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PubMed1989

Plasmid library for the transcription of RNA probes complementary to the entire genome of the human immunodeficiency virus type 1 (HIV-1).

A plasmid (pBH10R3) containing a 9-kb Sst I fragment of HIV-1 (clone BH-10) inserted in pSP64, an in vitro expression vector, has been used for the transcription of anti-sense HIV-1 RNA. With this system, the transcripts obtained in vitro were not usually full length (1 to 2 kb long) and they predominantly span the 3' end ORF and ENV regions of the viral genome. We have rearranged the HIV-1 genomic sequences with respect to the SP6 promoter in the pSP64 vector and have obtained a series of new constructs allowing the expression in vitro of RNA transcripts complementary to other regions in the HIV-1 genome, including the 5' end of the ENV region as well as the TAT, POL, and GAG regions. In fact, the combined use of these constructs as templates for in vitro transcription allows the production of RNA probes spanning the entire viral genome. Compared with the 1- to 2-kb probes mentioned above, the combined use of such probes results in a several-fold increase in the sensitivity of molecular hybridization for the detection of HIV-1 nucleic acid sequences. Also, these constructs enable the preparation of RNA probes that have the potential to detect restriction polymorphisms throughout the HIV-1 genome.

Gene Library↗
PubMed1993

Detection of polymerase chain reaction-amplified human immunodeficiency virus type 1 proviral DNA with a digoxigenin-labeled RNA probe and an enzyme-linked immunoassay.

An enzyme-linked immunoassay (EIA) combined with a solution hybridization (SH) reaction was devised to detect human immunodeficiency virus type 1 (HIV-1) provirus amplified by the polymerase chain reaction (PCR). In this nonisotopic PCR assay, designated PCR-EIASH, a fragment of the HIV-1 gag gene from peripheral blood mononuclear cells (PBMCs) was first amplified with biotinylated primers. The biotinylated amplified DNA segment was reacted in solution with an internal RNA probe labeled with digoxigenin-11-UTP. Hybrids were captured in a microtiter plate coated with streptavidin. Specific bound hybrids were quantitated by the addition of an enzyme-labeled antibody against digoxigenin and a fluorogenic substrate. The hybridization, immunological, and amplification parameters of PCR-EIASH were optimized as follows: 12.5 pmol of each primer was used in the PCR; the reannealing reaction of amplified products with the RNA probe, which was used at 0.30 microgram/ml, was completed in 30 min at 70 degrees C in 2x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate). Five copies of HIV-1 DNA diluted in a lysate of 100,000 PBMCs from a seronegative control could be detected by PCR-EIASH with a signal of 41 +/- 3 fluorescent units above a background noise of 13 +/- 2 fluorescent units. A total of 91 PBMC lysates from 91 seropositive patients sampled once and 20 PBMC lysates from 10 seropositive patients sampled twice were tested in duplicate in the PCR-EIASH; 107 samples were positive in duplicate tests, 1 sample was indeterminate, and 3 samples were negative. Of the latter three samples, one became positive by diluting the cell lysate, suggesting the presence of an inhibitor of Taq polymerase. The three samples negative for HIV-1 by PCR-EIASH were also negative when amplified with SK145-SK39 and detected with 32P-labeled SK102.

Base Sequence↗
PubMed1997

Genotype-specific RNA probes for direct identification of wild polioviruses by blot hybridization.

We have developed RNA probes for the direct identification of wild poliovirus isolates by blot hybridization. The probes are complementary to sequences of the first 30 to 32 codons of VP1, which evolve more extensively (approximately 1.5-fold) than the rest of VP1. To illustrate our general approach, we describe the design of probes specific to each of four major genotypes recently endemic (1981 to 1991) to the Americas: Andean type 1, Brazil type 1, Brazil type 3, and Central America-Mexico type 3. A wild isolate of each genotype was selected according to molecular and epidemiologic criteria to be representative of the principal lineages in circulation. Variable VP1 sequences of the representative isolates were amplified by the reverse transcriptase PCR and were inserted into a plasmid vector containing a T7 promoter. The in vitro transcripts, labeled with digoxigenin, served as probes. These formed stable hybrids only with RNAs of isolates of the corresponding genotypes. Hybrids were detected by a sensitive chemiluminescence assay, capable under normal diagnostic conditions of detecting specific wild poliovirus sequences in samples containing up to a 100-fold excess of Sabin vaccine strain-related sequences of the same serotype.

