Nonradioactive Oligonucleotide Probes Research Articles

The use of digoxigenin-labeled oligonucleotide probes for the specific detection of Salmonella in foods

Three oligonucleotide fragment TS11 ,TS21,and TS31 were labeled with digoxigenin, and the hybridization specificities for three oligonucleotides confirmed with Salmonella and non-Salmonella isolates. Three non-radioactive oligonucleotide probes were used for the specific detection of Salmonella in contaminated food samples, including pork, fish and shrimp samples. It was found that enrichment of Salmonella in food samples using lactose combined tetrathionate broth followed by streaking of the culture on Salmonella-Shigella agar and spotting suspected cells on nitrocellulose paper placed on Luria agar prior to colony hybridization yield unambiguous results. Salmomella at 3 cfu per gram of food could be detected.

Rapid In Situ Hybridization using Oligonucleotide Probes on Paraformaldehyde-prefixed Brain of Rats with Serotonin Syndrome.

3,4-Methylenedioxymethamphetamine (MDMA; ecstasy) toxicity may cause region-specific changes in serotonergic mRNA expression due to acute serotonin (5-hydroxytryptamine; 5-HT) syndrome. This hypothesis can be tested using in situ hybridization to detect the serotonin 5-HT2A receptor gene htr2a. In the past, such procedures, utilizing radioactive riboprobe, were difficult because of the complicated workflow that needs several days to perform and the added difficulty that the technique required the use of fresh frozen tissues maintained in an RNase-free environment. Recently, the development of short oligonucleotide probes has simplified in situ hybridization procedures and allowed the use of paraformaldehyde-prefixed brain sections, which are more widely available in laboratories. Here, we describe a detailed protocol using non-radioactive oligonucleotide probes on the prefixed brain tissues. Hybridization probes used for this study include dapB (a bacterial gene coding for dihydrodipicolinate reductase), ppiB (a housekeeping gene coding for peptidylprolyl isomerase B), and htr2a (a serotonin gene coding for 5-HT2A receptors). This method is relatively simply, cheap, reproducible and requires less than two days to complete.

Modification of expression of stem cell factor by various cytokines.

The local production of stem cell factor (SCF) may be an important mechanism for regulating proliferation, differentiation, and migration of various cells bearing c-kit receptors, and might be susceptible to the cytokines that serve in inflammation and tissue repair. We have demonstrated that in three murine cell lines, Balb/3T3A31, MC3T3-E1, and C3H-2K, which constitutively produced SCF with different quantity, the SCF mRNA expression was greatly enhanced in response to basic fibroblast growth factor (bFGF) or transforming growth factor beta1 (TGF-beta1). The study was carried out by in situ hybridization utilizing nonradioactive oligonucleotide probes and quantitative image analysis. Leukemia inhibitory factor (LIF) or interleukin-4 (IL-4) moderately increased SCF mRNA in all cell lines, but IL-3 did not. The dot-blot enzyme-linked immunosorbent assay (ELISA) further confirmed that SCF protein production in these cell lines and bone marrow stromal cells was markedly enhanced by TGF-beta1, although TGF-beta1 suppressed the proliferation of all these cells. bFGF also enhanced the SCF production in these cell lines, but did not in bone marrow stromal cells, suggesting a difference in their susceptibility to the cytokine. Our results suggest that TGF-beta1 and bFGF potentially modulate the biological function of cells bearing c-kit receptors through the modulation of SCF production in fibroblasts.

Detection of mycobacterial nucleic acids by polymerase chain reaction in fixed tissue specimens of patients with human immunodeficiency virus infection. Swiss HIV Cohort Study.

A polymerase chain reaction (PCR) method, which amplifies a fragment of the 16S ribosomal RNA (rRNA) gene present in all mycobacterial species, was developed and tested on 84 formalin-fixed paraffin-embedded tissue specimens from 51 patients with human immunodeficiency (HIV) infection. The PCR products were characterized either by sequencing or by hybridization with nonradioactive oligonucleotide probes specific for Mycobacterium tuberculosis complex, M. avium, or M. genavense. Sequencing was successful for 26 samples compared with the 45 samples for probe hybridization. The sensitivity of DNA amplification compared with microscopic examination was 79.5%. A mixed infection was detected with M. genavense for only one patient who was infected with M. tuberculosis complex. In the group of 22 control patients, where no diagnosis of mycobacterial infection was made during life and no acid-fast bacteria were seen during the autopsy, four samples of one patient were positive by hybridization with the M. tuberculosis probe. This patient had a clinical history compatible with tuberculosis. This PCR method may be a powerful tool for the precise diagnosis of mycobacterial infections from histopathologic material, provided that several sections from the same specimen block are tested.

Rapid detection of toxoplasmic nucleic acid by enzyme-linked immunofiltration-assay after membrane transfer.

