Comparison of radioactive (32P and 35S) and biotinylated probes for detection of cytomegalovirus DNA

In vitro high-throughput screening assay for modulators of transcription

We developed a 96-well microtiter-plate high-throughput screening (HTS) assay for the detection of modulators of transcription. This HTS assay consists of three steps: (1) the in vitro transcription reaction; (2) modification and hybridization of RNA products; and (3) washing and quantification. During the first step, a DNA template containing the promoter of interest upstream of a cassette lacking guanosine residues in one of its strands (G-less cassette) is incubated with nuclear extract and the necessary cofactors/activators and substrates. During the second step, the in vitro synthesized transcripts are digested with RNase T1 and hybridized to two DNA oligonucleotides. One oligonucleotide is biotinylated for trapping of the RNA products to a streptavidin-coated plate, and the other is europium-labeled for detection by time-resolved fluorescence. We show that this assay is highly reproducible and robust, yielding results comparable to those obtained by standard methodologies employing radioactive nucleotide incorporation and gel electrophoresis while offering a very significant advantage in terms of throughput (>2000 assay points per operator per day). We demonstrate the usefulness of the assay for the discovery of small molecule inhibitors of transcription, and applications of this approach for the high-throughput discovery of transcriptional modulators are discussed.

A highly sensitive nonisotopic detection method for in situ hybridization

In situ hybridization is a technique that allows detection of specific DNA and RNA sequences in tissue sections. Nonisotopic techniques are fast and give a precise localization of the hybridization product, but a drawback is the low sensitivity. However, the sensitivity is dependent on the detection system used. To evaluate a sensitive in situ hybridization method with nonradioactive probes we compared three different detection systems, using biotin-labeled human papillomavirus (HPV) 16 probes. The three detection systems included (i) STAV-FITC method (streptavidin-fluorescein isothiocyanate/alkaline phosphatase anti-FITC), (ii) APAAP method (mouse anti-biotin/anti-mouse IgG/alkaline phosphatase mouse anti-alkaline phosphatase), and (iii) tyramide signal amplification (TSA) method (STAV-horseradish peroxidase (HRP)/biotinyl tyramide/STAV-HRP). The in situ hybridization methods were tested on CaSki and SiHa cells and two cervical carcinomas known to be HPV16 positive. The cells and tissues and been fixed in 4% buffered formalin and paraffin embedded. The three different detection systems gave satisfactory nuclear staining in CaSki cells (CaSki cells contain > 500 copies of HPV16 DNA) and the two cervical carcinomas. However, demonstration of HPV16 DNA in SiHa cells (SiHa cells contain one to two HPV16 genome copies) was possible only by use of the APAAP method. It was concluded that the APAAP method provides the best sensitivity among the nonisotopic detection systems and can detect single viral copies in formalin-fixed and paraffin-embedded material.

An ultrasensitive, nonisotopic immunoassay for hyaluronan using the streptavidin-biotin system

A time-resolved fluoroimmunoassay for measuring hyaluronan concentrations in plasma and several biological fluids is described. The solid-phase immunoassay is based on the competition between aggregation of hyaluronan with the cartilage proteoglycan monomer, followed by binding of a monoclonal antibody to keratan sulfate of the proteoglycan and a biotinylated anti-mouse IgG. Fluorescence can be measured by a time-resolved fluorometer after binding of Eu(3+)-labelled streptavidin to the biotinylated IgG. The assay is precise and correlates well (r = 0.986) with the only established radioimmunoassay known. The results show that it is essential to perform a blank run without addition of proteoglycan, as endogenous proteoglycan disturbs the measurement and causes underestimation of plasma hyaluronan. The distinguishing feature of this assay is its extreme sensitivity (< 0.24 microgram/l of plasma). The mean analytical recovery after serial dilutions and addition was 100.3 and 101.3%, the within-assay and between-assay coefficients of variation were 3.67% and 7.02%, respectively.

Nucleotide sequence of the Schizosaccharomyces japonicus var. versatilis ribosomal RNA gene cluster and its phylogenetic implications

Fission yeasts form a small but heterogeneous group of ascomycetes and it is still unclear whether they should be subdivided into three genera (Schizosaccharomyces, Octosporomyces, Hasegawaea) or remain a single genus (Schizosaccharomyces). In order to decide whether a new genus Hasegawaea should be established for the species Schizosaccharomyces japonicus and Schizosaccharomyces versatilis, we have characterized the entire rDNA cluster in Schizosaccharomyces japonicus var. versatilis and compared it with the homologous region from Schizosaccharomyces pombe and with complete rRNA gene sequences from other yeast genera. From a phage genomic library a recombinant lambda phage containing the entire rDNA repeat unit was isolated. In this paper we report the primary sequence of the 18s, 5.8s and 25s rRNA coding regions. The S. japonicus var. versatilis rRNA genes are 1823 (18s), 158 (5.8s) and 3422 (25s) nucleotides long. The two sequences of the larger rRNA genes exhibit 95.7% (18s) and 93% (25s) similarity with the homologous genes from S. pombe. The differences between the rRNA genes of S. japonicus and S. pombe, however, are much smaller than the intrageneric differences within the rDNA sequences of other yeast genera. Therefore, subdivision of fission yeasts into the genera Schizosaccharomyces and Hasegawaea does not to seem to be justified.

Cytomegalovirus DNA detection of an immediate early protein gene with nested primer oligonucleotides

A rapid and sensitive polymerase chain reaction (PCR) was developed to detect conserved sequences from the immediate early gene of human cytomegalovirus (HCMV). The primers sequences were from EcoRI J fragment of Ad169. The first primer set was selected to amplify a 242 bp fragment and the next primer set was nested within the first and amplified a 146 bp fragment. With the single PCR system it was possible to detect 100 fg HCMV DNA but with double PCR 5-10 fg were detectable. Specific amplification was seen in urines from patients with HCMV infections. 20 urine samples were analysed by single PCR, double PCR and virus cultivation. The double PCR was the most sensitive method. Urines from healthy seropositive persons and cells infected with other members of the herpes virus family were negative with all three methods. This suggests that specific amplification by double PCR is sensitive and can be used for rapid detection of HCMV DNA in cases with activated infection.

Detection of cytomegalovirus DNA using probes labelled with digoxigenin

Cloned HindIII restriction fragments of cytomegalovirus (CMV) DNA (strain AD169) were labelled with biotin, digoxigenin or 32P and used as probes to detect CMV DNA. Probes biotinylated by nick translation, random hexanucleotide priming (RHP) or "photobiotin" were able to detect 10-50 pg of homologous DNA. Probes labelled with digoxigenin or 32P by RHP detected 0.1 pg of homologous DNA, and 1-10 CMV-infected fibroblasts. Comparison of digoxigenin- and 32P-labelled probes in a DNA hybridisation assay on 186 urine specimens demonstrated that these probes were of similar sensitivity, detecting CMV DNA in 40 and 41 specimens, respectively. Positive results were obtained using this hybridisation assay with 11 of 14 specimens (79%) yielding CMV by virus isolation, and with 35 other specimens obtained from patients with laboratory evidence of CMV infection or symptoms compatible with CMV disease. Thus digoxigenin-labelled probes may provide an assay that can detect CMV DNA in specimens yielding a negative result by virus isolation.