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PubMed1984

Isolation of HLA locus-specific DNA probes from the 3'-untranslated region.

When human class I cDNA clones containing coding sequences are used to probe genomic DNA, 15-20 fragments, each containing a complete class I gene or pseudogene, are seen. Identification of which genomic DNA segments encode the HLA-A and -B antigens has to date required transfection of mouse L cells with cloned class I genes or analysis of HLA loss mutants. In this report we show that under high-stringency conditions, probes constructed from the 3'-untranslated region can be used to specifically identify the segments of DNA that encode the HLA-A and -B antigens in the human lymphoblastoid cell line 721. Examination of DNA from unrelated individuals indicates that these probes are locus specific and will permit identification of HLA-A and -B genes in the population.

Cell Line↗

PubMed1988

Comparison of cultural methods and DNA probe analyses for the detection of Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, and Bacteroides intermedius in subgingival plaque samples.

The purpose of this study was to compare DNA probe analyses to cultural methods for detecting three periodontal pathogens, Actinobacillus actinomycetemcomitans, Bacteroides gingivalis, and Bacteroides intermedius, in human subgingival plaque. Subgingival sites from patients diagnosed as either healthy or showing evidence of gingivitis or juvenile or adult periodontitis were sampled using two paper points. The number of these pathogens from one paper point was determined using microbiologic media and speciated by biochemical tests. Results were then compared to bacterial numbers obtained from the other paper point using species-specific DNA probes. In 60 samples from the disease group, DNA probe analysis demonstrated 100% effectiveness in detecting A. actinomycetemcomitans and B. intermedius and 91% effectiveness in detecting B. gingivalis at culture positive levels (greater than or equal to 10(3) cells). In addition, probe assays frequently identified these pathogens in samples that were culture negative. Probe analysis revealed a better correlation between presence of a pathogen and clinical evidence of disease on an individual patient basis. In contrast, most samples taken from sites of healthy individuals showed undetectable levels of all three pathogens as determined by both techniques. These results suggest that DNA probe technology is at least equivalent and often superior to cultural methods for detecting A. actinomycetemcomitans, B. gingivalis, and B. intermedius in human subgingival plaque samples.

Actinobacillus↗

PubMed2002

FISHing in the microwave: the easy way to preserve proteins. I. Colocalization of DNA probes and surface antigens in human leukocytes.

Most of the techniques for simultaneous visualization of proteic cell components and DNA probes are difficult to carry out. We have developed an alternative protocol for simultaneous visualization of DNA probes and cell surface antigens in human cells. The method exploits microwave energy to denature DNA and to anneal the probe after antigen fluorescent detection of unfixed cells previously embedded in a microgel. CD3 antigens and whole genome DNA probes or specific repetitive DNA sequences were colocalized in peripheral blood samples. The results show a strong, specific and consistent hybridization pattern in each cell that allowed correlation between cell subtype (PROTEINS) and nuclear phenotype (DNA).

CD3 Complex↗

PubMed1995

Production of digoxigenin-labelled DNA probe for detection of Muscovy duck parvovirus.

A chemiluminescent dot-blot hybridization assay was developed for the detection of Muscovy duck parvovirus (DPV) by using a non-radioactive DPV DNA probe. A 1030bp HindIII-Bg/II fragment of DPV DNA was labelled with digoxigenin-labelled dUTP. The hybridized DPV DNA probes were detected by an immunoenzymatic reaction using anti-digoxigenin-antibody Fab fragments conjugated to alkaline phosphatase and visualized by chemiluminescent reaction. The assay proved to be sensitive since up to 3 fg of homologous DPV DNA and 10(0.4) EID50 mul-1 of DPV infected amino-allantoic fluid could be visualized. It appeared to be specific for the detection of different strains of DPV and Derszy's disease virus (DDV). Nevertheless, the dot-blot assay showed a lower sensitivity to detect DDV infected samples. No hybridization was noticed between DPV DNA probe and the two mammalian parvovirus strains tested (canine and porcine parvoviruses), emphasizing nucleotidic sequence heterologies. The use of the probe for DPV diagnosis purpose is discussed. To our knowledge, this work constitutes the first description of a dot-blot hybridization assay for the detection of an avian parvovirus.

