Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “RNA Probes”

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 55 records · Page 3Linked to original sources
PubMed1994

A functional site of the GTPase-associated center within 28S ribosomal RNA probed with an anti-RNA autoantibody.

An anti-RNA autoantibody (anti-28S) was employed to identify structural and functional elements characteristic of a domain termed the 'GTPase center' in eukaryotic 28S ribosomal RNA. This antibody, an inhibitor of ribosome-associated GTP hydrolysis, has a unique property: it binds to the RNA domain of eukaryotes but not to that of prokaryotes. The antibody binding occurred in the presence of Mg2+ and protected from chemical modification three conserved bases (U1958, G1960 and A1990) and the base G1959 which is replaced by A in prokaryotic 23S rRNA (A1067 in Escherichia coli). In vitro substitution of G1959 to A drastically weakened the antibody binding, and the reciprocal substitution, A1067-->G of the E.coli domain conferred the binding ability. This suggests that the G base determines the specificity of antibody binding. The G1959 was also protected by the association of ribosomes with elongation factor EF-2. The result, together with protection of E.coli base A1067 by EFG [D.Moazed, I.M. Robertson and H.F. Noller (1988) Nature, 334, 362-364], suggests that the position of G1959 in eukaryotes and A1067 in prokaryotes constitutes at least part of the factor binding site irrespective of the base replacement during evolution.

Animals↗
PubMed1997

N-ethylmaleimide (NEM) can significantly improve in situ hybridization results using 35S-labeled oligodeoxynucleotide or complementary RNA probes.

We predicted that a significant source of background labeling after in situ hybridization (ISH) using 35S-labeled probes is attributable to a chemical reaction between the phosphorothioate moiety of the probe [O3P = S] and disulfides in tissue. These covalent bonds would immobilize probe in the tissue, thereby increasing background labeling. On the basis of this view, we have explored the use of N-ethylmaleimide (NEM) to irreversibly alkylate the phosphorothioate moiety of the probe and/or to alkylate free sulfhydryls in tissue to block the formation of disulfides as a method of reducing background labeling. We report that NEM can significantly decrease background labeling of 35S-labeled oligodeoxynucleotide or cRNA probes but does not affect specific labeling. We conclude that the use of NEM in ISH protocols, as outlined here, may be an additional element researchers may consider to improve the signal-to-noise ratio.

Brain Chemistry↗
PubMed1998

Detection of rabbit haemorrhagic disease virus (RHDV) by in situ hybridisation with a digoxigenin labelled RNA probe.

An in-situ hybridisation (ISH) technique for the detection of rabbit haemorrhagic disease virus (RHDV) was developed. Thirteen seronegative adult rabbits were infected oro-nasally using the BS89 RHDV strain. Liver and spleen samples were collected from 4 h post infection (p.i.) and repeated every 4 h till 44 h p.i. Each sample was tested immunohistochemically, by sandwich ELISA and by ISH. A 2.482-kb RNA probe, matching the genomic fragment coding for the VP60 structural protein of RHDV, was arranged. Two RNA probes (sense and antisense) were transcribed in vitro and UTP-digoxigenin-labelled. The antisense probe clearly detected positivity in the cytoplasm of the hepatocytes at 8 h p.i. Labelled hepatocytes were scattered throughout the sections until 24 h p.i. followed by a more diffuse perilobular positive reaction. A much weaker signal of similar distribution was detected up to 24 h p.i. using the sense RNA probe. All spleen samples tested negative for both probes. Liver samples were positive at 32 h p.i. using both ELISA and the immunoperoxidase test. Spleen samples were positive using only the ELISA at 32 h p.i. This study showed that RHDV replication occurred almost immediately after inoculation and that the liver appears to be the main site of replication.

Animals↗
PubMed1998

Production of digoxigenin-labelled RNA probes and the detection of cytokine mRNA in rat spleen and brain by in situ hybridization.