Base Sequence↗
PubMed1987

Molecular hybridization with RNA probes in concentrated solutions of guanidine thiocyanate.

Hybridizations with RNA probes were performed in 3-6 M guanidine thiocyanate concentrations where cells can be solubilized. At these concentrations the melting temperature of hybrids and the optimum temperature of hybrid formation are greatly reduced. The rate of hybridization in GuSCN at room temperature was greater than that in 50% formamide at 42 degrees C. Hybridizations were performed on DNA and RNA in cells dissolved in GuSCN without prior nucleic acid purification.

Animals↗
PubMed1989

Non-isotopic RNA probes. Comparison between different labels and detection systems.

Several studies have shown the use of non-radioactive labelled DNA probes for in situ hybridisation, mainly to identify cellular DNA. In this study mRNA in situ hybridisation was performed on rat pituitary with biotinylated complementary (c) RNA probes for rat prolactin and growth hormone (GH), and compared with radioactive 35S-radiolabelled probes. Biotinylated cRNA probes were labelled with either biotin-11-UTP or with allylamine-UTP, the latter method being able to produce a higher yield of labelled RNA. Different detection systems were tested, and hybridisation signal was seen in cells of anterior pituitary with both types of biotinylated probes. The signals were detected using either avidin-biotin-complex with peroxidase (ABC), peroxidase-anti-peroxidase (PAP) or gold-silver methods. ABC peroxidase detected using glucose oxidase-diaminobenzidine (DAB)-nickel solution appeared to be the best method for detecting labelled RNA probes, with very strong signal and low background. The biotinylated probes were comparable in sensitivity to the radiolabelled probes in detecting prolactin and GH mRNAs in the anterior lobe of the rat pituitary. These results indicate an alternative methods of labelling and detection of biotinylated probes which could have a potential role in research and diagnostic techniques.

Allylamine↗
PubMed1991

Detection of astrovirus in pediatric stool samples by immunoassay and RNA probe.

Two new astrovirus assays, a rapid biotin-avidin enzyme immunoassay (EIA) and RNA probe hybridization, were developed and compared with an established astrovirus assay, an indirect EIA, and immune electron microscopy. Sensitivity and specificity were evaluated by using a screening panel of 22 astrovirus-positive and 305 astrovirus-negative fecal specimens. The biotin-avidin assay was equivalent in performance to the reference indirect assay, and both could detect about 10 ng of viral protein. Although the probe was more sensitive than either EIA and could detect higher dilutions of virus in tissue culture and stool specimens, it did not detect more astrovirus-positive fecal specimens. Of the 22 astrovirus-positive specimens detected by the EIAs, 20 were confirmed by immune electron microscopy with hyperimmune rabbit antiserum. To determine the usefulness of EIAs for large epidemiologic studies, EIAs were used to screen 1,289 stool specimens from three studies of children with and without diarrhea. Astrovirus was detected in 3.5% of specimens from children with diarrhea and 1.9% of specimens from those without diarrhea. Our results indicate that the biotin-avidin EIA is an efficient, sensitive, and specific method for routinely screening large numbers of fecal samples and that its application in epidemiologic studies may yield higher rates of astrovirus infection than have been found previously by other methods.

Avidin↗
PubMed1991

In situ hybridization with single-stranded RNA probes to demonstrate infrequently elevated gli mRNA and no increased ras mRNA levels in meningiomas and astrocytomas.