We report the use of enzyme-linked immunofiltration-assay (ELIFA) for rapid detection of Toxoplasma gondii DNA after transfer to nitrocellulose or nylon membranes. Saturation, specific labeling with a nonradioactive oligonucleotide probe and washing steps are included in an active filtration process, which is controled by microcomputer regulating reagent flow. This method provides excellent specificity, reproducibility and repeatability. Recycling in a closed circuit or by reversing the direction of flow provides the advantage of reducing the required volume of costly reagents (e.g. probes). ELIFA does not require lengthy membrane manipulation, and hybridization as well as stringency and revelation steps can be automated. The procedure can be carried out in less than 2 h, which is a major time saving compared to conventional solid-phase molecular hybridization techniques.

Detection of human cytomegalovirus DNA in dried newborn blood filter paper

To detect human cytomegalovirus (HCMV) DNA, filter paper spotted with peripheral blood from newborns 4 to 7 days after birth was dried and subjected to the polymerase chain reaction (PCR) followed by Southern blot hybridization with a nonradioactive oligonucleotide probe. The detection rates were 25.1% in healthy individuals and 33.0% in low body weight neonates weighing not more than 2500 g at birth, most of whom appeared to have been infected transplacentally or by other means within the uterus. HCMV was detected after only heating the dried blood on the filter paper, and may be applied as a screening method for the early diagnosis of HCMV.

MODERN DIAGNOSIS (WITH MOLECULAR TESTS) OF ACUTE INFECTIOUS DIARRHEA

There have been three significant technical developments in the molecular genetic diagnosis of infectious diarrhea. The first was the replacement of polynucleotide probes with more specific synthetic oligonucleotide probes. The second was the replacement of radiolabeled markers with nonradiolabeled markers, and the third was PCR amplification. In the PCR procedure, it is possible to increase the quantity of target nucleotide sequences to quantities easily detectable with nonradioactive oligonucleotide probes. It is now possible to amplify nucleotide sequences of more than one enteric pathogen with different primers simultaneously and to detect these amplified nucleotide sequences with nonradiolabeled oligonucleotide probes. With a scanning laser system, the results of enteric PCRs will be used to identify enteric pathogens on a routine basis in clinical and public health laboratories. Computers need to be used to analyze these results and transfer this information rapidly to clinicians and public health officials.

Chemiluminescent detection of infectious bursal disease virus with a PCR-generated nonradiolabeled probe.

A polymerase chain reaction (PCR)-generated digoxigenin-labeled nonradioactive oligonucleotide probe was developed and utilized in slot-blot hybridization coupled with chemiluminescence for the detection of infectious bursal disease virus (IBDV). The probe was prepared from the RNA of the standard challenge strain (STC) of IBDV serotype 1 by reverse transcription followed by 2 PCR amplifications with 2 separate sets of primers. RNA of STC viruses prepared from bursae infected with STC viruses was subjected to the first PCR with the outer primers V8 and V9 that amplified a 607-base pair (bp) segment. The PCR product from the first PCR was eluted following agarose gel electrophoresis and subjected to the second PCR with the nested primers V6 and V7 that flanked a 351-bp segment. In the second PCR, dTTP was substituted by digoxigenin-11-dUTP in the PCR reaction mixture so that the amplified 351-bp DNA products were labeled with digoxigenin. The specificity of the PCR-generated digoxigenin-labeled probe was tested on different strains of IBDV, several unrelated avian viruses, and bacteria by slot-blot hybridization assay. Hybridization was detected by chemiluminescence. The sensitivity of the probe was assayed using 10-fold serial dilutions of purified RNA from the STC strain of IBDV. The PCR-generated digoxigenin-labeled probe hybridized with genomic RNA of STC and variant strains A, D, E, G, and GLS-5 of IBDV serotype 1 but not OH strain of IBDV serotype 2. The probe did not react with avian reovirus, infectious bronchitis virus, Salmonella enteritidis, Escherichia coli, or Staphylococcus aureus.(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of point mutation in bla T genes of Enterobacteriaceae by biotinylated oligonucleotide probes using microwell hybridization and enzymofluorometric method.

Point mutation in the nucleotide sequence of the structural genes for the TEM-type penicillinases can broaden their substrate spectrum towards all beta-lactams except cephamicins and imipenem. We describe here hybridization techniques for the detection of point mutations by non-radioactive oligonucleotide probes with plasmid DNA carrying bla T genes immobilized in polystyrene microwells. After hybridization in discriminating conditions with corresponding biotinylated oligonucleotide probes, the hybrids were detected by using a streptavidin-alkaline phosphatase conjugate and a fluorogenic substrate, 4-methylumbelliferyl-phosphate. The adsorption of DNA to microwells used in the present work was found to be independent of Mg2+ and Na+ concentrations. By this method, less than 3 fmols of target DNA were sufficient for the detection of point mutation.