Non-radioactive in situ hybridization is a sensitive method for determining the site of production for secretory molecules such as cytokines. We report here on the central and peripheral induction of proinflammatory cytokines by endotoxin, and outline procedures for the generation and application of rat-specific digoxigenin (Dig)-labelled RNA probes for the localization of mRNA by in situ hybridization. Rats were injected either intravenously (i.v.) or intracerebroventricularly (i.c.v.) with vehicle or lipopolysaccharide (LPS) and sacrificed at various time intervals post-injection. Rats were then perfused with 4% paraformaldehyde and the spleens and brains were removed and cryoprotected in 30% sucrose. Dig-labelled, rat-specific, antisense and sense RNA probes were generated by in vitro transcription from PCR-derived templates. Positive staining with all the antisense probes was cytoplasmic, whereas the sense probes showed no staining. Numerous tumor necrosis factor alpha (TNF-alpha) and interleukin-1 beta (IL-1beta) mRNA positive cells were observed in the marginal zone and in the red pulp of the spleen after iv LPS injections, whereas sections from saline-treated animals showed minimal cytokine mRNA expression. Cells positive for TNF-alpha and IL-1beta mRNA were detectable in the brain after i.c.v. injections of LPS, but not after icv injection of vehicle. An antisense probe for c-fos was utilized in these studies as a positive control for our procedure due to its anatomically specific expression in the rat brain after LPS. In conclusion we have demonstrated that in situ hybridization with Dig-labelled RNA probes is an efficient, sensitive and reliable tool to localize cytokine mRNA production in rat tissue.

Actins↗
PubMed1997

Detection of plasmids using DNA and RNA probes and the light-addressable potentiometric sensor.

Intact plasmids, plasmid fragments, and cDNA were detected using two DNA or RNA probes of varying lengths, each containing only biotin or fluorescein molecules. The probes were hybridized with the target plasmid/cDNA, bound with streptavidin, captured on nitrocellulose membranes, and detected using the urease-conjugate of an anti-fluorescein antibody via the light-addressable potentiometric sensor. The output of the silicon-chip sensor is in the form of rate, microV/s, and is directly proportional to the quantity of hybridized DNA captured on the membrane. Use of the larger probes (for beta-actin cDNA target) results in detection of intact plasmid at the level of approximately 106 target molecules; complementary DNA could be detected at similar levels. When the smaller probes are utilized (pGEM or pBSActB targets), plasmid fragmented targets could be detected only at levels 200 times greater than those observed when using the larger RNA probes.

Biotin↗
PubMed1989

Biotinylated RNA probes for the detection of potato spindle tuber viroid (PSTV) in plants.

Diseases caused by potato spindle tuber viroid (PSTV) are of significant agronomic importance, and early detection is vital. The objective of this paper was to synthesize biotinylated RNA probes in order to develop a specific, sensitive, and reliable assay system for detection of PSTV in infected plants. RNA probes were prepared by in vitro transcription of cloned PSTV, and were labelled with either biotin-11-UTP or [32P]UTP. Partially purified total RNAs from healthy and from PSTV-infected plants were spotted onto nitrocellulose filters and hybridized with either biotin-labelled or 32P-labelled probes. Our results showed that the sensitivity of biotinylated probes was similar to that for the 32P-labelled probes.

Biotin↗
PubMed1987

Quantitative molecular hybridization with unfractionated, solubilized cells using RNA probes and polyacrylamide gel electrophoresis.

Molecular hybridization with RNA probes was performed on unfractionated cells solubilized in guanidine thiocyanate solutions. Unhybridized probe was digested with ribonuclease, and protected probe fragments were resolved by polyacrylamide gel electrophoresis (PAGE). Since the same medium was used both for solubilization of the cells and as the hybridization buffer, RNA purification was not required and the analysis of large numbers of samples was facilitated. Using this method, specificity is superior to dot blot analysis because the size of hybridized fragments is determined and the signal of the probe hybridized to target RNA is separated from the background by PAGE.

