Genomes and Genes
Summary: A group of 13 or more ribonucleotides in which the phosphate residues of each ribonucleotide act as bridges in forming diester linkages between the ribose moieties.
- Wińska P, Miazga A, Poznański J, Kulikowski T. Partial selective inhibition of HIV-1 reverse transcriptase and human DNA polymerases ? and ? by thiated 3'-fluorothymidine analogue 5'-triphosphates. Antiviral Res. 2010;88:176-81 pubmed publisher..1995), 2-SFLT is a potent and selective anti-HIV-1 agent with the selectivity index 4-fold higher than that of FLT. Findings regarding the mechanisms of antiviral and cytotoxic activities of FLT and its thioanalogues are discussed. ..
- Bergamini A, Ercoli L, Perno C. [Inhibition of alfa interferon and ampligen of human immunodeficiency virus (HIV) replication in monocyte-macrophage subpopulations]. Medicina (Firenze). 1990;10:34-6 pubmed..Finally, HIV replication in chronically-infected M/M was not affected by alpha-IFN. These results suggest that alpha-IFN might be useful in combination with other anti-HIV drugs in the therapy of HIV-related disease. ..
- Kikuchi K, Shimizu S, Sato Y, Morishita E, Takenaka A. Crystallization of oligonucleotides containing A-rich repeats suggests a structural contribution to the autoregulation mechanism of PABP translation. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012;68:185-9 pubmed publisher..Otherwise, PABP at low concentration preferentially binds to the poly(A) tail of PABP mRNA. ..
- Wickstrom E. Escherichia coli initiation factor IF3 binding to AUG and AUG-containing single strands and hairpin loops, and nonspecific binding to polymers. Biochim Biophys Acta. 1974;349:125-30 pubmed..No binding was detected for GUA, A8 U, or the hairpin loop A5 GC5 U5. AUG-specific binding, per nucleotide, is strong; nonspecific binding, per nucleotide, is weak. ..
- Hubel A, Schöffl F. Arabidopsis heat shock factor: isolation and characterization of the gene and the recombinant protein. Plant Mol Biol. 1994;26:353-62 pubmed..The native size of recombinant ATHSF1 in vitro is consistent with a trimer as demonstrated by chemical cross-linking and pore exclusion limit analysis. ..
- Sinha R, Kumar G. Interaction of isoquinoline alkaloids with an RNA triplex: structural and thermodynamic studies of berberine, palmatine, and coralyne binding to poly(U).poly(A)(*)poly(U). J Phys Chem B. 2009;113:13410-20 pubmed publisher..84 and TDeltaS degrees = 7.44 kcal/mol) in coralyne. These results advance our knowledge on the binding of small molecule isoquinoline alkaloids that are specific binders of RNA structures, particularly triplexes. ..
- Ye X, Ng T. A novel and potent ribonuclease from fruiting bodies of the mushroom Pleurotus pulmonarius. Biochem Biophys Res Commun. 2002;293:857-61 pubmed..There was no activity toward poly U. The optimal pH for its activity was 7 and the optimal temperature was 55 degrees C. It inhibited cell-free translation in a rabbit reticulocyte lysate with an IC50 of 0.33 nM. ..
- Sun W, Godson G. Synthesis of polyribonucleotide chains from the 3'-hydroxyl terminus of oligodeoxynucleotides by Escherichia coli primase. J Biol Chem. 1998;273:16358-65 pubmed..We also show that the primed RNA is an effective primer for the synthesis of DNA chain by E. coli DNA polymerase III holoenzyme. The significance of this finding to primases generating multimeric length RNA is discussed. ..
- Costa Giomi M, Gomes I, Tiraboschi B, Auge de Mello P, Bergmann I, Scodeller E, et al. Heterogeneity of the polyribocytidilic acid tract in aphthovirus: changes in the size of the poly(C) of viruses recovered from persistently infected cattle. Virology. 1988;162:58-64 pubmed..These variations may lead to the production of new strains with altered biological properties that may contribute to the maintenance and spread of these viruses in the field. ..
