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PubMed1985

[Constraints on base sequences in a polynucleotide: I. Significance of the degeneration of the code].

The statistical study of polynucleotide sequences constituting the genes of E. coli, bacteriophages lambda and T7 reveals that constraints act upon nucleic acids (DNA or RNA) and contribute to determine the choice between the synonymous codons. The existence of synonymous codons seems to be the way of satisfying these constraints, keeping the possibility of specifying a large variety of polypeptides. At least in the case of amino acids with a small number of codons, these constraints are strong enough to influence the primary structure of proteins.

Bacteriophages↗
PubMedDate not supplied

[Amino acid composition of polynucleotide-peptide complexes isolated from algae].

The amino acid composition of the peptide moiety of sulphur containing polynucleotide-peptide complexes (S-PNPC) was studied with four species of green algae and two species of blue-green algae. S-PNPC contained almost all amino acids which were usually encountered in acid hydrolysates of proteins, and also unidentified ninhydrin-positive compounds. The amino acid composition of the peptide moiety of S-PNPC was rather similar in the case of different algae, and was characterized by the prevailence of acid amino acids.

Amino Acids↗
PubMed1979

Partial purification and characterisation of bat liver ribonuclease. Hydrolysis of purine and pyrimidine polynucleotides by bat liver RNase.

A ribonuclease has been extracted from bat liver and purified. From polyacrylamide gel electrophoresis, it was found that there is only one molecular weight unit in this enzyme and this has a molecular weight of about 28,000. This enzyme was found to hydrolyse both purine and pyrimidine polynucleotides (e.g. polyadenylic acid and polycytidylic acid respectively). Hydrolysis of polyadenylic acid was found to be faster than that of polycytidylic acid.

Animals↗
PubMed1982

Design of nucleoside, oligonucleotide and polynucleotide analogues as antiviral agents.

Several approaches can be envisaged in the design of nucleoside and oligo- or polynucleotide analogues with selective antiviral activity: (i) deoxythymidine (dThd) or deoxycytidine (dCyd) analogues which are specifically recognized as substrate by the virus-induced dThd-dCyd kinase; (ii) adenosine analogues which impair transmethylation reactions (or polyamine biosynthesis), by virtue of an inhibition of S-adenosylhomocysteine hydrolase; (iii) (2'-5')-oligonucleotide analogues derived from pppA(2'p5'A)2, an important intermediate in the antiviral action of interferon; (iv) oligo(deoxy)nucleotides that are complementary to a well-defined nucleotide sequence of the viral genome; (v) single-stranded homopolynucleotides that act as antitemplates for virus-associated RNA or DNA polymerases; and (vi) double-stranded homopolynucleotides that may be pursued for their interferon-inducing potentials.

Adenosine↗
PubMed1982

Independent locations of kinase and 3'-phosphatase activities on T4 polynucleotide kinase.

We have used two chemical modification reagents and three proteases to study the relationship between the two activities of T4 polynucleotide kinase. In each case, conditions were found where one of the two activities of the enzyme could be eliminated without greatly reducing the other. Taken together, these data indicate that the two activities are catalyzed by amino acid residues located in separate active sites on the polypeptide chain. Specific exopeptidase digestion indicates that the kinase activity lies in the NH2-terminal and the phosphatase in the COOH-terminal portion of the polypeptide chain. Partial trypsin digestion produces a 29,000-dalton fragment with no kinase activity and nearly normal 3'-phosphatase activity.

Binding Sites↗
PubMed1981

Function of nucleoside triphosphate and polynucleotide in Escherichia coli recA protein-directed cleavage of phage lambda repressor.

Escherichia coli recA protein catalyzes a specific proteolytic cleavage of repressors in vitro when it is activated by interaction with a single-stranded polynucleotide and nucleoside triphosphate. The ATP analogue adenosine-5'-O-(3-thiotriphosphate) (ATP gamma S) satisfies the NTP requirement. We show here that despite its activity in repressor cleavage, ATP gamma S is hydrolyzed at a negligible rate by the recA protein DNA-dependent nucleoside triphosphatase activity. In the presence of DNA, ATP gamma S binds tightly to recA protein in a complex that can be detected because it is trapped by a nitrocellulose filter. One ATP gamma S molecule is bound per recA monomer. These results suggest that a ternary complex of recA protein, DNA, and nucleoside triphosphate is the species active in repressor cleavage. The activation of recA protein by small, defined oligonucleotides in place of DNA is described and characterized.

