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Results for “RNA, Complementary”

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At least 145 records · Page 8Linked to original sources

PubMed1994

Ultrastructural in situ hybridization to nascent transcripts of highly transcribed rRNA genes in chromatin spreads.

The amplified rRNA genes of amphibian oocytes were used as a model system for the development of an in situ hybridization technique to label nascent transcripts in dispersed chromatin. A biotinylated complementary RNA probe was hybridized to nascent transcripts from dispersed nucleoli, and detected by a two step antibody technique utilizing colloidal gold as an electron dense marker. A specific sequence on the rRNA nascent transcript was labeled in a pattern consistent with its location; however, gene morphology was difficult to analyze following in situ hybridization owing to low sample contrast. Proteins associated with the transcripts were apparently lost during the procedure, leading to decreased electron density of the transcripts. The technique was systematically modified in an attempt to identify conditions that preserved gene morphology adequately for ultrastructural analysis, while simultaneously maintaining sufficient levels of specific labeling.

Animals↗

PubMed1996

Localization of urokinase-type plasminogen activator mRNA in the adult mouse brain.

Urokinase-type plasminogen activator (uPA) is an inducible serine protease, secreted by a variety of cell types, that functions in fibrinolysis and has been implicated also in events such as cell migration and tissue remodeling and repair. To explore the role of uPA in the adult brain we have now screened the whole mouse brain for cells expressing the uPA gene through in situ hybridization using 35S-complementary RNA. uPA mRNA was visualized predominantly in three regions: (1) the subicular complex, (2) the entorhinal cortex, (3) the parietal cortex, where the signal was somewhat lower and confined to layers IV and VI. Weaker signals were seen in the basolateral nucleus of the amygdala and in the anterodorsal thalamic nucleus, and also in the hilus of the dentate gyrus where labeling was slightly over background. Cells exhibiting uPA mRNA signaling were large neurons according to morphological criteria. These results support the view of uPA being involved in neuronal functions of the adult brain, specifically in the hippocampal formation and the parietal cortex.

Animals↗

PubMed1995

A syntaxin-related protein controls acetylcholine release by different mechanisms in Aplysia.

Polyclonal antibodies raised against rat syntaxin-1B and an affinity-purified fraction have been used to study the functional role of this protein in transmitter release from Aplysia neurons. In a ganglionic protein extract, this fraction recognized a 37,000 molecular weight protein which therefore might be the Aplysia homologue of rat brain syntaxin-1B. Immunoglobulins were injected in the presynaptic cell of an identified cholinergic synapse of the buccal ganglion of Aplysia californica. This treatment decreased the postsynaptic response due to a reduction of the number of quanta released in relation to a decline of presynaptic Ca2+ current. When antibodies were applied extracellularly, transmitter release also decreased. In contrast to intracellular injection, this reduction was not accompanied by a decrease of the Ca2+ current but by an increase of presynaptic outward current. When injected in the presynaptic neuron, syntaxin complementary RNA also depressed Ca2+ current and transmission. This work provides evidence that Aplysia neurons express a syntaxin-like protein which is involved in the control of the presynaptic Ca2+ influx triggering acetylcholine release from terminals. This protein appears to have an extracellular segment which might interact with outward current.

Acetylcholine↗

PubMedDate not supplied

32P- and biotin-labelled in vitro transcribed cRNA probes for the detection of potato spindle tuber viroid and chrysanthemum stunt viroid.

Replacing nick-translated DNA probes by in vitro transcribed complementary RNA (cRNA) probes considerably increased the sensitivity of dot-blot detection tests of potato spindle tuber viroid and chrysanthemum stunt viroid. As compared to the limit of detection of 5-10 pg of viroid obtained with 32P-labelled DNA probes, cRNA probes allow the detection of less than 1 pg of pure viroid. When labelled with biotin by incorporation of biotin-labelled ribonucleotides, the cRNA probes have a limit of detection of approximately 5 pg of purified viroid.

Biotin↗

PubMed1994

Detection of clonal T-cell populations in gastrointestinal lymphomas by analysis of cRNA conformational polymorphisms of rearranged T-cell-receptor-gamma genes.