Animals↗

PubMed1991

Design and testing of a functional group-specific DNA probe for the study of natural populations of acetogenic bacteria.

The acetogens, although phylogenetically diverse, can be characterized by their possession of the acetyl coenzyme A (acetyl-CoA) pathway for autotrophic CO2 fixation. The gene encoding formyltetrahydrofolate synthetase, a key enzyme of the acetyl-CoA pathway, was previously cloned from the thermophilic acetogen Clostridium thermoaceticum and has now been tested as a group-specific probe for acetogens. Stable hybrids were formed between the probe and single DNA fragments from eight known acetogens representing six genera. A hybrid was also formed between the probe and a DNA fragment from one sulfate reducer known to be capable of both autotrophic CO2 fixation and acetate catabolism. No such hybrid was formed between the probe and DNA from a homoacetate fermenter not known to use the acetyl-CoA pathway, with two known formyltetrahydrofolate synthetase-producing purine fermenters, or with DNA from 27 other species representing 16 genera of organisms that do not use the acetyl-CoA pathway. DNA purified from cells extracted from horse manure was also screened with the acetogen probe. Six hybrids, indicating at least six detectable acetogen "strains," were observed.

Acetyl Coenzyme A↗

PubMed1987

Two unusual cases of first trimester prenatal diagnosis of cystic fibrosis using DNA probes.

There are now several DNA probes which localize the cystic fibrosis mutation (CF) to chromosome 7q2.2-q3.1. The most tightly linked probes, pJ3.11 and met, are useful for first trimester prenatal diagnosis for many families provided that there is at least one living child affected by CF (Farrall et al., 1986). We describe here two families seeking prenatal diagnosis for CF which present unusual counselling problems. The first is an extended family in which there is no living affected member with CF; the second, a consanguinous marriage at risk both for cystic fibrosis and beta-thalassaemia. In both cases first trimester chorionic villus sampling and DNA haplotype analysis predicted that the fetus is a carrier for CF, and in the doubly affected family a carrier for beta-thalassaemia as well. Both pregnancies resulted in live births and subsequent immunoreactive trypsin estimations were both in the normal range.

Chorionic Villi↗

PubMed1993

Homologous DNA targeting with RecA protein-coated short DNA probes and electron microscope mapping on linear duplex molecules.

We demonstrate that RecA protein-coated, short single-stranded DNA probes paired with a specific homologous DNA sequence in a linear duplex target molecule and accurately targeted the selected DNA sequence. RecA protein-coated complementary ssDNA probes were reacted with linear duplexes, and the homologously paired molecules were observed by electron microscopy. The sites of interaction between the RecA protein-coated DNA probes and the uncoated duplex DNA targets were directly visible on individual target DNA molecules by high-resolution darkfield electron microscopy, without chemical fixation or sample shadowing. The efficiency and specificity of pairing were verified with 446 and 222 base single-stranded DNA probes that shared no homology with one another, and several linear duplex target DNAs with their respective probe homology sites at different locations with respect to the ends of the double-stranded DNA molecules. Measurements of the position of RecA protein-coated probes paired to individual target molecules, observed at high magnification, showed that DNA probes specifically paired at their corresponding homologous target sequences. This RecA protein-mediated DNA mapping method allows homologous sequence positioning and gene mapping on individual double-stranded DNA molecules. Targeting reactions in which two different probe/target sites were 900 bases apart on a single duplex target molecule allowed both sites to be mapped in the same targeting reaction; although targets displaying both probes simultaneously were seen much less frequently than expected. The possible torsional or mechanistic constraints related to these reactions are briefly discussed.

DNA Probes↗

PubMed1991

[Study of detailed conditions in DNA probe test by use of Gen-Probe Rapid Diagnostic System for identification of Mycobacterium avium complex and Mycobacterium tuberculosis complex].