- Tan L, Xie L, Sun X. Binding properties of Ru(II) polypyridyl complexes with poly(U)·poly(A)*poly(U) triplex: the ancillary ligand effect on third-strand stabilization. J Biol Inorg Chem. 2013;18:71-80 pubmed publisher..5 to 48.4 °C. The results reveal that the ancillary ligands have an important effect on third-strand stabilization of the triplex RNA poly(U)·poly(A)*poly(U) when metal complexes contain the same intercalative ligands. ..
- Gokhale K, Newnam G, Sherman M, Chernoff Y. Modulation of prion-dependent polyglutamine aggregation and toxicity by chaperone proteins in the yeast model. J Biol Chem. 2005;280:22809-18 pubmed..As many stress-defense proteins are conserved between yeast and mammals, these data shed light on possible mechanisms modulating polyglutamine aggregation and toxicity in mammalian cells. ..
- Shapiro R, Riordan J, Vallee B. Characteristic ribonucleolytic activity of human angiogenin. Biochemistry. 1986;25:3527-32 pubmed..These results may bear importantly on the physiological function of angiogenin. ..
- Van Aerschot A, Meldgaard M, Schepers G, Volders F, Rozenski J, Busson R, et al. Improved hybridisation potential of oligonucleotides comprising O-methylated anhydrohexitol nucleoside congeners. Nucleic Acids Res. 2001;29:4187-94 pubmed..Upon incorporation of the hexitols within RNA sequences in an effort to induce a beneficial pre-organised structure, the positive effect of the 3'-O-methyl derivative 1 proved larger than that of 2. ..
- Diaz E. Analysis of the interband optical transitions: characterization of synthetic DNA band structure. J Chem Phys. 2008;128:175101 pubmed publisher..We propose that a comparison between the obtained spectra and the experiments can provide an insight into the electronic band structure of DNA. ..
- Habara Y, Doshita M, Hirozawa S, Yokono Y, Yagi M, Takeshima Y, et al. A strong exonic splicing enhancer in dystrophin exon 19 achieve proper splicing without an upstream polypyrimidine tract. J Biochem. 2008;143:303-10 pubmed..This compensation was only seen in living cells but not in 'in vitro splicing'. This suggests the possibility that the previous splicing experiments using an in vitro splicing system could underestimate the activity of ESEs. ..
- Bobba G, Bretonniere Y, Frias J, Parker D. Enantiopure lanthanide complexes incorporating a tetraazatriphenylene sensitiser and three naphthyl groups: exciton coupling, intramolecular energy transfer, efficient singlet oxygen formation and perturbation by DNA binding. Org Biomol Chem. 2003;1:1870-2 pubmed
- Li X, Peng Y, Qu X. Carbon nanotubes selective destabilization of duplex and triplex DNA and inducing B-A transition in solution. Nucleic Acids Res. 2006;34:3670-6 pubmed..Our circular dichroism, competitive binding assay and triplex destabilization studies provide direct evidence that SWNTs induce DNA B-A transition in solution and they bind to the DNA major groove with GC preference. ..
- Prodi G, Grilli S, Mazzullo M, Colacci A, Arfellini G. Comparison between photo-induction and microsomal activation of polycyclic hydrocarbons with different oncogenic potency. Toxicol Pathol. 1984;12:185-8 pubmed..DBA), benzo(a)pyrene (BP) and 7,12-dimethylbenz(a)anthracene (DMBA)) to calf thymus DNA and synthetic polyribonucleotides was studied...
- Islam M, Chowdhury S, Kumar G. Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides. J Phys Chem B. 2009;113:1210-24 pubmed publisher..These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences. ..
- Miyata S, Yoshida Y, Kihara H. Purification and characterization of a protease from Xenopus embryos. Eur J Biochem. 1989;186:49-54 pubmed..0 to pH 4.5. The protease was activated by addition of total RNA from Xenopus embryos, by poly(rU) or poly(rG). In contrast, after addition of tRNA or poly(rC), no activation of the protease was observed...