Detection of 14 HLA-DQB1 alleles by oligotyping

Fourteen alleles have been identified by analysis of the nucleotide sequences encoding the HLA-DQB1 chain. This study describes the detection of these 14 alleles by selective gene amplification and sequence-specific hybridization with nonradioactive oligonucleotide probes. These techniques were employed to create an oligotyping system with two levels of resolution that provide versatility and the capacity for comprehensive detection of all polymorphic sequences. An initial low-resolution assay was employed to detect four major groups of alleles that are associated with the DQw1-w4 serological specificities. A further high-resolution assay was then employed to differentiate 14 individual DQB1 alleles. Appropriate control measures were also included to detect carry-over and to confirm hybridization specificity. This system was used to analyze the allele frequencies of DQB1-0301, -0302, and -0303 in 115 DQB1-03 ∗∗ Caucasian blood donors. Allele frequencies of oligotypes DQB1-05 ∗∗ and DQB1-06 ∗∗ were analyzed in 112 DQB1-01 ∗∗ Caucasian blood donors. This system was also utilized to identify oligotypes designated DQB1-0501 through DQB1-0503 and DQB1-0601 through DQB1-0605 in 35 Tenth International Histocompatibility Workshop DQw1 cell lines to examine the correlation with serological and cellular specificities. In one of these cell lines, an unexpected linkage was discovered between the DRB1 and DQB1 loci, suggesting a recombination event. Oligotyping is a precise and accurate method for directly defining polymorphic sequences and it promises to have a major impact on the future direction of HLA typing.

Genotypic identification of pathogenic Mycobacterium species by using a nonradioactive oligonucleotide probe

Commercial DNA hybridization assays (Syngene, Inc., San Diego, Calif.) utilizing alkaline phosphatase-labeled oligonucleotide probes for the identification of Mycobacterium tuberculosis complex and M. avium complex (MAC) were evaluated with 261 isolates of mycobacteria. On the basis of biochemical criteria, the test for MAC was 98% specific and more sensitive (95 of 99, 95%) than Gen-Probe (88 of 99, 89% sensitivity); the major difference in sensitivity noted between the two systems was related to the hybridization of seven MAC strains to the SNAP X probe. The M. tuberculosis complex probe correctly identified all 62 isolates of M. tuberculosis and all 11 isolates of M. bovis, for a sensitivity of 100%. There were two discrepant reactions with mycobacteria other than M. tuberculosis complex isolates.

Rapid typing of HLA-DQB1 DNA polymorphism using nonradioactive oligonucleotide probes and amplified DNA

The allelic sequence diversity at the HLA-DQB1 locus has been analyzed by polymerase chain reaction (PCR) amplification and sequencing. Fifteen amino acid sequence-defined alleles (one previously unreported) and several silent nucleotide polymorphisms which subdivide these alleles have been identified. Here, we describe the specific amplification of the DQB1 second exon by several different PCR primer pairs and a simple and rapid typing procedure using a panel of 16 horseradish peroxidase (HRP)-labeled oligonucleotide probes capable of distinguishing these DQB1 alleles.

Rapid typing of DNA sequence polymorphism at the HLA-DRB1 locus using the polymerase chain reaction and nonradioactive oligonucleotide probes

An HLA-DR typing system that uses sequence-specific oligonucleotide (SSO) probes conjugated to horseradish peroxidase (HRP) for analyzing DRB alleles amplified by the polymerase chain reaction has been developed. Using 25 HRP-SSO probes and two primer pairs for generic and for DRB1 locus-specific amplification, we can distinguish 31 of 34 HLA-DRB1 alleles. This procedure is suitable for typing heterozygous samples from a variety of sources, including cDNA templates, and can detect in a simple and rapid dot-blot format allelic variants not distinguishable by serological methods. It should prove valuable for tissue typing, determining individual identity, and studies of disease susceptibility.

The Use of Non-Radioactive Oligonucleotide Probes to Analyze Enzymatically Amplified DNA for Prenatal Diagnosis and Forensic HLA Typing

Non-radioactive oligonucleotide probes for specific alleles of the HLA-DQα and β-globin loci have been synthesized and applied to forensic analysis and prenatal diagnosis. The results obtained with biotin-labeled, enzyme-labeled, and 32P-labeled probes are compared in the individuality analysis of different autopsy samples and the diagnosis of two fetuses at risk for sickle-cell anemia.

Non-radioactive oligonucleotide probe for detection of clinical enterotoxigenic Escherichia Coli isolates of bovine origin

Oligonucleotides (32 or 34 mer) corresponding to enterotoxigenic Escherichia coli ST Ia (ST-P) toxin were tailed with Bio-11-dUTP using terminal deoxynucleotidyl transferase. Plasmids from clinica E.Coli isolates were prepared by modified rapid alkaline lysis procedure and dot-spotted. Biotinylated oligonucleotide probes were hybridized to detect the St Ia toxin gene. The results were in agreement with that obtained by radioactive oligonucleotide probes. Of 135 clinical isolates (sampled from 6 different regions of France), only 7 (5.2 %) were found to be ST Ia +. These 7 isolates were the only ones to be found positive for the K99 adhesive pili antigen. Both the proves were specific to the ST Ia toxin gene and failed to detect the closely related ST Ib (ST-H) toxin gene. Possibilities of their wide usage in clinical labs are discussed.

Identification of individuality using non-radioactive oligonucleotide probes to analyze enzymatically amplified polymorphic DNA sequences

Identification of individuality using non-radioactive oligonucleotide probes to analyze enzymatically amplified polymorphic DNA sequences