In order to improve feasibility of technical procedures in Gen Probe Rapid Diagnostic System (Gen Probe Inc., San Diego, CA, U.S.A.) for identification of Mycobacterium avium complex (MAC) and M. tuberculosis complex (MTC), we studied several test conditions in the DNA probe testing, such as stability of test bacterial suspension, optimal duration of bacterial cultivation, the number of organisms in test bacterial suspension required for accurate determination, and so on. With respect to concentration of organisms (MAC and MTC) in test bacterial suspension (0.1ml), we found that 5-fold dilution as well as 5-fold condensation of the standard bacterial suspension (McFarland No.1) gave substantially the same result as in the case where bacterial suspension at the standard concentration was used. This indicates that the test bacterial suspensions (0.1ml) containing either 1.5 X 10(7)-5 X 10(8) of MAC or 3 X 10(5)-8 X 10(6) of MTC are available for the DNA probe testing. Test bacterial suspension at McFarland No.1 prepared from fresh cultures (3-4 week-old) could be stored either at -80, -20 or 4 degrees C at least for 17 weeks without significant loss of reactivity to M. avium, M. intracellulare and MTC DNA probes. In this case, stability of DNA probe-reactivity was preserved in the following order: MTC, M. avium and M. intracellulare. Concerning the age of bacterial cultures, at least 16-week-old cultures of MAC and MTC after initial appearance of cell growth on 1% Ogawa's egg media were sufficiently reactive to either MAC or MTC DNA probe. In this case, MTC showed most stable reactivity during the course of long-term cultivation.(ABSTRACT TRUNCATED AT 250 WORDS)

DNA Probes↗

PubMed1986

DNA probes for identification of clinically important Bacteroides species.

Conventional procedures for identifying gram-negative anaerobes such as Bacteroides spp. are cumbersome and time-consuming. A simpler approach would be to use DNA probes to identify these organisms. Since many different species of gram-negative anaerobes are isolated from clinical specimens, the most useful DNA probes would be probes that identify a few clinically significant groups of anaerobes. To obtain such probes, we cloned HindIII-digested chromosomal DNA from various Bacteroides species and then screened these probes, labeled with 32P by nick translation, for hybridization to DNA from various species of Bacteroides, Fusobacterium, and other gram-negative bacteria. We identified three DNA probes (pBFII-4, pBFII-5, and pBFII-6) that hybridized specifically to DNA from Bacteroides fragilis, the species that accounts for about half of all isolates from clinical specimens containing anaerobes. We identified one DNA probe (pBE-3) that hybridized to all members of the B. fragilis group, a group of species that resemble B. fragilis with respect to fermentation pattern and antibiotic resistances. We also identified one probe (pBO-21) that hybridized to DNA from all Bacteroides sp. strains as well as to DNA from strains of Fusobacterium necrophorum and Fusobacterium nucleatum. pBO-21, but not pBE-3, cross-hybridized with a cloned Bacteroides sp. 16S rRNA gene. The limit of detection for these probes was 10(6) bacteria. The probes could detect B. fragilis in blood culture medium and in mixed cultures with other gram-negative bacteria. Attempts to use biotin-labeled DNA probes instead of 32P-labeled probes were not successful because the Bacteroides sp. extracts contained material that bound the streptoavidin-peroxidase detection reagent.

Animals↗

PubMed2002

Molecular cloning of verrucosidin-producing Penicillium polonicum genes by differential screening to obtain a DNA probe.

A differential molecular screening procedure was developed to obtain DNA clones enriched for verrucosidin-related genes that could be used as DNA probes to detect verrucosidin-producing Penicillium polonicum. Permissive and nonpermissive conditions for verrucosidin production were selected to obtain differentiated poly (A)+ RNA for the cloning strategy. P. polonicum yielded the highest amount of verrucosidin when cultured in malt extract broth at 25 degrees C without shaking. These conditions were selected as verrucosidin permissive conditions. When shaking was applied to the verrucosidin permissive conditions, verrucosidin was not detected. Approximately 5000 transformants were obtained for the library of DNA fragments from verrucosidin-producing P. polonicum and hybridized with cDNA probes obtained from poly (A)+ RNA of permissive and nonpermissive conditions. A total of 120 clones hybridized only with the permissive cDNA probes. From these, eight representative DNA inserts selected on the basis of size and labelled with fluorescein-dUTP were assayed as DNA probes in the second differential screening by Northern hybridization. Probe SVr1 gave a strong hybridization signal selectively with poly (A)+ RNAs from high verrucosidin production. When this probe was assayed by dot blot hybridization with DNA of different moulds species, hybridization was detected only with DNA from the verrucosidin-producing strain. The strategy used in this work has proved to be useful to detect unknown genes related to mycotoxins. In addition, the DNA probe obtained should be considered for the detection of verrucosidin-producing moulds.