- Tan L, Liu J, Shen J, Liu X, Zeng L, Jin L. First ruthenium(II) polypyridyl complex as a true molecular "light switch" for triplex RNA structure: [Ru(phen)2(mdpz)]2+ enhances the stability of Poly(U)·Poly(A)*Poly(U). Inorg Chem. 2012;51:4417-9 pubmed publisher..In this article, [Ru(phen)(2)(mdpz)](2+) (Ru1) is the first metal complex able to enhance the stability of the RNA triplex Poly(U)·Poly(A)*Poly(U) and serve as a prominent molecular "light switch" for the RNA triplex. ..
- Mundus D, Bulygin K, Yamkovoy V, Malygin A, Repkova M, Vratskikh L, et al. Structural arrangement of the codon-anticodon interaction area in human placenta ribosomes. Affinity labelling of the 40S subunits by derivatives of oligoribonucleotides containing the AUG codon. Biochim Biophys Acta. 1993;1173:273-82 pubmed..The proteins S5 and S9 were labelled by the 5' end derivative of pAUGU3, and the protein S17 was modified by the 5' end derivative of pAUG. ..
- Kasparov A, Kasparova E, Pavliuk A. [Local express auto-cytokine therapy (a complex of cytokines) in the treatment of viral and nonviral eye lesions]. Vestn Oftalmol. 2004;120:29-32 pubmed
- Lee F, Vallee B. Characterization of ribonucleolytic activity of angiogenin towards tRNA. Biochem Biophys Res Commun. 1989;161:121-6 pubmed..0, 100-200 mM, and approximately 65 degrees C, respectively, for RNase A. Polyanions and metals both inhibit angiogenin and RNase A but to different extents. ..
- Duke G, Palmenberg A. Cloning and synthesis of infectious cardiovirus RNAs containing short, discrete poly(C) tracts. J Virol. 1989;63:1822-6 pubmed
- Diebold S, Kaisho T, Hemmi H, Akira S, Reis E Sousa C. Innate antiviral responses by means of TLR7-mediated recognition of single-stranded RNA. Science. 2004;303:1529-31 pubmed..These results identify ssRNA as a ligand for TLR7 and suggest that cells of the innate immune system sense endosomal ssRNA to detect infection by RNA viruses. ..
- Thore S, Mauxion F, Seraphin B, Suck D. X-ray structure and activity of the yeast Pop2 protein: a nuclease subunit of the mRNA deadenylase complex. EMBO Rep. 2003;4:1150-5 pubmed..This first structure of a nuclease involved in the 3'-5' deadenylation of mRNA in yeast provides information for the understanding of the mechanism by which the Ccr4-Not complex achieves its functions. ..
- Gryaznov S, Winter H. RNA mimetics: oligoribonucleotide N3'-->P5' phosphoramidates. Nucleic Acids Res. 1998;26:4160-7 pubmed..The properties of the oligoribonucleotide N3'-->P5' phosphoramidates indicate that these compounds can be used as hydrolytically stable structural and functional RNA mimetics. ..
- Meister W, Lindau S, Hauser A, Bohley C, Gromann U, Naumann S, et al. Biomesogenic matrix systems. J Biomol Struct Dyn. 2000;18:385-92 pubmed..The results indicate the importance of biomesogenic (pre)ordering in nucleic acid native and artificial matrix reactions. ..
- Takahashi A, Muramatsu H, Takagi S, Fujisawa H, Miyake Y, Muramatsu T. A splicing factor, Prp8: preferential localization in the testis and ovary in adult mice. J Biochem. 2001;129:599-606 pubmed..Prp8 was shown to bind to midkine (MK), a heparin-binding growth factor. Since Prp8 expression partially overlaps with the sites of action of MK, it is possible that binding to Prp8 is involved in part of MK signaling. ..
