well as double-stranded poly(A).poly(U) with dodecylamine (DDA) and dodecyltrimethylammonium bromide (DTAB) has been studied by UV-, CD-, IR-spectroscopy and fluorescence analysis of hydrophobic probe pyrene. DDA and DTAB were shown to bind cooperatively with DNA and polyribonucleotides, resulting in the formation of complexes containing hydrophobic micelle-like clusters. Critical aggregation concentration (CAC) of DDA and DTAB shifts sharply to lower values (30-50 times) in the presence of DNA and polynucleotides as compared to critical micelle concentration (CMC) of free DDA and DTAB in solution. The analysis of binding isotherms within the frame of the model of cooperative binding of low-molecular ligands to linear polymers allowed us to determine the thermodynamic parameters of complex formation and estimate the contribution of electrostatic interaction of positively charged heads of amphiphiles with negatively charged phosphate groups of DNA and polyribonucleotides, and hydrophobic interaction of aliphatic chains to complex stability. Electrostatic interaction was shown to make the main contribution to the stability of DNA complexes with DDA, while preferential contribution of hydrophobic interactions is characteristic of DTAB complexes with DNA. The opposite effect of DDA and DTAB on the thermal stability of DNA double helix was demonstrated from UV-melting of DNA-while DTAB stabilizes the DNA helix, DDA, to the contrary, destabilizes it. The destabilizing effect of DDA seems to originate from the displacement of intramolecular hydrogen bonds in complementary Watson-Crick A.T and G.C base pairs with intermolecular H-bonds between unsubstituted DDA amino groups and proton-accepting sites of nucleic bases.

Amines↗
PubMed1999

Inosine and N1-methylinosine within a synthetic oligomer mimicking the anticodon loop of human tRNA(Ala) are major epitopes for anti-PL-12 myositis autoantibodies.

Sera of some patients afflicted with the inflammatory disease myositis contain antibodies of the anti-PL-12 type. A fraction of these polyclonal autoantibodies specifically precipitates the fully matured human tRNA(Ala) bearing the anticodon IGC (PL-12 antigen). Earlier work (Bunn & Mathews, 1987, Science 238:116-119) had shown that the epitopes are located entirely within the anticodon stem-loop of the tRNA(Ala). Here we demonstrate that human anti-tRNA(Ala) autoantibodies immunoprecipitate a synthetic polyribonucleotide containing inosine (I) and N1-methylinosine (m1I) separated by 2 nt as in the anticodon stem-loop of human tRNA(Ala). The shortest polyribonucleotide that can be immunoprecipitated corresponds to the pentanucleotide IpGpCpm1IpUp, which corresponds to part of the anticodon loop of human tRNA(Ala) and lacks the stem-loop structure. The efficiency of immunoprecipitation was about four times greater with longer polyribonucleotides capable of forming a stem-loop structure, and was abolished by altering the relative positions of I and m1I within the synthetic polynucleotide. Synthetic oligodeoxyribonucleotide analogs of the tRNA(Ala) stem-loop, containing the sequence dIpdGdCdm1Ip, are not antigenic. Our results show that human anti-tRNA(Ala) autoantibodies selectively recognize chemical details of modified nucleotides (the 6-keto group of inosine-34 and the 6-keto group and the N1-methyl groups of N1-methylinosine-37) within an anticodon loop structure of a tRNA molecule. We also describe the chemical synthesis of the phosphoramidite derivatives corresponding to N1-methylinosine and N1-methyl-2'-deoxyinosine for use in the automatic chemical synthesis of oligonucleotides containing N1-methylinosine and N1-methyl-2'-deoxyinosine.

Antibodies, Antiphospholipid↗
PubMed1971

Primer requirement and template specificity of the DNA polymerase of RNA tumor viruses.

Polyribonucleotides will act as efficient templates for the DNA polymerases found in the virions of avian myeloblastosis virus and mouse leukemia virus if a short complementary oligodeoxyribonucleotide primer is added. Synthesis of the complementary polydeoxyribonucleotide continues until an amount of polymer equal to the amount of initial template has been produced. The two viruses show slightly different specificities toward the four homoribopolymers. Polydeoxyribonucleotides are generally much poorer templates than the homologous polyribonucleotides, in most cases yielding no detectable synthesis. The DNA polymerase of RNA tumor viruses, therefore, have the same requirements for activity as do other DNA polymerases, except that they prefer polyribonucleotides over polydeoxyribonucleotides as templates.

Adenine Nucleotides↗
PubMed1986

Protein synthesis in yeast Saccharomyces cerevisiae. Purification of Co-eIF-2A and 'mRNA-binding factor(s)' and studies of their roles in Met-tRNAf.40S.mRNA complex formation.