Adenosine Triphosphate↗
PubMed1980

Non-stepwise methods in the preparation of building blocks for polynucleotide synthesis.

Oligonucleotide fragments of the general sequence ABn, BnC and ABnC as building units for polynucleotide synthesis can be obtained by three types of reactions, namely the sequence-specific co-condensation of nucleic acid constituents, the sequence-specific degradation of copolymers and the limited addition of nucleotides to primers. Examples for these reactions are described and the scope and application of the approach discussed.

Base Sequence↗
PubMed1981

The purification of polynucleotide phosphorylase from Thermus aquaticus by the use of heparin-sepharose 4B affinity chromatography.

The polynucleotide phosphorylase of Thermus aquaticus was purified using ammonium sulfate fractionation and column chromatography on DEAE-cellulose, heparin-Sepharose 4B and DEAE-Sephadex A25. The enzyme was purified 1500-fold and was 90-95% homogeneous as checked by polyacrylamide gel electrophoresis. It has a molecular weight of 275 000 and consists of four identical subunits. The Km values for the enzyme as determined in polymerization (ADP, GDP, UDP) and phosphorolytic reactions (poly A, poly U) are in the same concentration range as in the case of the enzyme deriving from mesophilic microorganisms. Furthermore, the enzyme is primer dependent and its activity is lost gradually at temperatures higher than 65 degrees C. In the base ratio of the copolymers followed the input base ratio polymerization reactions with polyUA, while with polyAG and polyUG a marked difference between the initial base ratio and the base composition of copolymers was observed.

Base Composition↗
PubMedDate not supplied

[A method of comparison of DNA polynucleotide sequences].

The results of a comparative analysis of the kinetic curves of reassociation of DNA of closely related species of Microtus (Microtus arvalis, Microtus oeconomus oeconomus, Microtus oeconomus Chachlovi) are presented. A five power polynomial was used as a mathematical model of the kinetic DNA reassociation curves. The values of polynomial coefficients and the theoretical value, both with statistical deviations dispersion, have been estimated with the help of a standard computer programme. The modified Fischer criterium was used for comparing the model kinetic curves of reassociation of the above species and of subspecies of Microtus, and to estimate the significance of the difference between two random means. A pair-wise comparison of the model curves shows that the similarity of the DNA polynucleotide sequences in two subspecies is less expressed than in two species of Microtus. A method of comparison of DNA nucleotide sequences is suggested on the basis of mathematical models of kinetic curves of DNA reassociation.

Animals↗
PubMed1994

Novel approach to molecular cloning and polynucleotide synthesis using vaccinia DNA topoisomerase.

Construction of chimaeric DNA molecules in vitro relies traditionally on two enzymatic steps catalyzed by separate protein components. Site-specific restriction endonucleases are used to generate linear DNAs with defined termini that can then be joined covalently at their ends via the action of DNA ligase. A novel approach to the synthesis of recombinant DNAs exploits the ability of a single enzyme, vaccinia DNA topoisomerase, to both cleave and rejoin DNA strands with extreme specificity at each step. Placement of the CCCTT cleavage motif for vaccinia topoisomerase near the end of a duplex DNA permits efficient generation of a stable, highly recombinogenic protein-DNA adduct that can religate only to acceptor DNAs that contain complementary single-strand extensions. Linear DNAs containing CCCTT cleavage sites at both ends (bivalent substrates) can be activated by topoisomerase and inserted into a plasmid vector in a simple and rapid in vitro procedure that is especially well suited to the molecular cloning of polymerase chain reaction-amplified DNAs. Activation of polyvalent (e.g. branched) DNA substrates by topoisomerase offers a potentially powerful method for the synthesis of two- and three-dimensional polynucleotide networks.

Base Sequence↗
PubMed1994

A poly(A) binding protein-specific sequence motif: MRTENGKSKGFGFVC binding to mRNA poly(A) and polynucleotides and its role on mRNA translation.

A consensus sequence (GKSKGFGFV) was recognized in all the sequenced poly(A) binding proteins. We synthesized a 15-amino acid peptide (corresponding to 354-368 in the yeast poly(A) binding protein) which includes the consensus sequence to test its binding affinity to different nucleotides, polynucleotides and mRNA with or without a poly(A) tail. Biochemical and biophysical studies revealed that the 15-amino acid peptide has a strong binding affinity to poly(A) alone or poly(A) attached at the 3' end of mRNA. Circular dichroism spectroscopy demonstrated that the secondary structure of the 15-mer is consistent with that expected based on the structure of the native RNP domain. Furthermore, among the various mononucleotides performed in the present studies, ATP was preferentially found to bind to the 15-mer. To further examine the biological significance of the binding of the 15-mer to the poly(A) tail of mRNA, in vitro translation of the mRNA poly(A)+ in the presence of the 15-mer drastically increased globin synthesis by almost 2-fold, while translation of the deadenylated mRNA in the presence of the 15-mer almost did not alter the rate of incorporation of radiolabeled leucine into globin.

