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At least 721 records · Page 40Linked to original sources
PubMed1979

Addition of short guanylyl blocks to oligonucleotide primers with a thermophilic polynucleotide phosphorylase. Its application to the synthesis of oligonucleotides containing guanylyl residues.

Polynucleotide phosphorylase from Thermus thermophilus catalyzed the addition of short guanylyl blocks from GDP to the 3'-hydroxyl termini of oligonucleotide primers at low temperature in a simple reaction mixture. Polyguanylic acid formation was inhibited at 37 degrees C, but the addition of one or two guanylyl residues to oligonucleotide primers proceeded in high yields. The reaction was applied to the synthesis of oligonucleotides containing guanylyl residues at the 3'-end. Using (Ap)2A and (Up)2U as primers, (Ap)3G, (Ap)3GpG, and (Up)3G were synthesized in yields of 25--52%. (Ap)2GpG was synthesized from ApA and GDP in a yield of 13%.

Guanine↗
PubMed1980

Electrostatic components of drug-receptor recognition. I. Structural and sequence analogues of DNA polynucleotides.

The electrostatic fields associated with the important biological receptor DNA have been studied by means of stereoscopic displays to investigate drug-receptor recognition processes. This revealed great differences between A- and B-type structures and enabled significant nucleotide sequence effects to be detected for the latter helix. These variations were further investigated by topological analysis of the surface potential in the two grooves of the B-DNA duplex at different radii from the helix axis. This made it possible to characterize the potential surface and to allocate curvature changes to specific atomic groupings. A general finding was that larger potential fields were found in the space encompassed by the narrow groove with strong potential gradients from the ends of the helix to the centre in both grooves. This gradient may provide a motive force for translating small molecules on the surface of a polynucleotide.

DNA↗
PubMed1975

Interferon induction by viruses and polynucleotides: a differential effect of comptothecin.

The plant alkaloid comptothecin inhibits interferon production induced by Newcastle disease virus (NDV) or ultraviolet-irradiated NDV in chick and human cells, and by Sindbis virus in chick cells. It has no effect on interferon production induced by poly (rI).poly(rC) in chick and human cells. No effect of comptothecin could be detected on the multiplication of NDV, and it is concluded that the inhibition reflects a difference between interferon induction by viruses and by polynucleotides.

Animals↗
PubMed1992

Plasmid content and localisation of the STaI (STaP) gene in enterotoxigenic Escherichia coli with a non-radioactive polynucleotide gene probe.

Enterotoxigenic Escherichia coli (ETEC) strain P2200 of porcine origin possessed eight possibly plasmid-determined characters (K88+ Raf+ Hly+ Col+ Smr Tcr Su(r) STa+) and six plasmid DNA bands of 4.2-93 kb. Analysis of the spontaneous loss of characters and the results of matings with other E. coli strains revealed that the K88, Raf, Hly, Smr, Tcr and Su(r) characters could be transferred, and that the presence of the K88 and Raf characters was associated with an 83-kb plasmid. The presence and location of the STaI gene was investigated in several ETEC strains of bovine or porcine origin. Hybridisation with a non-radioactive polynucleotide probe associated the STaI gene with a plasmid in each strain; these plasmids were of 32-142 kb. In contrast, plasmids from a P2200 STa- variant and plasmids from two STa- variants of the bovine ETEC strain B41* (strain B41 obtained from a different source) did not hybridise with the probe. One of the B41*STa- variants had lost the STa plasmid, whereas the second variant retained a plasmid of the same size which did not hybridise. In contrast, a third B41*STa- variant retained a plasmid of the same size that still hybridised with the STaI probe. Plasmid DNA restriction fragment analysis, followed by hybridisation with the STaI probe, showed that the STaI gene was associated with 8.3-, 6.8- and 3.5-kb plasmid fragments in strain B41, and with 4.9-, 6.8- and 3.5-kb plasmid fragments in strain B41*, following digestion with EcoRI, BamHI, or EcoRI + BamHI, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2006

RNA 3'-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase.

