Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA, Complementary”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,639 records · Page 91Linked to original sources
PubMed2006

Aptamers targeted to an RNA hairpin show improved specificity compared to that of complementary oligonucleotides.

Aptamers interacting with RNA hairpins through loop-loop (so-called kissing) interactions have been described as an alternative to antisense oligomers for the recognition of RNA hairpins. R06, an RNA aptamer, was previously shown to form a kissing complex with the TAR (trans-activating responsive) hairpin of HIV-1 RNA (Ducongé and Toulmé (1999) RNA 5, 1605). We derived a chimeric locked nucleic acid (LNA)/DNA aptamer from R06 that retains the binding properties of the originally selected R06 aptamer. We demonstrated that this LNA/DNA aptamer competes with a peptide of the retroviral protein Tat for binding to TAR, even though the binding sites of the two ligands do not overlap each other. This suggests that upon binding, the aptamer TAR adopts a conformation that is no longer appropriate for Tat association. In contrast, a LNA/DNA antisense oligomer, which exhibits the same binding constant and displays the same base-pairing potential as the chimeric aptamer, does not compete with Tat. Moreover, we showed that the LNA/DNA aptamer is a more specific TAR binder than the LNA/DNA antisense sequence. These results demonstrate the benefit of reading the three-dimensional shape of an RNA target rather than its primary sequence for the design of highly specific oligonucleotides.

Aptamers, Nucleotide↗
PubMed1978

Synthesis of Sindbis virus complementary DNA by avian myeloblastosis virus RNA-directed DNA polymerase.

Sindbis virus 42 S RNA was efficiently transcribed into complementary DNA (CDNA) by avian myeloblastosis virus alphabeta DNA polymerase using oligo- (dT) or single-stranded calf thymus DNA as primers. Both of the Sindbis virus cDNA products were able to protect 60% of 125I-labeled Sindbis virus RNA, at near equal weight ratios, from RNAase A and T1 digestion. Using hybridization kinetics, the Crt 1/2 value for hybridization of the calf thymus-primed cDNA product with excess Sindbis RNA was determined to be 1.8 9 10-2 mol . s . 1-1. Thes data demonstrate that the Sindbis virus cDNA products are relatively uniform representations of Sindbis virus RNA sequences.

Avian Myeloblastosis Virus↗
PubMed1990

Control of ColE1 plasmid replication. Intermediates in the binding of RNA I and RNA II.

Replication of plasmid ColE1 is regulated by a plasmid-specified small RNA (RNA I). RNA I binds to the precursor (RNA II) of the primer for DNA synthesis and inhibits primer formation. The process of binding of RNA I to RNA II that results in formation of a stably bound complex consists of a series of reactions forming complexes differing in the stability. Formation of a very unstable early intermediate that was previously inferred from the inhibition of stable binding caused by a second RNA I species was firmly established by more extensive studies. This complex is converted to a more stable yet reversible complex that was identified by its RNase sensitivity, which was altered from that of the earlier complex or from that of free RNA I or RNA II. In these complexes, most loops of RNA II interact with their complementary loops of RNA I. The kinetic and structural analyses of the binding process predict formation of a complex interacting at a single pair of complementary loops that precedes formation of these complexes. Thus the process of binding of RNA I to RNA II is seen to consist of a sequence of reactions producing a series of progressively more stable intermediates leading to the final product.

Bacteriocin Plasmids↗
PubMed1995

Modified oligonucleotides as therapeutic and diagnostic agents.

Modified oligonucleotides and their analogs represent an exciting new class of agents with potential therapeutic and diagnostic applications. Among the most extensively investigated analogs are oligonucleoside phosphorothioates, some of which incorporate 'hairpin' structures at the 3' end and 'chimeras' that bear two modified oligonucleotides, all potential therapeutic candidates. To further enhance their potential, bio-reversible analogs of oligonucleotides have been synthesized. Several isosteric analogs of phosphoric diester oligonucleotides with neutral achiral backbones, and other novel molecules, such as peptide nucleic acids and circular oligonucleotides, are also reported to form stable duplexes with complementary RNA/DNA and are currently under investigation. Additionally, oligonucleotides carrying a variety of fluorescent tags have been used as probes with potential for diagnostic applications.

Animals↗
PubMed2004

Synthesis and properties of a novel bridged nucleic acid analogue bearing a P3'-->N5' phosphoroamidate linkage, 5'-amino-3', 5'-BNA.