Analysis of complementary RNA molecules of junctional regions of rearranged T-cell-receptor-gamma genes show a pattern of conformational polymorphisms which is specific for an individual lymphocytic clone. In a blinded study we analysed formalin-fixed, paraffin-embedded histological specimens from gastrointestinal lymphomas and control tissues (lymphomas: pleomorphic T-cell 10, anaplastic large cell [Ki1+] 9, centroblastic 5, immunocytoma 1, B-CLL 2, Hodgkin's 2, centroblastic-centrocytic 1, MALT [mucosa associated lymphoid tissue] 1, T-cell acute lymphoblastic leukaemia 1, non-lymphoid or polyclonal lymphoid tissues 5). Junctional regions of rearranged TCR-gamma genes were amplified by the polymerase chain reaction and the products were transcribed into cRNA. Conformational patterns of cRNA molecules were analysed by polyacrylamide gel electrophoresis. 13/20 T-lineage lymphomas and the T-cell acute lymphocytic leukaemia displayed a distinct cRNA band pattern, all B-lineage lymphomas and the non-lymphoid control tissues were negative. Only one case of nasopharyngeal (lymphoepithelial, Schmincke-Regaud) carcinoma showed a faint cRNA banding pattern. This novel and non-radioactive assay allows for the rapid detection and molecular characterization of clonal lymphoid populations in minute histological biopsy specimens.

Base Sequence↗

PubMed1994

Quantitation of mucin mRNA in respiratory and intestinal epithelial cells.

Mucin glycoproteins (mucins) are the major macromolecular constituents of mucus gels in mammalian respiratory, gastrointestinal, and reproductive tracts. Disorders of mucin glycosylation, which may result from either abnormal post-translational processing or differences in mucin protein gene expression, have been indicated in several diseases. Quantitation of mucin gene expression has been hindered by two features of human mucin genes: variable numbers of tandemly repeating nucleotides per mRNA molecule and polydisperse mRNA transcripts. We report here a method to quantitate mucin mRNA levels in epithelial cells and have evaluated three mucin genes, MUC1, MUC2, and MUC5, which are expressed in respiratory epithelium. The method uses the 3' non-tandem repeat mucin cDNA sequences, as they were shown to have a single-size transcript when amplified by the polymerase chain reaction, consistent with a one-to-one relationship with the mRNA molecule. The 3' non-tandem repeat cDNA sequences were cloned and transcribed in vitro to prepare complementary RNA (cRNA) standards. By comparison to a cRNA standard curve, mucin gene expression was evaluated in colon adenocarcinoma, pancreatic adenocarcinoma, and transformed respiratory epithelial cells and in nasal polyp tissue by slot blot analysis. CFPAC-1, a pancreatic adenocarcinoma cell line, expressed the highest MUC1 transcript levels. Colon adenocarcinoma cell lines varied in MUC2 expression levels, and one colon adenocarcinoma cell line, HT-29, had higher levels of MUC5 than MUC2. Nasal polyp tissue expressed more MUC5 mRNA than MUC1 or MUC2 mRNA. This mucin mRNA slot blot method provides a quantitative method for investigating the regulation of mucin gene expression in health and disease.

Adenocarcinoma↗

PubMed1993

In vitro selection of fast-hybridizing and effective antisense RNAs directed against the human immunodeficiency virus type 1.

The rate of double strand formation between procaryotic antisense RNA and complementary RNA in vitro is known to correlate with the effectiveness of antisense RNA in vivo. In this work, an in vitro assay for determining the hybridization rates of a large number of antisense RNA species was developed. A set of HIV-1-directed antisense RNAs with the same 5'-end but successively shortened 3'-ends was produced by alkaline hydrolysis of a 150 nt HIV-1-directed antisense transcript. This mixture was used to determine hybridization rates for individual chain lengths with a complementary HIV-1-derived RNA in vitro. The second order binding rate constants of individual antisense RNA species differed by more than a factor of 100, although in some cases, slow-hybridizing and fast-hybridizing antisense RNAs differed by only two or three 3'-terminally-located nucleotides. The results indicated that there was not a trivial dependence of binding rates on the chain length of antisense RNAs. Further, the binding rate constants determined in vitro for individual antisense RNA species correlated with the extent of inhibition of HIV-1 replication in vivo.

Cloning, Molecular↗

PubMed1975

Complexity of cytoplasmic RNA in different mouse tissues measured by hybridization of polyadenylated RNA to complementary DNA.