Using computer-assisted digital image-analysis, the level of ras and gli messenger RNA (mRNA) in neoplasms of meningeal and glial origin was determined in an attempt to correlate these parameters with histological tumor severity. We used single-stranded, asymmetric, radiolabelled RNA probes to detect the amount of ras and gli mRNA present in formalin-fixed, paraffin-embedded tumor material. Such archival material can provide an immediate, larger sample base than with fresh samples. The extent of ras mRNA expression in 25 brain tumors was not significantly different than normal cerebellum. However, five of 74 astrocytomas of relatively high malignant potential demonstrated gli mRNA levels above normal cerebellum.

Analysis of Variance↗
PubMed1993

Use of a digoxigenin-labeled RNA probe to detect all 24 serotypes of bluetongue virus in cell culture.

A digoxigenin-labeled RNA probe, corresponding to the section of the bluetongue virus (BTV) serotype 17 genome coding for nonstructural protein-1 (NS1), was applied to noninfected cell cultures and cell cultures infected with 24 different serotypes of BTV, 2 serotypes of epizootic hemorrhagic disease virus, and African horse sickness virus type 4. The probe hybridized to all cell cultures infected with the various BTV serotypes but did not hybridize to noninfected cell cultures or cell cultures infected with any of the other orbiviruses.

Animals↗
PubMed2006

Nonisotopic detection of microRNA using digoxigenin labeled RNA probes.

MicroRNAs (miRNAs) are an important class of endogenously derived, small approximately 22 nucleotide noncoding regulatory RNAs that have recently become implicated in development, cell regulation and cancers of various tissues. Here we report a nonisotopic Northern analysis method for miRNA detection using 3'-digoxigenin (DIG)-labeled RNA oligo probes. Northern blot analysis was performed using miRNA or total RNA fractions extracted from human leukemic cell lines, and blots were hybridized with either 32P- or DIG-labeled RNA probe for miR-181, miR-155 or miR-16. A labeled probe for U6 small nuclear RNA served as an internal control. The use of DIG-labeled RNA probes was equally sensitive compared to 32P-labeled probes in detecting miRNA quantities as low as 50 ng. The ability to use nonisotopic methods and yet obtain sensitive and reliable results offers an advantage to investigators who prefer to avoid isotopes.

Blotting, Northern↗
PubMed1994

Determination of isozyme-specific mRNAs of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase in glutamate obese rats by RNA probes.

To study the possible alterations in the metabolism of fructose 2,6-bisphosphate in glutamate induced obese rats, the mRNA levels of different isozymes coding for the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFK-2/F2,6Pase) were determined in various rat tissues obtained from fed and starved animals. For Northern analysis and dot blotting radioactively labeled RNA probes were synthesized by in vitro transcription. A modified ligase-free subcloning method was applied to obtain the plasmid vectors containing specific fragments of the cDNAs coding for the muscle, liver and heart isozymes of PFK-2/F2,6Pase. In liver but not in heart and skeletal muscle of glutamate obese rats the content of mRNA of PFK-2/F2,6Pase is significantly lower than in normal rats. As in normal rats short-term starvation has no effect on mRNA levels of the bifunctional enzyme. These results are compared with the maximum activities of PFK-2 and F2,6Pase determined in cell-free extracts prepared from the three organs.

Animals↗
PubMed1990

Enzyme immunoassay for detection of hybrids between PCR-amplified HIV-1 DNA and a RNA probe: PCR-EIA.

An enzyme immunoassay was developed to detect human immunodeficiency virus type 1 (HIV-1) DNA amplified by polymerase chain reaction (PCR-EIA). A set of primers (outer set) was used in PCR to amplify a segment of the HIV-1 gag gene from peripheral blood mononuclear cells. Hybrids between the amplified DNA and a RNA probe were measured in a microtiter plate immunoassay using a beta-D-galactosidase-conjugated monoclonal antibody to DNA-RNA hybrids and a fluorescent substrate. A second set of primers (nested set) located within the outer set was used in PCR with a known template to prepare the probe. One primer of the nested set included the T7 RNA polymerase promoter at its 5' end allowing transcription of a single-stranded RNA probe. Ten copies of HIV-1 DNA could be detected by PCR-EIA (42 fluorescent units with a background of 18 fluorescent units) compared with a detection limit of 1000 copies by ethidium bromide-stained agarose gel. HIV-1 DNA was detected by PCR-EIA in peripheral blood mononuclear cells from 32 of 33 seropositive patients (range 54-810 fluorescent units), and 0 of 25 seronegative patients (range 20-40 fluorescent units) (sensitivity 97%; specificity 100%). PCR-EIA offers a practical and nonisotopic method to objectively measure PCR-amplified HIV-1 DNA and has the potential for the measurement of other microbial pathogens in human body fluids.