We have designed and successfully synthesized a novel bridged nucleic acid analogue with a P3'-->N5' phosphoramidate linkage, 5'-amino-3',5'-BNA. X-ray crystallographic analysis demonstrated that the 5'-amino-3',5'-BNA had C1-exo-O4-endo sugar puckering and a constrained gamma dihedral angle of 22.8 degrees. The oligonucleotides containing 5'-amino-3',5'-BNA exhibited strong binding affinity towards complementary strands. In addition, the 5'-amino-3',5'-BNA oligonucleotide was easily hydrolyzed at its phosphoramidate linkage under mild acidic conditions.

Amides↗
PubMed2003

Synthesis and hybridization properties of l-oligodeoxynucleotide analogues fixed in a low anti glycosyl conformation.

We have synthesized l-type enantiomers (cU and cA) of nucleoside analogues, whose glycosyl bonds are fixed in a low anti conformation (ap glycosyl conformation, [small chi][approximate] 180[degree]), and incorporated them into oligonucleotides to evaluate the hybridization ability with natural DNA and RNA sequences. Although the incorporation of the modified nucleosides into oligonucleotides decreased the hybridization ability with unmodified complementary DNA sequences, the fully-substituted 12mers (cU(12) and cA(12)) still retained the hybridization ability with the complementary unmodified DNA 12mers, regardless of their unnatural l-chirality. In contrast, cU(12) and cA(12) showed different hybridization behavior with complementary unmodified RNA 12mers. cU(12) forms a more stable duplex with rA(12) than the corresponding natural 12mer (dT(12)), whereas cA(12) cannot hybridize with rU(12). Based on the model structure of cU(12)-rA(12), we discuss these experimental results.

Animals↗
PubMed1990

Androgen dependence and tissue specificity of renin messenger RNA expression in mice.

Testosterone, a steroid hormone which increases blood pressure by hitherto unknown mechanisms, is known to induce renin synthesis in the submandibular gland (SMG) of mice. Since renin as well as all other components of the renin-angiotensin system are present in organs important for cardiovascular control, e.g. the kidney, heart, adrenal gland and brain, it is of interest to study the effect of testosterone on renin gene expression in these organs. Renin messenger (m) RNA concentrations were measured by a solution hybridization assay using a 32P-labeled mouse SMG renin complementary (c) RNA as a radioactive probe (detection limit: 1 pg renin mRNA). Measurements were performed after 2 h and after 2, 7, 14 and 21 days of dihydrotestosterone (DHT) treatment in female NMRI mice. Renin mRNA concentration (values are expressed as pg renin mRNA/ micrograms total RNA) in the SMG was significantly increased after 7 days (108 +/- 22 in controls versus 630 +/- 101 in DHT-treated mice), after 14 days (83 +/- 15 in controls versus 743 +/- 83 in DHT-treated mice) and after 21 days (107 +/- 30 in controls versus 579 +/- 76 in DHT-treated mice), but did not reach levels found in untreated male NMRI mice (1021 +/- 84). In the kidney, a decrease was observed within 21 days, from 43 +/- 4 and 40 +/- 4 to 29 +/- 2 and 22 +/- 1.7 pg/micrograms in controls and DHT-treated groups, respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Adrenal Glands↗
PubMed1990

Molecular cloning and functional expression of the cardiac sarcolemmal Na(+)-Ca2+ exchanger.

The Na(+)-Ca2+ exchanger of the cardiac sarcolemma can rapidly transport Ca2+ during excitation-contraction coupling. To begin molecular studies of this transporter, polyclonal antibodies were used to identify a complementary DNA (cDNA) clone encoding the Na(+)-Ca2+ exchanger protein. The cDNA hybridizes with a 7-kilobase RNA on a Northern blot and has an open reading frame of 970 amino acids. Hydropathy analysis suggests that the protein has multiple transmembrane helices, and a small region of the sequence is similar to that of the Na(+)- and K(+)-dependent adenosine triphosphatase. Polyclonal antibodies to a synthetic peptide from the deduced amino acid sequence react with sarcolemmal proteins of 70, 120, and 160 kilodaltons on immunoblots. RNA, synthesized from the cDNA clone, induces expression of Na(+)-Ca2+ exchange activity when injected into Xenopus oocytes.

Adenosine Triphosphate↗
PubMed1977

The use of a complementary DNA probe to detect accumulation of mengo RNA in infected cells pretreated with interferon.