The kinetics of hybridization of polyadenylated RNA from mouse L-cells with complementary DNA (cDNA) synthesized with reverse transcriptase revealed three classes of differing abundance. The simplest interpretation requires three frequency classes representing polyadenylated RNA; 5, 45, and 50 percent of the total polyadenylated RNA and about 3, 300, and 7600 different RNA sequences of 6 times 10-5 daltons, respectively. The complementary DNA synthesized with L-cell polyadenylated RNA as template hybridized efficiently with RNA from different mouse tissues, indicating that most species of the L-cell RNA in the highand middle frequency class are present in all mouse tissues. Kinetics of hybridization of complementary DNA synthesized with cytoplasmic polyadenylated brain RNA as template suggested a higher complexity for brain RNA. Thirty-five percent of this brain cDNA failed to hybridize with L-cell RNA. This complementary DNA fraction, isolated by hydroxylapatite chromatography, represented approximately 11,000 RNA sequences specific for the brain. On the other hand, hybridization of complementary DNA synthesized on polyadenylated mouse liver RNA with L-cell RNA failed to demonstrate differences between these two groups of polyadenylated RNA.

Adenine Nucleotides↗

PubMed1996

Intracellular expression of RNA transcripts complementary to the human immunodeficiency virus type 1 gag gene inhibits viral replication in human CD4+ lymphocytes.

Intracellular expression of antisense transcripts was evaluated for its potential to interfere with human immunodeficiency virus type 1 (HIV-1) replication. Retroviral vectors encoding HIV-1 psi-gag complementary sequences downstream of a selectable gene (neo, puromycin gene, or Lyt2 gene) were stable and yielded high titers. Human CEMSS T cells were transduced with amphotropic retroviral vectors to express RNA complementary to the psi-gag sequence of HIV-1. Replication of laboratory-adapted HIV-1 strains was inhibited by more than 1 order of magnitude (log10) in these transduced cells even at high inoculation doses (4 x 10(4) 50% tissue culture infective doses). Antisense-mediated anti-HIV efficacy was further demonstrated by survival of CD4+ cells in these cultures relative to controls. The level of anti-HIV-1 activity of the psi-gag antisense sequence correlated with the length of the antisense transcript. Maximal anti-HIV efficacy was observed with complementary sequence more than 1,000 nucleotides long, whereas transcripts less than 400 nucleotides long failed to inhibit HIV-1 replication. Expression of psi-gag antisense RNA also reduced HIV-1 JR-CSF replication 10-fold in primary CD4+ lymphocytes. These results obtained with a T-cell line and primary peripheral blood lymphocytes indicate the potential of long antisense RNAs as an efficient anti-HIV-1 therapeutic agent for gene therapy.

Anti-HIV Agents↗

PubMed1993

Antiviral activity of a phosphorothioate oligonucleotide complementary to RNA of the human cytomegalovirus major immediate-early region.

Phosphorothioate oligonucleotides complementary to mRNA of the human cytomegalovirus (HCMV) DNA polymerase gene or to RNA transcripts of the major immediate-early regions 1 and 2 (IE1 and IE2) of HCMV were evaluated for antiviral activity in a 96-well immunoassay with primary human dermal fibroblasts as host cells. Oligonucleotides complementary to RNA of the IE2 region exhibited the most potent antiviral activity. One of these oligonucleotides, ISIS 2922, was at least 30-fold more potent than the nucleoside analog, ganciclovir, with a 50% effective concentration of 0.37 microM in the 96-well immunoassay. In an infectious virus yield reduction assay, ISIS 2922 and ganciclovir reduced production of infectious virus by 2 log units at concentrations of 2.2 and 36 microM, respectively. A control oligonucleotide showed no inhibition of virus production at concentrations as high as 3 microM. ISIS 2922 reduced IE protein synthesis in HCMV-infected cells in a dose-dependent manner which correlated with antiviral activity. The antiviral activity of ISIS 2922 was not due to oligonucleotide-induced cytotoxicity since effects on cell viability or proliferation were observed only at concentrations well in excess of effective antiviral concentrations. The specificity and potency of ISIS 2922 suggest that it may be useful for the treatment of cytomegalovirus disease in humans.

Antiviral Agents↗

PubMed1979

Program of bacteriophage gh-1 DNA transcription in infected Pseudomonas putida.