Antibodies prepared against a homogeneous preparation of Co-eIF-2A20 [Ahmad et al. (1985) J. Biol. Chem. 260, 6955-6959] reacted with several polypeptides including an 80-kDa polypeptide present in a crude yeast ribosomal salt wash. This 80-kDa polypeptide, containing Co-eIF-2A (Co-eIF-2A80) activity, has been extensively purified using a two-step purification procedure involving an immunoaffinity column chromatograph prepared using antibodies against Co-eIF-2A20 (fraction II) and hydroxyapatite chromatography (fraction III). The factors, eIF-2 + homogeneous Co-eIF-2A80 (fraction III) promoted Met-tRNAf.40S complex formation with an AUG codon but not with a physiological mRNA or a polyribonucleotide messenger poly(U,G) whereas eIF-2 + a partially purified Co-eIF-2A80 preparation (fraction II) promoted Met-tRNAf.40S complex formation with an AUG codon as well as with globin mRNA and poly(U,G) messenger. This factor-promoted Met-tRNAf binding to 40S ribosomes depends absolutely on the presence of a polyribonucleotide messenger containing an initiation codon (such as AUG or GUG). Other polyribonucleotide messengers tested, such as poly(U), poly(A) and poly(A,C) were completely ineffective in this binding reaction. This result indicates that the Met-tRNAf.40S.mRNA complex is formed by a direct interaction between Met-tRNAf, 40S ribosomes and the initiation site in mRNA. A mechanism has been proposed for Met-tRNAf.40S.mRNA complex formation in yeast.

Carrier Proteins↗
PubMed1993

[Are immunomodulators capable to improve the activity of nucleoside antiretroviral agents?].

Synthetic polyribonucleotides stimulate cells to produce interferons and other cytokines and increase both humoral and cell-mediated immunity. The polynucleotide complexes affect host defense system and may have antiviral properties. Studies in animal models of experimental viral infection may therefore be performed to define a possible strategy for their use in human disease. Antiviral properties of polyribonucleotides have been demonstrated in animals, especially in murine models of retroviral infection. In the early treatment of Friend virus infection, the antiretroviral effect of zidovudine is enhanced by combination with poly I poly C or poly A poly U. Polyribonucleotides also enhance the inhibitory effect of zidovudine on HIV replication in lymphocyte T or macrophage cultures. Therefore this class of compounds could be used in combination with antiviral agents in the treatment of HIV infection, especially when they induce no significant toxicity as it is the case for poly A poly U.

Adjuvants, Immunologic↗
PubMed1975

Polynucleotide phosphorylase from Streptomyces aureofaciens: purification and properties.

1. Polynucleotide phosphorylase from a chlortetracycline-producing strain of Streptomyces aureofaciens was isolated by Polymin P fractionation. Using chromatography on DEAE-cellulose and Sephadex G-150 the enzyme, which appears homogeneous in gel chromatography and sedimentation analysis, was purified 2000-fole giving a final yield of 15%. 2. The sedimentation coefficient (s-o 20, w) of the native enzyme in 0.2 M NaCl is 9.15 S and its molecular weight is 210 000 plus or minus 15 000. Molecular weight estimated by sodium dodecylsulfate gel electrophoresis was about 100 000. 3. We have determined the optimal conditions for nucleoside 5'-diphosphate polymerization, their phosphate exchange and phosphorolysis of polyribonucleotides catalysed by polynucleotide phosphorylase from S. aureofaciens. 4. Chlortetracycline is a competitive inhibitor of S. aureofaciens polynucleotide phosphorylase. 5. Polynucleotide phosphorylase is activated in the polymerization reaction by ionic strength (K+, Na+, NH4+) while polyribonucleotide phosphorolysis is activated only by NH4+.

Ammonia↗
PubMed1975

An improved fluorescence probe cytotoxicity assay.

The phenanthridine dye, ethidium bromide, which is actively excluded by viable cells, undergoes a significant fluorescence enhancement at 5900 A upon binding intracellular double-stranded polyribonucleotides. A rapid and sensitive assay of antibody mediated cytotoxicity to cells grown in vitro has been developed using this phenomenon. In this communication, we describe this fluorescence probe cytotoxicity assay and a sensitive electro-optical system designed to measure the fluorescence enhancement of ethidium bromide as it intercalates with intracellular polyribonucleotides. Basic characteristics of the fluorescence enhancement resulting from the interaction of ethidium bromide and non-viable cells are presented as well as examples of this assay as it has been used to study surface membrane neoantigens of cells tranformed by the oncogenic DNA virus, SV40.

Animals↗
PubMed1972

Purification and properties of bacteriophage T4-induced RNA ligase.