Complementary DNA (cDNA) from Mengo virus RNA has been synthesized and used as a probe to measure the synthesis and accumulation of viral RNA in Mengo infected L cell cultures, treated or untreated with interferon. Under experimental conditions used (200 units interferon/ml and 50 virus plaque-forming units/cell) results show that there is some synthesis of Mengo virus RNA in cells treated with interferon. One hour after infection, treated cells contain three times less viral RNA than untreated cells; five hours after infection, this difference has increased to ten fold. As in the control, no fragmented Mengo virus RNA molecules were found in interferon treated cells. The smaller recovery of infectious particles from interferon treated cells as compared to RNA accumulation suggests that not only RNA accumulation is inhibited but also a step posterior in viral maturation.

Cytoplasm↗
PubMed1982

A candidate gene for human U1 RNA.

Clones containing sequences complementary to the small nuclear RNA U1 were isolated from the human DNA library of Lawn et al. (1978). Three clones were studied by hybridization and restriction enzyme cleavage. The results showed that the inserts in all three clones were different and that each clone contains one single copy of a sequence which hybridizes to U1 RNA. The results revealed moreover that only one of the three clones contains all the cleavage sites which can be predicted from the known sequence of human U1 RNA, suggesting that the three clones comprise one candidate U1 gene and two pseudogenes. A fragment from the recombinant with the candidate U1 gene was subcloned in the pPR322 plasmid and part of its sequence was determined. The results showed that the subclone contains a sequence which matches that of the human U1 RNA perfectly. The sequence "TATAT" which often is found adjacent to RNA polymerase II start sites, was identified 33-37 base pairs upstream from the beginning of the U1 sequence. Two ten base pairs long, nearly perfect, direct repeats were also identified in the vicinity of the U1 sequence and an imperfect inverted repeat follows immediately after the U1 gene.

Base Sequence↗
PubMed1985

Injected anti-sense RNAs specifically block messenger RNA translation in vivo.

As a test for a method to analyze gene function in embryogenesis, the translation of a specific mRNA has been blocked in vivo by microinjection of complementary (anti-sense) RNA. RNA complementary to globin mRNA was synthesized in vitro by transcription of an inverted globin cDNA clone. After injection into frog oocyte cytoplasm, the anti-sense globin RNA forms a hybrid with globin mRNA and selectively prevents its translation. Deletion mapping of the anti-sense RNA shows that the 5' region of the globin mRNA must be covered in order to block translation. This method may allow one to study the function of many genes for which DNA clones are available by preventing the expression of the endogenous gene as protein.

Animals↗
PubMed1978

Diversity and abundance of polyadenylated RNA from Achlya ambisexualis.

The diversity, abundance, and DNA sequence representation of poly(adenylic acid) containing RNA derived from cells of Achlya ambisexualis cultured in defined and undefined media have been determined. The kinetics of hybridization of polyadenylated RNA with complementary DNA were the same for both culture conditions and revealed the presence of three frequency classes containing 29, 220, and 3000 different sequences of an average length of 1150 nucleotides. Complexity estimates derived from experiments in which polyadenylated RNA was hybridized to unique sequence DNA were in good agreement with these results. The kinetics of hybridization of complementary DNA with an excess of nuclear DNA indicate that approximately 10% of the RNA is transcribed from reiterated DNA sequences while the remainder is transcribed from single copy sequences.

Base Sequence↗
PubMed2005

Single-molecule FRET studies of important intermediates in the nucleocapsid-protein-chaperoned minus-strand transfer step in HIV-1 reverse transcription.

The minus-strand transfer step of HIV-1 reverse transcription is chaperoned by the nucleocapsid protein (NC), which has been shown to facilitate the annealing between the transactivation response element (TAR) RNA and complementary TAR DNA stem-loop structures. In this work, potential intermediates in the mechanism of NC-chaperoned TAR DNA/TAR RNA annealing have been examined using single-molecule fluorescence resonance energy transfer. The interaction between TAR DNA and various DNA oligonucleotides designed to mimic the initial annealing step was monitored to capture potential intermediates along the reaction pathway. Two possible mechanisms of annealing were examined, namely nucleation through the 3'/5' termini, termed the "zipper" complex, or nucleation through the hairpin loops in a "kissing" complex. Intermediates associated with both mechanisms were observed in the presence of NC, and the kinetics of formation of these intermediates were also measured. Thus, the single-molecule experiments support the notion that NC-assisted annealing of TAR DNA:TAR RNA may occur through multiple pathways.