The program of transcription in phage gh-1-infected Pseudomonas putida was examined. It was found that the host P. putida RNA polymerase transcribes early RNA from the L strand of gh-1 DNA during the initial stages of infection. The host RNA polymerase is also undoubtedly responsible for transcription of complementary RNA late in the infectious cycle because complementary RNA was not transcribed when rifampin was added to the infected cell culture. The gh-1-induced RNA polymerase transcribes late RNA from the L strand of gh-1 DNA late in the infectious cycle. The P. putida RNA polymerase transcribed only early RNA from primarily the L strand of gh-1 DNA in vitro when the molar ratio of enzyme to gh-1 DNA was 0.5. When the molar ratio was 50 the P. putida RNA polymerase transcribed RNA from the H strand of gh-1 DNA as well as complementary RNA. Thgh-1 RNA polymerase transcribed only the L strand of gh-1 DNA in vitro but transcribed both early and late RNA.

Bacteriophages↗

PubMed1992

Heterologous expression of the human potassium channel Kv2.1 in clonal mammalian cells by direct cytoplasmic microinjection of cRNA.

The cloned human delayed rectifying K+ channel Kv2.1 (drk1) was expressed in clonal mouse fibroblasts (L-cells) and rat basophilic leukemia cells (RBL-1) by direct cytoplasmic microinjection of complementary RNA (cRNA). Within six hours, cells microinjected with Kv2.1 cRNA expressed a large sustained outward current as determined from whole-cell patch-clamp recordings. Nearly 100% of cells injected with cRNA expressed outward current. Current density was 30-70 pA/pF when measured at a potential of +50 mV. Steady-state activation and inactivation parameters for Kv2.1 were similar when expressed in either L-cells or RBL-1 cells. These results are the first to demonstrate that functional ion channel proteins can be expressed in mammalian clonal cell lines by direct cytoplasmic microinjection of cRNA.

Animals↗

PubMed1986

Biological characteristics of a cold-adapted influenza A virus mutation residing on a polymerase gene.

The biological function of a cold-adapted (ca) mutation residing on the PB2 gene of an influenza A/Ann Arbor/6/60 (A/AA/6/60) ca variant virus in the viral replication cycle at 25 degrees C was studied. The viral polypeptide synthesis of A/AA/6/60 ca variant at 25 degrees C was evident approximately 6 hours earlier than the wild type (wt) virus and yielded twice as many products. The quantitative analysis of viral complementary RNA (cRNA), synthesized in the presence of cycloheximide, revealed that A/AA/6/60 ca variant and a single gene reassortant that contains only the PB2 gene of the ca variant with remaining genes of the wt virus produced equal amount of cRNA at 25 degrees and 33 degrees C, which was an amount approximately four fold greater than the wt virus' cRNA synthesized at 25 degrees C. These results strongly suggest that the ca mutation residing on the PB2 gene of A/AA/6/60 ca variant affects the messenger RNA synthesis at 25 degrees C in the primary transcription.

Cold Temperature↗

PubMed1976

Inhibition of influenza RNA synthesis by virazole (ribavirin).

Virazole (ribavirin) inhibits the RNA synthesis of an influenza A virus (fowl plague). Neither virion RNA nor complementary RNA are produced. Although the effect of virazole can be counteracted by guanosine the inhibitor does not interfere with the uptake or incorporation of labelled guanosine into chick embryo cells, nor does replacement of glucose by mannose amplify the effect of virazole. Thus virazole seems not to act via an interference with the GTP pool. Synthesis of Semliki Forest virus RNA is not affected by virazole.

Culture Techniques↗

PubMed1997

Modulation of RNase H activity by modified DNA probes: major groove vs minor groove effects.

We have previously prepared ribozyme mimics and chemical nucleases from modified DNA containing pendant bipyridine and terpyridine groups. The ability of these modified DNA probes to support RNase H cleavage of complementary RNA is described. DNA/RNA duplexes were formed using DNA probes designed to deliver metal complexes via either the major groove or the minor groove of the duplex. The duplexes were treated with Escherichia coli RNase H. Modifications in the major groove produced the same RNA cleavage pattern as unmodified DNA probes. However, minor groove substituents inhibited RNA cleavage over a four-base region. Comparison was made with a DNA probe containing a 2'-OMe modification. Our results support enzyme binding in the minor groove of a DNA/RNA duplex. We do not observe cleavage directly across from the modified nucleoside. The RNA cleavage efficiency effected by RNase H and a DNA probe decreases as follows: unmodified DNA > or = C-5 modified DNA >> c2'-modified DNA > C1'-modified DNA. Results with 28-mer RNA substrates roughly parallel those obtained with a 159-mer RNA target. The differences observed between low and high MW RNA substrates can be explained by a much higher enzyme-substrate binding constant for the high MW target.