As in other bacteria, 3'-tails are added post-transcriptionally to Streptomyces coelicolor RNA. These tails are heteropolymeric, and although there are several candidates, the enzyme responsible for their synthesis has not been definitively identified. This paper reports on three candidates for this role. First, it is confirmed that the product of S. coelicolor gene SCO3896, although it bears significant sequence similarity to Escherichia coli poly(A) polymerase I, is a tRNA nucleotidyltransferase, not a poly(A) polymerase. It is further shown that SCO2904 encodes an RNase PH homologue that possesses the polymerization and phosphorolysis activities expected for enzymes of that family. S. coelicolor RNase PH can add poly(A) tails to a model RNA transcript in vitro. However, disruption of the RNase PH gene has no effect on RNA 3'-tail length or composition in S. coelicolor; thus, RNase PH does not function as the RNA 3'-polyribonucleotide polymerase [poly(A) polymerase] in that organism. These results strongly suggest that the enzyme responsible for RNA 3'-tail synthesis in S. coelicolor and other streptomycetes is polynucleotide phosphorylase (PNPase). Moreover, this study shows that both PNPase and the product of SCO3896 are essential. It is possible that the dual functions of PNPase in the synthesis and degradation of RNA 3'-tails make it indispensable in Streptomyces.

Bacterial Proteins↗
PubMed2001

Stretch-induced hairpin-coil transitions in designed polynucleotide chains.

The structural property of a poly( dG-dC) or poly( dA-dT) nucleotide is investigated. At low force and room temperatures, the polymer takes on compact hairpin structures. An abrupt transition from hairpin to random coil occurs at certain critical forces, its high cooperativity is related to the unfavorable formation of hairpin and other kinds of looped structures. It is hence necessary to consider the enthalpic effects of single-stranded loops in realistic models of RNA folding. A possible new way to obtain the statistical weights of elementary nucleotide arrangements is by single-macromolecular mechanical measurements on specifically designed polynucleotides.

Base Pairing↗
PubMed1975

A rapid technique for the estimation of polynucleotide adenylyltransferase and ribonucleic Acid polymerase in plant tissues.

Nucleic acid-dependent polynucleotide adenylytransferase (EC 2.7.7.19) and ribonucleic acid polymerase (EC 2.7.7.6) have been partially purified from maize tissues (Zea mays L.) utilizing ammonium sulfate precipitation and batch diethylaminoethylcellulose chromatography. The technique is applicable to the simultaneous processing of up to eight samples of plant tissue and affords a rapid and reproducible means of assaying these two enzymes from small quantities of kernels or seedlings. The kinetic characteristics of the partially purified enzymes resemble those from more extensively purified preparations.

Journal Article↗
PubMed2003

Domain analysis of the chloroplast polynucleotide phosphorylase reveals discrete functions in RNA degradation, polyadenylation, and sequence homology with exosome proteins.

The molecular mechanism of mRNA degradation in the chloroplast consists of sequential events, including endonucleolytic cleavage, the addition of poly(A)-rich sequences to the endonucleolytic cleavage products, and exonucleolytic degradation. In spinach chloroplasts, the latter two steps of polyadenylation and exonucleolytic degradation are performed by the same phosphorolytic and processive enzyme, polynucleotide phosphorylase (PNPase). An analysis of its amino acid sequence shows that the protein is composed of two core domains related to RNase PH, two RNA binding domains (KH and S1), and an alpha-helical domain. The amino acid sequence and domain structure is largely conserved between bacteria and organelles. To define the molecular mechanism that controls the two opposite activities of this protein in the chloroplast, the ribonuclease, polymerase, and RNA binding properties of each domain were analyzed. The first core domain, which was predicted to be inactive in the bacterial enzymes, was active in RNA degradation but not in polymerization. Surprisingly, the second core domain was found to be active in degrading polyadenylated RNA only, suggesting that nonpolyadenylated molecules can be degraded only if tails are added, apparently by the same protein. The poly(A) high-binding-affinity site was localized to the S1 domain. The complete spinach chloroplast PNPase, as well as versions containing the core domains, complemented the cold sensitivity of an Escherichia coli PNPase-less mutant. Phylogenetic analyses of the two core domains showed that the two domains separated very early, resulting in the evolution of the bacterial and organelle PNPases and the exosome proteins found in eukaryotes and some archaea.