- Semenenko T, Selkova E, Nikitina G, Gotvyanskaya T, Yudina T, Amaryan M, et al. Immunomodulators in the prevention of acute respiratory viral infections. Russ J Immunol. 2002;7:105-14 pubmed..6 (amixin) and 2.1 (poludan), and corresponding protection indices of 72.1% and 52.7%. Having the same chance of getting infected, individuals protected with these drugs often have the disease in a milder or asymptomatic form. ..
- Duke G, Osorio J, Palmenberg A. Attenuation of Mengo virus through genetic engineering of the 5' noncoding poly(C) tract. Nature. 1990;343:474-6 pubmed..We propose that analogous synthetic strains of foot and mouth disease virus could serve as the basis for new attenuated vaccines. ..
- Kasparova E, Fadeeva L, Pavliuk A, Pereverzina O, Kasparov A. [Theoretical validation of local express auto-cytokine therapy]. Vestn Oftalmol. 2002;118:25-7 pubmed
- Bab I, Smith E, Gavish H, Attar Namdar M, Chorev M, Chen Y, et al. Biosynthesis of osteogenic growth peptide via alternative translational initiation at AUG85 of histone H4 mRNA. J Biol Chem. 1999;274:14474-81 pubmed..Together, our results demonstrate that H4 gene expression diverges at the translational level into the simultaneous parallel production of both H4, a nuclear structural protein, and OGP, an extracellular regulatory peptide. ..
- Hattori M, Frazier J, Miles H. Poly(8-aminoguanylic acid): formation of ordered self-structures and interaction with poly(cytidylic acid). Biochemistry. 1975;14:5033-45 pubmed..The properties of the ordered structures are interpreted in terms of a strong tendency of the 8-amino group to form a third interbase hydrogen bond, when this possibility is not prevented by high pH. ..
- Murthy C, Deeble D, von Sonntag C. The formation of phosphate end groups in the radiolysis of polynucleotides in aqueous solution. Z Naturforsch C. 1988;43:572-6 pubmed..This is possibly linked to the decomposition of unstable hydroperoxides which are formed in high yields in poly(U) and poly(C) (G = 0.7 and 0.19 mumol J-1, resp.).(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Kocic G, Bjelakovic G, Saranac L, Kocic R, Jevtovic T, Sokolovic D, et al. Altered degradation of circulating nucleic acids and oligonucleotides in diabetic patients. Diabetes Res Clin Pract. 2008;79:204-13 pubmed..Decreased RNase activity and related increase of circulating oligonucleotides may favor the increase of nucleic acid "danger motifs", leading to TLRs activation. ..
- Barciszewska M, Sucha A, Bałabańska S, Chmielewski M. Gel electrophoresis in a polyvinylalcohol coated fused silica capillary for purity assessment of modified and secondary-structured oligo- and polyribonucleotides. Sci Rep. 2016;6:19437 pubmed publisher..Also, we demonstrate the use of PVA-coated capillaries to identify and separate phosphorylated siRNAs and secondary structures (e.g. siRNA duplexes). ..
- Odean M, Trachte G, Johnson A. Characterization of immune suppression induced by polyribonucleotides. Int J Immunopharmacol. 1991;13:339-48 pubmed..Thus, the polyribonucleotide complexes appear to suppress antibody synthesis by inducing macrophages to secrete PGE, a known immune suppressant. ..
- Kovtun A, Shirokikh N, Gudkov A, Spirin A. The leader sequence of tobacco mosaic virus RNA devoid of Watson-Crick secondary structure possesses a cooperatively melted, compact conformation. Biochem Biophys Res Commun. 2007;358:368-72 pubmed..In this work we synthesized the polyribonucleotides containing either the natural omega sequence or the regular (CAA)(n) sequence, and studied them using UV ..
- Shumilov V, Ivannikov I, Ogarkov P, Lobastov S, Olontsev V. [Epidemiologic effectivness of poludane in preventing influenza and other acute respiratory diseases in troops]. Voen Med Zh. 2002;323:45-7, 93 pubmed..058). The coefficient of effectiveness was 50%, i.e. the incidence has decreased in two times. The use of poludanum according to scheme 2 caused no decrease in ARD incidence. ..