An enzyme, purified 300-fold from Escherichia coli infected with bacteriophage T4, catalyzes the conversion of 5'-termini of polyribonucleotides to internal phosphodiester bonds. The reaction requires ATP and Mg(++). For every 5'-(32)P terminus rendered resistant to alkaline phosphatase, an equal amount of AMP and PPi are formed. Various polyribonucleotides are substrates in the reaction; to date, the best substrate is [5'-(32)P]polyriboadenylate. With the latter substrate, no evidence of intermolecular reaction was obtained. However, the 5'-(32)P termini of poly(A) rendered resistant to alkaline phosphatase are also resistant to attack by RNase II, polynucleotide phosphorylase, and low concentrations of venom phosphodiesterase. Since the product formed with poly(A) lacks 3'-hydroxyl ends, as measured with these exonucleases, the enzyme appears to convert linear molecules of polyriboadenylate to a circular form by the intramolecular covalent linkage of the 5'-phosphate end to the 3'-hydroxyl terminus.

Adenosine Monophosphate↗
PubMed1977

Effect of homopolyribonucleotides on messenger ribonucleoprotein particles.

A discrete set of polypeptides copurify with and appear to be specifically attached to mRNA from polysomes of eukaryotic cells. This report describes the effect of homopolyribonucleotides on mRNA-protein complexes separated from ribosome subunits by oligo(dT)-cellulose chromatography. It is shown that poly (U) and poly (A) can release mRNA-protein complexes adsorbed to oligo(dT)-cellulose, whereas poly (C) and poly(I) are much less effective in this process. Analysis of polyribonucleotide released material showed that poly(U) effectively dissociated the mRNA-protein complexes while poly(A) caused no or only partial derangement of these particles. The specificities seen in the polyribonucleotide effects in turn suggest a high degree of specificity in the interaction between the proteins and mRNA.

Adenoviridae↗
PubMed1995

2'-Fluoropolynucleotide-directed reverse transcriptase reactions. Effect of homologous polynucleotides.

Several homologous polynucleotides have been tested as inhibitors on the reactions catalyzed by avian myeloblastosis virus (AMV) reverse transcriptase, in the presence of polyribonucleotides and 2'-fluorinated polynucleotides as templates. Polynucleotides differentially inhibited the reactions catalyzed by reverse transcriptase in the presence of these synthetic templates. Polyriboadenylic acid (poly(rA), poly(2'-O-methyladenylic acid) (poly(Am)), poly(2'-fluoro-2'-deoxyadenylic acid) (poly(dAfl), polyinosinic acid (poly(rI)) and polyuridylic acid poly(rU)) inhibited the polyribonucleotide-, but not the 2'-fluorinated polynucleotide-directed reverse transcriptase activity.

Avian Myeloblastosis Virus↗
PubMed1985

Calcium-dependent endoribonuclease of Trypanosoma brucei has a base-preferential affinity to adenylate.

The substrate specificity of a calcium-dependent endoribonuclease of Trypanosoma brucei cytoplasm has been further determined. The actions of the enzyme on transfer RNA, ribosomal RNA and various synthetic polyribonucleotides indicate that the enzyme degrades double-stranded as well as single-stranded RNAs; while it preferentially hydrolyses polyribonucleotides having adenylic acid residues, and has a pronounced preference for poly (adenylic acid). Its apparent Michaelis constant (Km) values using different substrates also suggest a base-preferential affinity of the enzyme to adenylate. The relative activity of the ribonuclease against homopolyribonucleotides is poly(A) greater than poly(U) greater than poly(C); while poly(G) is completely resistant to the activity. Poly(A) segments on poly(A)-rich RNA are selectively hydrolyzed by the endoribonuclease. A possible implication of this enzyme in the post-transcriptional modification and turnover of mRNA molecules is suggested.

Adenosine Monophosphate↗
PubMed1984

Proximity of polyriboguanylic acid-reactive sites in mammalian DNA to portions of DNA preferentially hybridizing with cellular RNA.

Transcribed portions of mouse nuclear DNA are adjacent to sites reacting preferentially with polyriboguanylic acid [poly(G)]. This spatial relationship was suggested by hybridization of radioactively labeled Ehrlich ascites RNA with denatured mouse DNA, the latter fractionated by centrifugation in CsCl equilibrium density gradients both in the presence and in the absence of various synthetic polyribonucleotides. The fractions of DNA which preferentially reacted with guanylic acid-rich polyribonucleotides hybridized with radioactive RNA to a higher degree than did the bulk of cellular DNA. This ability to react with polyriboguanylic acid-containing polymers was further enhanced by breaking DNA by sonication. No increased tendency for such hybridization was seen with the DNA that preferentially reacted with polyribouridylic acid.

Animals↗