Amino Acid Sequence↗
PubMed1975

Quaternary structure of polynucleotide phosphorylase from Escherichia coli: evidence of a complex between two types of polypeptide chains.

A new form of polynucleotide phosphorylase containing alpha and beta subunits was isolated (form B) by purification without preparative electrophoresis; this form was compared to the enzyme obtained by preparative electrophoresis purification (form A). The Stokes radius of these two forms are very different: 6.4 nm for form A and 8.7 - 9.0 nm for form B; on the other hand the sedimentation coefficients are close: 8.9 S and 9.9 S respectively. Such a result suggests that form B is very asymmetric. The apparent molecular weights, calculated from the Stokes radii and from the sedimentation coefficients, are approximately 365000 for form B and 252000 for form A. The latter is homogeneous on polyacrylamide gel, whereas the former yields two components, one of which behaves similarly to form A. Finally, whereas form A is composed of only one type of subunit, alpha, form B contains two types of chains: alpha (Mr 86000 +/- 5000) and beta (Mr 48000 +/- 2000) in stoichiometric proportions. From these results we believe that one should assume for form B the existence of a complex between form A and beta chains; the role of the latter still remains to be specified.

Binding Sites↗
PubMed1994

Spectroscopic observation of renaturation between polynucleotides with RecA in the presence of ATP hydrolysis.

To obtain mechanistic insights about RecA-promoted base pairing between complementary polynucleotides, the complex formation of RecA with poly(dA) and poly(dT) in the presence of ATP (and ATP-regenerating system) has been studied. The reaction was followed using a fluorescent probe, benzopyrenediolepoxide (BPDE), covalently attached to less than 1% of the adenine bases of poly(dA). BPDE is sensitive to its environment and has been found useful for detection of interactions between DNA strands, in the three binding positions of the RecA filament, in the presence of adenosine 5'-O-3-thiotriphosphate (ATP[S]) [Wittung, P., Nordén, B. & Takahashi, M. (1994) J. Biol. Chem. 269, 5799-5803]. The emission spectrum of RecA:BPDE-poly(dA) formed in the presence of ATP is similar to that observed with ATP[S] supporting similar structures of the complexes. However, the fluorescence anisotropy is considerably reduced, suggesting a higher degree of freedom of DNA in the presence of ATP hydrolysis. Upon addition of a complementary strand, poly(dT), to a preformed filament of RecA:BPDE-poly(dA) in the presence of ATP, the fluorescence intensity slowly decreases and a change of emission profile consistent with Watson-Crick base pairing is observed. This contrasts with the case of ATP[S] in which normal base pairing is never observed. Hence, ATP hydrolysis appears necessary for the RecA filament to be able to promote true renaturation. The renaturation reaction is found more effective when one of the complementary DNA strands is bound in the primary RecA DNA-binding position and the other is added as the third strand, but the reaction can also occur between DNA strands in any combination of binding positions in the RecA filament. This observation suggests the importance of the third DNA-binding position of the RecA filament. Renaturation between DNA strands in the other two combinations of binding positions is speculated to have a role in aborting the strand-exchange reaction when the strands are insufficiently complementary.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1991

Excited-state properties of the alternating polynucleotide poly(dA-dT).poly(dA-dT).