Base Sequence↗
PubMed1986

Diversity of gene expression in goldfish brain.

The sequence complexity of nuclear and polysomal RNA from goldfish brain and kidney was measured by RNA-driven hybridization reactions with single-copy [3H]DNA. At saturation, brain nuclear and polysomal RNA were complementary to 23.2 and 6.7% of the DNA probe, respectively. In contrast to these findings, nuclear and polysomal RNA from kidney hybridized to 16.1 and 3.1% of the single-copy DNA, values that were significantly lower than that obtained in the CNS. Taken together, the results focus attention on the striking diversity of gene expression in goldfish brain and extend to lower vertebrates the observation that nervous tissue expresses significantly more genetic information than other somatic tissues or organs.

Animals↗
PubMed1979

SV40 DNA injected into Xenopus oocyte nuclei is transcribed by RNA polymerase B.

SV40 DNA I. injected into Xenopus oocyte nuclei is transcribed. The SV40-specific RNA molecules migrate on sucrose gradients as do viral RNAs formed in infected green monkey cells but a variable proportion of RNA sequences complementary to SV40 DNA is also found in the light region of the gradients. All SV40-specific RNA species seem to be synthesized by RNA polymerase B as their synthesis is completely sensitive to low concentrations (0.1 microgram/ml) of alpha-amanitin. Concomittantly, the formation of SV40-specific proteins (tumor antigens) is inhibited by injecting alpha-amanitin together with the SV40 DNA.

Amanitins↗
PubMedDate not supplied

Mutant viral RNAs synthesized in vitro show altered aminoacylation and replicase template activities.

A remarkable feature of the genomic RNAs of several plant viruses is the presence at the 3' end of a region that exhibits tRNA-like functions, including aminoacylation. The three genomic and single subgenomic RNAs of brome mosaic virus (BMV) accept tyrosine in vitro and in vivo, the smallest 3' fragment that can be aminoacylated being about 135 nucleotides long. The roles of the tRNA-like properties are incompletely understood, but an involvement in replication rather than translational functions is likely. We have recently shown (J.J.B. et al., in preparation) that the features recognized by the BMV RNA-specific RNA-dependent RNA polymerase (replicase) for the use of BMV RNA for complementary strand synthesis also lie within the tRNA-like structure. To distinguish between the roles of BMV RNA as a substrate for tyrosyl-tRNA synthetase and BMV replicase, we have now produced BMV RNAs with mutations at two separate loci within the tRNA-like structure. This has been achieved by transcription in vitro from specifically mutagenized cDNA, an approach permitting the generation of targeted mutants without regard to their viability in vivo.

Mosaic Viruses↗
PubMed1975

RNA polymerase associated with virions of pike fry rhabdovirus.

The association of an RNA-dependent RNA polymerase activity with virions of pike fry rhabdovirus has been demonstrated by both in vitro and in vivo studies. The temperature optimum for the in vitro assay is around 20 C, although enzyme activity can be observed at 4 C. Preparations of pike fry virus possess a glycoprotein, a membrane protein, a nucleoprotein, an L protein, and a phosphoprotein, as well as an RNA of about 3.8 times 10-6 mol wt. A protein kinase activity has been found associated with virus preparations. In vitro RNA product analyses indicate that the virus-associated enzyme functions principally as a transcriptase synthesizing viral-complementary, heteropolymeric RNA.

Animals↗
PubMed2002

Identification of cadmium-sensitive genes in the Antarctic fish Chionodraco hamatus by messenger RNA differential display.

To investigate the ability of cadmium to affect gene transcription in fish, the messenger RNA (mRNA) differential display technique was used to analyze gene expression in the Antarctic icefish Chionodraco hamatus exposed to sublethal doses of cadmium salt. Seven DNA complementary to RNA (cDNA) bands whose steady-state levels of expression significantly changed in response to cadmium exposure were identified. The results obtained show that two groups of genes are affected by cadmium in icefish liver. The first group comprises genes that are up-regulated by the metal: in particular, a gene encoding the heat-shock protein HSP70 and another encoding a protein homologous to GP49 of Sparus aurata egg envelope. The other group comprises genes down-regulated by cadmium. These are the transferrin gene and a gene encoding a protein presenting homology to mouse T2K, a kinase having a role in the prevention of apoptosis. Three cDNAs had no homology to known gene sequences, thus suggesting that may either encode not yet identified proteins, or correspond to untranslated regions of mRNA molecules.

Animals↗