- Hyde R, Buckheit R, Broom A. "Senseless" antiviral polyribonucleotides: poly (1-propargylinosinic acid). Nucleosides Nucleotides Nucleic Acids. 2002;21:45-54 pubmedPrevious work has shown that novel amphipathic oligo and polyribonucleotides exhibiting secondary structure in solution are potent inhibitors of HIV and HCMV replication and cytopathicity in tissue culture...
- Markosian M, Hyde R. Oligonucleotides and polyribonucleotides: a review of antiviral activity. Antivir Chem Chemother. 2005;16:91-102 pubmed..In an effort to find new therapeutics, oligo- and polyribonucleotides are being studied for their antiviral capabilities...
- Bocharov V, Ivanov M, Gantsovskiĭ P. [Intraocular correction of aphakia in patients after kidney transplantation]. Vestn Oftalmol. 2004;120:21-4 pubmed
- Sorrentino S, Naddeo M, Russo A, D Alessio G. Degradation of double-stranded RNA by human pancreatic ribonuclease: crucial role of noncatalytic basic amino acid residues. Biochemistry. 2003;42:10182-90 pubmed..These data and the wide distribution of the enzyme in different organs and body fluids suggest that HP-RNase has evolved to perform both digestive and nondigestive physiological functions. ..
- Manzano A, Mohri Z, Sperber G, Ogris M, Graham I, Dickson G, et al. Failure to generate atheroprotective apolipoprotein AI phenotypes using synthetic RNA/DNA oligonucleotides (chimeraplasts). J Gene Med. 2003;5:795-802 pubmed..We conclude that, although an evolving technology with enormous potential, chimeraplast-directed gene repair remains problematical. ..
- Murakami K, Abe M, Kageyama T, Kamoshita N, Nomoto A. Down-regulation of translation driven by hepatitis C virus internal ribosomal entry site by the 3' untranslated region of RNA. Arch Virol. 2001;146:729-41 pubmed
- Sana B, Ghosh D, Saha M, Mukherjee J. Purification and characterization of an extracellular, uracil specific ribonuclease from a Bizionia species isolated from the marine environment of the Sundarbans. Microbiol Res. 2008;163:31-8 pubmed..This RNase degrades uracil containing nucleic acids only. Our isolate could be a novel renewable source of deoxyribonuclease (DNase)--free RNase enzyme. ..
- Fathi R, Huang Q, Coppola G, Delaney W, Teasdale R, Krieg A, et al. Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates. Nucleic Acids Res. 1994;22:5416-24 pubmed..2-Aminoethyl)phosphonates represent a novel approach to the introduction of positive charges into the backbone of oligonucleotides. ..
- Chaires J, Ren J, Hamelberg D, Kumar A, Pandya V, Boykin D, et al. Structural selectivity of aromatic diamidines. J Med Chem. 2004;47:5729-42 pubmed..New insights into the molecular recognition of nucleic acid structures emerged from these studies, adding to the list of available design principles for selectively targeting DNA and RNA. ..
- Gamberi C, Contreas G, Romanelli M, Morandi C. Analysis of the yeast NSR1 gene and protein domain comparison between Nsr1 and human hnRNP type A1. Gene. 1994;148:59-66 pubmed..The biochemical data, therefore, would support the hypothesis that the two RRM domains in hnRNP A1 and Nsr1 interact with RNA in a similar manner in both mammalian and yeast cells, respectively. ..
- Yang H, Duckett C, Lindsten T. iPABP, an inducible poly(A)-binding protein detected in activated human T cells. Mol Cell Biol. 1995;15:6770-6 pubmed..In most tissues, poly(A)-binding activity is likely to be the result of the combined effects of constitutively expressed PABP and iPABP, whose expression is subject to more complex regulation. ..