Animals↗
PubMed2006

Solid-phase detection of RNA using bispyrene-modified RNA probe.

Bispyrene modified 2'-O-methyl oligoRNA (OMUpy2), which is a useful fluorescent probe for specific RNA detection, was immobilized on a glass substrate via various linker molecules to develop a more convenient RNA detection chip for gene expression study. As the fluorescence intensity of OMUpy2 enhanced greatly when it hybridized with its complementary RNA, it was expected that RNA detection by OMUpy2-immobilized chip (RNA-chip) required neither fluorescent labels to target nucleic acid nor washing protocol after the hybridization. As the linker molecules, oligo(dT), agarose, and poly(ethylene glycol) (PEG) were chosen, and the fluorescence from the chip was measured by a fluorescence microscope. Results indicated that the RNA-chip was able to detect the complementary oligoribonucleotide (cORN) without target labeling and washing protocols. Furthermore, the background emission was reduced as the length of the linker increased. In the case of PEG linker, 25-fold enhancement of the fluorescence intensity of the OMUpy2 was observed upon the addition of cORN.

Fluorescent Dyes↗
PubMed1990

Quantitative in situ hybridization using strand specific RNA probes: expression of the bunyavirus Germiston S segment in mosquito cells.

Infection of Vero (monkey) cells by Germiston bunyavirus is highly cytopathic with cell lysis and virus production at a high titre, whereas infection of Aedes albopictus C6/36 (mosquito) cells leads, after an acute primary phase, to a persistent non-cytopathic infection with a loss in virus production. In this report we demonstrate that single-stranded RNA probes can be successfully used in an in situ hybridization assay to quantify viral expression during this persistent infection. The steady-state levels of viral S-RNA segment (genomic and messenger sense) during the acute phase were similar to those observed in lytically infected Vero cells, but appeared delayed. Both senses of S-RNA were detected throughout persistent infection but in lower amounts, in less than 10% of the cells and always in the cytoplasm of infected cells. The number of copies per cell of messenger sense S-RNAs remained low during persistent infection whereas a higher fluctuation was observed for genomic S-RNAs. In situ hybridization with specific stranded RNA probes provides both qualitative and quantitative informations, that can lead to a better understanding of virus-cell interactions.

Aedes↗
PubMed1999

Epstein-Barr virus (EBV)-infected cells were frequently but dispersely detected in T-cell lymphomas of various types by in situ hybridization with an RNA probe specific to EBV-specific nuclear antigen 1.

Association of Epstein-Barr virus (EBV) with T-cell lymphomas was examined by in situ hybridization (ISH) with an antisense probe specific to abundantly expressed EBV-encoded small RNA-1 (EBER1). In addition to EBER1, EBV-specific nuclear antigen-1 (EBNA-1) is commonly expressed in EBV-associated tumors and latently infected B-lymphocytes. We examined paraffin sections of T-cell lymphomas except those of nasal origin for expression of latent viral transcripts by ISH. Using ISH with improved antisense RNA probe specific to EBNA-1 mRNA, the virus was detected in 19 (59%) of 32 cases, whereas the EBER1 transcript was found in only 15 (47%) of 32 cases by conventional EBER-ISH, resulting in 21 EBV-positive cases (66%) by combining the two methods. Latent membrane protein 1 (LMP1) mRNA of EBV was detected in 15 of 32 cases (47%), while no EBNA2 expression was observed in any these tumors. Patients with these lymphomas positive for LMP1 expression showed lower survival rates than those without expression of the viral mRNA. These results indicate that, in addition to EBER-ISH, RNA-RNA ISH with EBNA1 probes could be useful for detection of EBV-infected cells in paraffin sections, and detection of LMP1 mRNA expression in tumor cells could be a useful prognostic factor for T-cell lymphoma.