Amino Acid Sequence↗
PubMed1977

Purification and characterization of core-associated polynucleotide 5'-triphosphatase from Vaccinia virus.

A core-associated enzyme, designated as polynucleotide 5'-triphosphatase, has been purified from vaccinia. Fractionation on ADP-agarose of the soluble extract from detergent-disrupted cores followed by chromatography on poly(U)-agarose produced an 80-fold purification of the enzyme. The enzyme has an approximate molecular weight of 113,000 and is composed of two polypeptides with approximate molecular weights of 90,000 and 26,000. Divalent metal ions are necessary for enzymatic activity, which occurs optimally at pH 8.4. The enzyme acts upon 5'-ATP- and 5'-GTP-terminated RNA and also on 5'-ATP-terminated poly(A), catalyzing the hydrolysis of only the gamma-phosphate. The presumed biological role of the enzyme based upon this specificity is the participation in the initial step in the sequence of reactions through which the primary 5' termini of vaccinia messenger RNA are capped with the groups m7G(5')ppp(5')NmpN-.

Chemical Phenomena↗
PubMed1995

Interaction of yeast elongation factor 3 with polynucleotides, ribosomal RNA and ribosomal subunits.

In addition to the two usual eukaryotic elongation factors (EF-1 alpha and EF-2) fungal ribosomes need a third protein, elongation factor 3, for translation. EF-3 is essential for in vivo and in vitro protein synthesis. Functionally, EF-3 stimulates EF-1 alpha dependent binding of aminoacyl-tRNA to the ribosomal A site when E site is occupied by deacylated tRNA. EF-3 has intrinsic ATPase activity which is regulated by the functional state of the ribosome. EF-3 ATPase is activated by both 40S and 60S ribosomal subunits. However intact 80S ribosomes are needed for efficient activation of EF-3 ATPase. EF-3 appears to be an RNA binding protein with high affinity for polynucleotides containing guanosine rich sequences. To determine whether guanosine rich sequence of ribosomal RNA is involved in EF-3 binding, an antisense oligonucleotide dC6 was used to block EF-3 interaction with the ribosome. The oligonucleotide suppresses activation of EF-3 ATPase by 40S ribosomal subunit and not by the 60S or the 80S particles. Poly(U)-directed polyphenylalanine synthesis by yeast ribosomes is inhibited by dC6. To define the binding site of the oligonucleotide and presumably of EF-3 on 18S ribosomal RNA, hydrolysis of rRNA by RNase H was followed in the presence of dC6. These experiments reveal an RNase H cleavage site at 1094GGGGGG1099 sequence of 18S ribosomal RNA. This guanosine rich sequence of rRNA is suggested to be involved in EF-3 binding to yeast ribosome. Data presented in this communication suggest that the activity of EF-3 involved a direct interaction with the guanosine rich sequence of rRNA.

Fungal Proteins↗
PubMedDate not supplied

Polynucleotide sequence divergence among strains of Salmonella sub-genus IV and closely related organisms.

Polynucleotide sequence relatedness studies were carried out to determine the extent of divergence present in Salmonella sub-genus IV strains, related strains of Salmonella of other sub-genera and the Citrobacter genus. Salmonella sub-genus IV were 91-97% related. The Salmonella of sub-genus I, II and III showed lower binding (79-87%) to Salmonella sub-genus IV. The change in thermal elution midpoint closely followed the reassociation data. Relatedness of Salmonella sub-genus IV and C. freundii ranged between 44 and 57%, which confirms that these organisms belong to different genera. The taxonomic position of Salmonella sub-genus IV is discussed according to the actual classification of the family Enterobacteriaceae.

Base Sequence↗
PubMed2002

Polysaccharide-polynucleotide complexes VIII. Cation-induced complex formation between polyuridylic acid and schizophyllan.