Measurements of the steady-state fluorescence spectrum and anisotropy, r, of the alternating polynucleotide poly(dA-dT).poly(dA-dT) were carried out in order to characterize its photophysical properties at room temperature. The shape of the fluorescence spectrum depends on the excitation wavelength, namely, the relative fluorescence intensity of the short-wavelength peak decreases for excitation at short wavelengths. When monitoring the emission at short wavelengths, r is 0.18 and independent of the excitation wavelength. When monitoring the emission at long wavelengths, however, r is very low, about 0.03. These results suggest that: (i) the short-wavelength emission stems from thymine; and (ii) the long-wavelength emission stems from an excited-state complex (excimer), with the same one being formed regardless of whether thymine or adenine is excited. The corresponding fluorescence spectra have been resolved. The occurrence of transfer of electronic energy is discussed.

Fluorescence Polarization↗
PubMed1991

Room-temperature fluorescence properties of the polynucleotide polydA.polydT.

The room-temperature fluorescence spectrum of the non-alternating polynucleotide polydA.polydT is found to have its maximum at about 325 nm and, when exciting in the spectral region where both adenine (A) and thymine (T) absorb, to coincide with that obtained for excitation at 293 nm where thymine is selectively excited. The fluorescence anisotropy is found to be equal to 0.18 and independent of the excitation and emission wavelengths. These observations are consistent with: (i) emission stemming from T; and (ii) transfer of electronic energy from A to T being not efficient. These inferences are also supported by the observed dependence of the fluorescence quantum yield on the excitation wavelength.

Fluorescence Polarization↗
PubMed1992

Base release from DNA and polynucleotides upon 193 nm laser excitation.

Release of bases form calf thymus DNA and three polynucleotides, induced by 20 ns excitation at 193 nm in aqueous solution at pH 7, was detected by HPLC. The quantum yields of formation of free bases (phi B) from double-stranded DNA (0.4 mM) are independent of intensity, indicating a one-quantum mechanism of N-glycosidic bond cleavage. The phi B values increase in the order guanine, thymine, adenine, cytosine, the latter being phi C approximately 7 x 10(-4) for double-stranded DNA under Ar and O2. The larger phi B values in N2O-saturated solution, e.g., phi C = 1.2 x 10(-3), are ascribed to additional base release via OH-adduct radicals. The phi B values of homopolynucleotides increase in the order poly(G), poly(A) and poly(C), e.g. phi C = 7 x 10(-3) under Ar, as do the efficiencies for base release per radical cation (eta B). A comparison of the eta B values with the efficiencies of single-strand breakage for poly(C), poly(A) and DNA shows a similar trend; both are markedly larger for pyrimidines than for purines. Pathways to undamaged bases, initiated from base radical cations, are proposed.

Adenine↗
PubMed1993

Improved high-performance liquid chromatographic analysis of 8-methoxypsoralen monoadducts and cross-links in polynucleotide, DNA, and cellular systems: analysis of split-dose protocols.

The distribution of 8-methoxypsoralen-thymidine photoadducts from polynucleotides, calf thymus DNA and mammalian cells treated with [3H]8-methoxypsoralen under a variety of irradiation conditions was determined using high-performance liquid chromatography and scintillation analysis. The split-dose protocol, with samples treated with 8-methoxypsoralen and low doses of long-wavelength UV radiation to generate monoadducts, washed to remove unreacted 8-methoxypsoralen, then irradiated further to convert the monoadducts to cross-links, was examined. The photoadduct distribution in the first step is dependent upon the UVA dose and the wavelength of the radiation, but it is relatively independent of 8-methoxypsoralen concentration. Low fluence and longer wavelengths generate mainly 4',5'-monoadducts, whereas higher fluences and shorter wavelengths yield more cross-links. The second irradiation step converts the 4',5'-monoadducts to cross-links as well as to 3,4-monoadducts. The overall yield of cross-links after the second irradiation step is not dependent upon the wavelength used in the first step. Cellular studies demonstrated that the split-dose protocol is applicable to mammalian systems. These results may affect the interpretation of mutagenesis studies based on the split-dose protocol, because the second step can convert 4',5'-monoadducts to both 3,4-monoadducts, the expected cross-links. Therefore, interpretations that link increases in mutagenicity after the second step in a split-dose study solely to cross-link formation may need re-examination.