Base Sequence↗
PubMed1990

Localization by in situ hybridization of gamma-glutamyl transpeptidase mRNA in the rat kidney using 35S-labeled RNA probes.

gamma-Glutamyl transpeptidase (GGT) is involved in the extraction of plasma glutathione in the postglomerular compartment of the kidney. The enzyme is distributed in the proximal tubule associated with the apical brush border. Using in situ hybridization with 35S-labeled anti-sense and sense RNA GGT probes on rat kidney cryostat sections, the present study demonstrates that GGT mRNA transcripts are detected in proximal tubules localized in the inner cortex, outer medulla, and medullary rays of the cortex. Such a distribution suggests that the GGT gene is mainly expressed in the more distal part of the proximal tubule, i.e., the pars recta. As a control, in situ hybridization has also been performed using a 35S-labeled beta-actin anti-sense RNA probe showing a diffuse pattern of distribution of beta-actin RNA transcripts particularly in the outer cortex. This highly sensitive method using single strand asymetric RNA probes, with a markedly reduced nonspecific binding is promising for the study of gene expression patterns in the kidney in order to clarify their heterogeneity in the various segments of the nephron.

Animals↗
PubMed2005

Antisense and sense RNA probe hybridization to immobilized crude cellular lysates: a tool to screen growth hormone antagonists.

The growth-promoting effect of growth hormone (GH) is primarily mediated by insulin-like growth factor-1 (IGF-1). The liver is the main source of circulating IGF-I. The authors have used rodent primary hepatocytes for studies on pharmacological intervention of IGF-I mRNA expression. A 96-well nonradioactive IGF-1 mRNA quantification assay was developed, based on the hybridization of sense and antisense RNA probes, to replicate membranes with crude hepatocyte lysates. The sense hybridization was used as an internal standard. The antagonistic properties of a set of GH-receptor binding compounds were evaluated. Two compounds were found to down-regulate IGF-I mRNA. Effects due to metabolic inhibition or toxicity were excluded using a cell proliferation assay. To investigate potential unspecific transcriptional effects, the mRNA levels of the housekeeping genes, beta-actin and glyceraldehyde-3-phosphate dehydrogenase (GAPDH), were determined. Two other GH-regulated genes, cytochrome P450 2C12 (CYP2C12) and a rat homologue to the human alpha1B-glycoprotein (A1BG), were quantified by RNase protection assays and found to be down-regulated, confirming the antagonistic property of 1 compound. In conclusion, a direct filter hybridization assay of hepatocyte lysates using nonradioactive sense and antisense probes can be used for quantitative mRNA measurements and could constitute a valuable tool in screening for pharmacologically active compounds.

Animals↗
PubMed1993

Synthesis of RNA probes by the direct in vitro transcription of PCR-generated DNA templates.

We describe a novel method for the generation of RNA probes based on the direct in vitro transcription of DNA templates amplified by polymerase chain reaction (PCR) using primers with sequence hybrids between the target gene and those of the T7 and T3 RNA polymerases promoters. This method circumvents the need for cloning and allows rapid generation of strand-specific RNA molecules that can be used for the identification of genes in hybridization experiments. We have successfully applied this method to the identification of DNA sequences by Southern blot analysis and library screening.

Base Sequence↗
PubMed2001

Developmental patterns of ceramide glucosyltransferase (GlcT-1) expression in the mouse: in situ hybridization using DIG-labeled RNA probes.