Base Sequence↗

PubMedDate not supplied

Synthesis, hybridization properties, nuclease stability, and cellular uptake of the oligonucleotide--amino-beta-cyclodextrins and adamantane conjugates.

Synthesis of the oligonucleotides conjugated with amino derivatives of beta-cyclodextrin and adamantane, at the 3'-end of host oligonucleotide, has been described. The oligonucleotide conjugates were examined for their nuclease stability, hybridization properties, and cellular uptake. The oligonucleotide conjugates had increased nuclease resistance compared to their parent oligonucleotides. Conjugation of adamantane to the oligonucleotides did not adversely affect the ability of the oligonucleotides to hybridize with their complementary RNA. Conjugation with amino derivatives of beta-cyclodextrin, however, significantly destabilized the duplex formation. In the cellular uptake studies, we found that amino derivatives of beta-cyclodextrin attached at 3'-end of the oligonucleotides did not help to increase the uptake by cells. Cellular uptake of oligonucleotide-adamantane conjugates in association with 2-(hydroxypropyl)-beta-cyclodextrin (HPCD) as a "carrier" was significantly higher than that of control oligonucleotides.

Adamantane↗

PubMed1997

Antisense gene inhibition by C-5-substituted deoxyuridine-containing oligodeoxynucleotides.

Antisense oligodeoxynucleotides (ODNs) are capable of inhibiting gene expression via a RNase H mechanism in which the complementary RNA is degraded by RNase H. C-5 propyne dU phosphorothioate ODNs bind selectively and with high affinity to RNA within cells leading to potent antisense inhibition of RNA translation. The effect that increasing steric bulk of C-5-substituted deoxyuridine analogs has on affinity for RNA and ability to inhibit gene expression is discussed. The relative binding affinity was measured by thermal denaturation (Tm) analysis, and antisense activity was determined by inhibition of SV40 T-antigen (TAg) expression in CV1 cells. The results show that antisense activity is not directly correlated to Tm measurements. In vitro analysis (RNase H cleavage, on-rates, and off-rates) and pre-formed ODN/RNA experiments indicate that RNase H activity and intracellular dissociation appear to be major determinants of the antisense potency of the various substituted ODNs. The results of our analysis point to the unique ability of C-5 propyne dU ODNs to selectively bind to RNA within cells and activate cleavage of RNA by RNase H leading to potent inhibition of gene expression.

Animals↗

PubMed1999

Structure and stability of the consecutive stereoregulated chiral phosphorothioate DNA duplex.

The duplex structures of the stereoregulated phosphorothioate DNAs, [R(p),R(p)]- and [S(p),S(p)]-[d(GC(ps)T(ps)ACG)] (ps, phosphorothioate; PS-DNA), with their complementary RNA have been investigated by combined use of (1)H NMR and restrained molecular dynamics calculation. Compared to those obtained for the unmodified duplex structures (PO-DNA.RNA), the NOE cross-peak intensities are virtually identical for the PS-DNA.RNA hybrid duplexes. The structural analysis on the basis of the NOE restraints reveals that all of the three DNA.RNA duplexes take a A-form conformation and that there is no significant difference in the base stacking for the DNA.RNA hybrid duplexes. On the other hand, the NOE cross-peak intensities of the protons around the central T(ps)A step of the PS-DNA.DNA duplexes are apparently different from those of PO-DNA. DNA. The chemical shifts of H8/6 and H1' at the T(ps)A step are also largely different among PS-DNA.DNAs and PO-DNA.DNA, suggesting that the DNA.DNA structure is readily changed by the introduction of the phosphorothioate groups to the central T(p)A step. The structure calculations indicate that all of these DNA.DNA duplexes are B-form although there exist some small differences in helical parameters between the [R(p),R(p)]- and [S(p),S(p)]PS-DNA.DNA duplexes. The melting temperatures (T(m)) were determined for all of the duplexes by plotting the chemical shift change of isolated peaks as a function of temperature. For the PS-DNA.RNA hybrid duplexes, the [S(p),S(p)] isomer is less stable than the [R(p),R(p)] isomer while this trend is reversed for the PS-DNA.DNA duplexes. Consequently, although the PS-DNA.RNA duplexes take the similar A-form structure, the duplex stability is different between PS-DNA.RNA duplexes. The stability of the DNA.RNA duplexes may not be governed by the A-form structure itself but by some other factors such as the hydration around the phosphorothioate backbone, although the T(m) difference of the DNA.DNA duplexes could be explained by the structural factor.

DNA↗