Animals↗
PubMed1989

Template-directed oligomerization catalyzed by a polynucleotide analog.

A pyrophosphate-linked analog of polycytidylic acid has been synthesized and shown to catalyze the oligomerization of the complementary monomer 2'-deoxyguanosine 3',5'-bisphosphoimidazolide. Analogs of polynucleotides are of interest in studies of the origins of life as possible precursors of the first RNA molecules. These results demonstrate that such molecules are capable of serving as templates for further synthesis.

Catalysis↗
PubMed1997

Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles.

A highly selective, colorimetric polynucleotide detection method based on mercaptoalkyloligonucleotide-modified gold nanoparticle probes is reported. Introduction of a single-stranded target oligonucleotide (30 bases) into a solution containing the appropriate probes resulted in the formation of a polymeric network of nanoparticles with a concomitant red-to-pinkish/purple color change. Hybridization was facilitated by freezing and thawing of the solutions, and the denaturation of these hybrid materials showed transition temperatures over a narrow range that allowed differentiation of a variety of imperfect targets. Transfer of the hybridization mixture to a reverse-phase silica plate resulted in a blue color upon drying that could be detected visually. The unoptimized system can detect about 10 femtomoles of an oligonucleotide.

Biosensing Techniques↗
PubMed1990

A synthetic oligonucleotide probe and a cloned polynucleotide probe based on the yopA gene for detection and enumeration of virulent Yersinia enterocolitica.

We compared a synthetically produced 19-mer oligonucleotide probe with a polynucleotide probe consisting of a cloned fragment of the virulence gene yopA for their relative efficiencies in identification and enumeration of virulent Yersinia enterocolitica. The probes were used in DNA-DNA colony hybridization assays to differentiate 70 Yersinia strains with known plasmid profiles. All 19 strains harboring the 40- to 50-megadalton virulence plasmid were positive in the hybridization assay, whereas their isogenic derivatives lacking this plasmid were negative. Both probes correctly identified plasmid-bearing variants of Y. enterocolitica serogroups O:3, O:5,27, O:8, O:9, O:13, and O:21 from three continents. In contrast, none of the probes hybridized with DNA from 32 environmental yersiniae belonging to 26 serogroups not associated with disease. Colony hybridization was used to detect and enumerate virulent Y. enterocolitica in three artificially contaminated food samples. Despite a large background of indigenous bacteria (3 x 10(4) CFU), the efficiency of enumeration ranged from 33 to 82%. The use of nylon filters did not impair the growth of virulent yersiniae. Both probes showed a perfect concordance in their specific differentiation and enumeration of virulent Y. enterocolitica. DNA colony hybridization with these two probes permitted rapid and reliable identification of all common pathogenic serogroups without the need for enrichment or esoteric identification protocols.

Animals↗
PubMed1994

PCR-based preparation of 23S rRNA-targeted group-specific polynucleotide probes.

DNA coding for a variable region within domain III of bacterial 23S rRNA was used as the target for group-specific polynucleotide hybridization probes. The corresponding rDNA was amplified in vitro by the PCR technique in combination with a pair of primers specific for flanking conserved target sites. The amplified fragments were cloned or used directly as probes. RNA probes were generated by in vitro transcription of cloned or amplified rDNA. The probes were labeled by incorporating modified nucleotides during in vitro DNA amplification or in vitro transcription or by random priming. The use of in vitro transcribed single-stranded RNA probes instead of double-stranded DNA probes provided stronger hybridization signals. Group-specific probes were prepared from genomic DNAs or directly from cells of Acinetobacter calcoaceticus, Alcaligenes faecalis, Aeromonas hydrophila, Nannocystis exedens, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Pseudomonas stutzeri.

Bacteria↗