Glycosphingolipids (GSLs) play significant roles in a variety of cell membrane events, including cellular interactions, signaling, and trafficking. Ceramide glucosyltransferase (glucosylceramide synthase, GlcT-1, EC 2.4.1.80) catalyzes the initial step in GSL synthesis, the transfer of glucose from UDP-glucose to ceramide. The reaction product of glucosylceramide serves as a core structure for over 400 species of GSLs. The enzyme is a key regulatory factor controlling intracellular levels of ceramide and GSLs. Appearance and differential distribution of GlcT-1 mRNA during mice postimplantation embryogenesis [embryonic (E) days; E9, E11, E13, E15] were investigated by in situ hybridization with digoxigenin-labeled RNA probes, coupled with alkaline phosphatase detection. On E9, tissues of the mesencephalon, myelecephalon, diencephalons, and telencephalon expressed GlcT-1. On E11, it was expressed to a detectable extent in various tissues including mesencephalon, myelecephalon, diencephalon, telencephalon, nose, lung, liver, vertebra, tail, spinal cord, and tongue. The expression patterns of E13 were similar to those of E11, except that the heart and stomach became positive. On E15, a specific signal for GlcT-1 was detected in all organs of the embryo. These results provide the first evidence that GlcT-1 is differentially expressed during postimplantation embryogenesis.

Animals↗
PubMed2000

Developmental patterns of mST3GalV mRNA expression in the mouse: in situ hybridization using DIG-labeled RNA probes.

mST3GalV synthesizes ganglioside GM3, the precursor for simple and complex a- and b- series gangliosides, and the expression and regulation of mST3GalV (CMP-NeuAc: lactosylceramide alpha2,3-sialyltransferase) activity is central to the production of almost all gangliosides, a class of glycosphingolipids implicated in variety of cellular processes such as transmembrane signaling, synaptic transmission, specialized membrane domain formation and cell-cell interactions. To understand the developmental expression of mST3GalV in mice, we investigated the spatial and temporal expression of mST3GalV mRNA during the mouse embryogenesis [embryonic (E) days; E9, E11, E13, E15] by in situ hybridization with digoxigenin-labeled RNA probes. All tissues from E9 and E11 were positive for mST3GalV mRNA. On E13, mST3GalV mRNA was expressed in various neural and non-neural tissues. In contrast to these, on E15, the telencephalon and liver produced a strong expression of mST3Gal V which was a quite similar to that of E13. In this stage, mST3GalV mRNA was also expressed in some non-neural tissues. These data indicate that mST3GalV is differently expressed at developmental stages of embryo, and this may be importantly related with regulation of organogenesis in mice.

Animals↗
PubMed1999

Developmental patterns of GalBeta1,3(4)GlcNAc alpha2,3-sialyltransferase (ST3Gal III) expression in the mouse: in situ hybridization using DIG-labeled RNA probes.

Sialic acids are key determinants for biological processes, such as cell-cell interaction and differentiation. Sialyltransferases contribute to the diversity in carbohydrate structure through their attachment of sialic acid in various terminal positions on glycolipid and glycoprotein (N-linked and O-linked) carbohydrate groups. Galbeta 1,3(4)GlcNAc alpha2,3-sialyltransferase (ST3Gal III) is involved in the biosynthesis of sLe(x)and sLe(a) known as selectin ligands and tumor-associated carbohydrate structures. The appearance and differential distribution of ST3Gal III mRNA during mice embryogenesis [embryonic (E) days; E9, E11, E13, E15] were investigated by in situ hybridization with digoxigenin-labeled RNA probes coupled with alkaline phosphatase detection. On E9, all tissues were positive for ST3Gal III mRNA expression, whereas ST3Gal III mRNA on E11 was not detected throughout all tissues. On E13, ST3Gal III mRNA was expressed in different manner in various tissues. In this stage, ST3Gal III mRNA was positive only in the liver, pancreas and bladder. On E15, specific signal for ST3Gal III was detected in the liver, lung and forebrain. These results indicate that ST3GAI III is differently expressed at developmental stages of mice embryo, and this may be importantly related with regulation of organogenesis in mice.

Alkaline Phosphatase↗