Animals↗
PubMed1997

The use of RNA probes for the analysis of gene expression.

The monomeric bacteriophage RNA polymerases allow the synthesis of virtually any RNA molecule in unlimited quantity. In this protocol, we describe the preparation of plasmid and PCR-derived templates. A basic transcription protocol is provided with several optional modifications. The use of RNA probes in Northern blot hybridization and in RNase protection assays is described. The relative advantages and pitfalls of these two methods to quantitatively detect mRNA targets are discussed.

Animals↗
PubMed1996

A rapid and sensitive dot-blot hybridization assay for the detection of citrus exocortis viroid in Citrus medica with digoxigenin-labelled RNA probes.

A rapid and sensitive dot-blot hybridization assay using in vitro-transcribed digoxigenin-labelled RNA probes (riboprobes) was developed aiming at detection of citrus exocortis viroid (CEVd) in crude sap of infected Citrus medica plants. The protocol includes a very quick and simple preparation of RNA extracts from samples using a denaturation step with formaldehyde. From our results, the employment of this step is highly recommended because the hybridization signals in formaldehyde-denatured samples were significantly stronger when compared with that of extracts without formaldehyde treatment. The assay was found to be sensitive enough to detect 0.1 ng of purified CEVd RNA and was able to detect viroid in 0.2 mg of symptomatic Citrus medica leaves. The use of riboprobes also allowed hybridization under high temperature conditions, avoiding non-specific background.

Digoxigenin↗
PubMed1989

Detection of rabies virus RNA in the central nervous system of experimentally infected mice using in situ hybridization with RNA probes.

Rabies virus is usually demonstrated in human or animal tissues using antigen-detection or viral isolation techniques. Rabies virus RNA can be demonstrated in paraffin-embedded tissues using in situ hybridization. Negative (-) sense 35S- and 3H-labeled RNA probes, specific for rabies virus nucleocapsid protein mRNA, were used for the detection of rabies virus RNA in the nervous system of mice experimentally infected with fixed and street strains of rabies virus. In situ hybridization signals were compared with rabies virus antigen demonstrated with immunoperoxidase staining. Rabies virus RNA and antigen were also demonstrated in the same neurons using a double-labeling technique. In situ hybridization has potential applications as a diagnostic test for rabies and in studies of rabies pathogenesis.

Animals↗
PubMed1995

Use of digoxigenin-labeled RNA probe to test hepatitis A virus antiviral drugs.

A nucleic acid hybridization assay was used to evaluate inhibitory activity of antiviral compounds against hepatitis A virus (HAV) in cell culture and compared to radioimmunoassay by analysis of variance procedure. The 5' genomic end of the HM-175 strain was used as digoxigenin-labeled RNA probe. Dot-blot examination showed a reduction of detectable HAV RNA in infected cells when treated with amphotericin B. An antiviral dose-effect was shown by statistical analysis of densitometric measures of hybridization signals. Comparison between molecular hybridization assay and radioimmunoassay by analysis of variance procedure showed the equivalence of both methods. Data previously obtained on selected drugs by antigen and infectious titres determinations were confirmed by hybridization assay and make possible digoxigenin-labeled RNA probe use to measure an antiviral dose-effect for screening of hepatitis A antiviral compounds.

Amides↗
PubMed1992

Detection of rabies virus mRNA in mouse brain by using in situ hybridization with digoxigenin-labelled RNA probes.

A non-isotopic method of in situ hybridization (ISH) was developed for the detection of rabies virus RNA in paraffin-embedded tissues. Digoxigenin-labelled RNA probes for rabies virus glycoprotein mRNA were used. The method had good sensitivity and low backgrounds, and there was excellent cellular localization of signals. ISH wih digoxigenin-labelled probes was compared with ISH with 3H-labelled probes. This non-isotopic method of ISH is more convenient than the radiolabelled method, and it is quicker because a long autoradiographic exposure is not required.

Animals↗