Schizophyllan belongs to the beta-1,3-D-glucan family, and dissolves as a single chain in dimethyl sulfoxide (DMSO) and as a triple helix in water, respectively. It is already known that when we prepare a mixture of poly(C) and schizophyllan in DMSO and subsequently exchange the solvent to water, poly(C) and schizophyllan can form a complex. When we applied this procedure to the poly(U) system, we could not induce the complex formation between poly(U) and schizophyllan at all. However, we found that addition of some alkaline cations is necessary to induce the complexation between poly(U) and schizophyllan. The complex stability strongly depends on both the cation species and the salt concentration. The complexation is sensitively reflected in the CD spectrum. The magnitude of the spectral change is followed by the order; Rb(+) >> K(+) > Na(+) ? Cs(+). This cation order in the stability is confirmed by the fluorescence polarization measurements. (23)Na-NMR spectroscopy reveals that the product system is stabilized by addition of the cations, suggesting that the OH group in schizophyllan and the phosphate anion in poly(U) synergistically form a specific ligand system for the cations. To the best of our knowledge, such a cation-induced specific interaction between saccharides and polynucleotides has not been reported, and may provide a new clue to understand the biological role of beta-1,3-D-glucans.

Circular Dichroism↗
PubMed1975

Polynucleotide aggregates enhance the transport of protein at the surface of cultured mammalian cells.

It was known that polycationic polymers enhance the entry of macromolecules into cells. We now show that polynucleotides may have similar effects, when used as large aggregates. Poly(1-vinylcytosine):polyinosinic acid, an inducer of interferon production in human cells, can cause at 40 mug/ml a 75-fold enhancement of albumin uptake by sarcoma cells in culture. Most of this activity (85%) is related to the presence of aggregates retained by 0.65 mu millipore membranes. The prior finding that enhancers of albumin transport have increasing effects with increasing molecular sizes may thus extend to complexes of supramolecular sizes.

Adsorption↗
PubMed1993

The influence of DNA structure on the in vitro stimulation of murine lymphocytes by natural and synthetic polynucleotide antigens.

Although DNA is generally considered to be a poor immunogen, recent evidence suggests that DNA from various species differ in their immunological activity and that bacterial DNA can induce the in vitro proliferation of normal murine B cells. To delineate structural features of DNA associated with mitogenic activity, the response of murine lymphocytes to various natural and synthetic polynucleotides was determined. Both ss and dsDNA from two different bacterial strains were equally effective in inducing proliferation. This response was independent of adenosine methylation, since DNA from dam- Escherichia coli stimulated proliferation. Among the synthetic polymers tested, only the duplexes poly(dG).poly(dC), and poly(dG.dC) were mitogenic, while polymers containing dA, dT, or dI alone or in combination with dG and dC were inactive. The mitogenic activity of poly(dG.dC) was eliminated, however, upon substitution of rG for dG or 5medC for dC. The mitogenic activity did not require high molecular weight DNA since active polymers ranged in size from approximately 260 to 800 base pairs. In addition, E. coli DNA fragments of 50-300 and 125-600 bases were mitogenic. Together, these data suggest that the mitogenic activity of DNA is dependent on sequence-specific determinants that can be presented by synthetic DNA duplexes as well as bacterial ss and dsDNA.

Animals↗
PubMed1994

Nucleolytic inactivation and degradation of the RNase III processed pnp message encoding polynucleotide phosphorylase of Escherichia coli.

The two cleavages made by RNase III in the transcripts of the pnp gene of Escherichia coli, 80 nucleotides upstream of the coding sequence of polynucleotide phosphorylase, were previously demonstrated to trigger the rapid degradation of the pnp messenger. In this paper, we demonstrate that the 5' end of the RNase III processed pnp mRNA is attacked by ribonucleases more efficiently than the rest of the molecule. Several 5' extremities resulting from cleavages occurring in the first 500 nucleotides of the pnp transcript have been identified. Three of them referred to as X, Y and W occur in the wild-type strain at the beginning of the coding sequence of the pnp mRNA. The mRNA appears to be cleaved more efficiently at the X site, proximal to the initiation codon, than at sites Y and W located downstream. In vitro, the maturation at X is catalysed by RNase E but not by RNase III. Accumulation of RNA processed at X in RNase E deficient strains leads us to postulate that X is a high affinity primary site which is slowly cleaved by the residual activity of thermosensitive RNase E at non-permissive temperature and that secondary sites located downstream are processed less efficiently than X. Taken together, our results suggest that in wild-type E. coli the degradation of the RNase III processed mRNA is mediated by RNase E.

Base Sequence↗