Blotting, Northern↗

PubMed1989

Simple chemical synthesis and hybridization properties of non-radioactive DNA probes.

A simple chemical method for the synthesis of non-radioactive DNA probes is described: triazolyl-containing sequences were built by incorporation of 4-triazolylpyrimidin-2-ones instead of cytidines during oligodeoxyribonucleotide synthesis. The activating triazolyl groups were then displaced by a diamine which was further derivatized by a label, such as biotin. Synthesized DNA probes were oligonucleotides complementary to a cloned human antithrombin III DNA sequence. These probes, containing the same label at different positions of the sequence, were hybridized to their target DNA immobilized on nitrocellulose. Their hybridization specificity and stability were studied. Hybrid detection was performed either colorimetrically by the streptavidin-alkaline phosphatase-based system or by autoradiography after 5'-32P labeling of the probes: 15 fmol (0.05 microgram) of complementary sequence could be visualized in the two cases.

Antithrombin III↗

PubMed1983

Identification of human papillomavirus DNA in cervical and vaginal intraepithelial neoplasia with molecularly cloned virus-specific DNA probes.

The presence of human papillomavirus (HPV) DNA was identified in the tissues of cervical and vaginal intraepithelial neoplasia by Southern blot DNA hybridization under conditions of low stringency. The specific types of HPV present in the tissues were identified by using molecularly cloned types 1 through 6 (HPV-1 through HPV-6) HPV DNA probes under high-stringency conditions. All tissues of cervical and vaginal intraepithelial neoplasia analyzed contained HPV genomes. Fifteen of 19 samples (79%) contained HPV-6 DNA, and 10 of 19 samples (53%) HPV-3 DNA. Hybridization with HPV-1, HPV-2, HPV-4, and HPV-5 DNAs was also observed in several of the samples. Four of the samples did not hybridize with any of the probes tested (HPV-1 through HPV-6); yet, all showed hybridization with an HPV-EV DNA (a type 3-related DNA) probe under low-stringency conditions, indicating the presence of HPV types other than those belonging to HPV-1 through HPV-6.

Carcinoma in Situ↗

PubMed1993

Detection of polymorphisms among Theileria parva stocks using repetitive, telomeric and ribosomal DNA probes and anti-schizont monoclonal antibodies.

A total of 21 Theileria parva stocks from 6 countries were characterized using T. parva repetitive and ribosomal DNA probes, a Plasmodium berghei telomeric oligonucleotide and a panel of anti-schizont monoclonal antibodies (MAbs). Hybridization of the repetitive DNA probe to Southern blots of EcoRI-digested T. parva DNA revealed 20 different restriction fragment patterns among DNA samples isolated from infections initiated using 16 parasite stocks. The panel of anti-schizont MAbs defined 8 different profiles among schizont-infected lymphoblastoid cell-cultures infected with the same 16 T. parva stocks. Many stocks, which were differentiated by the repetitive DNA probe, could not be distinguished using the anti-schizont MAbs. A cloned T. parva small subunit ribosomal RNA (SSUrRNA) gene probe separated 17 T. parva stocks into 2 groups, exhibiting either 1 or 2 restriction fragments, when hybridized to EcoRI-digested T. parva DNA. When hybridized to PvuII-digested DNA from 8 T. parva stocks, the ribosomal probe identified 4 groups with similar restriction fragment patterns. A synthetic oligonucleotide derived from a P. berghei telomeric sequence hybridized to 7 or 8 size-polymorphic restriction fragments in the EcoRI-digested DNA of most T. parva stocks. The telomeric and ribosomal probes defined the same 4 groups among 8 T. parva stocks as assessed by similarities in restriction fragment patterns. Based on the comparison of repetitive DNA sequences from the T. parva Uganda and Muguga stocks, a synthetic oligonucleotide was developed which distinguished the DNA of the T. parva Uganda stock from that of 4 other T. parva stocks on a positive/negative basis.

Animals↗

PubMed1993

Quantitative and sensitive northern blot hybridization using PCR-generated DNA probes labeled with digoxigenin by nick translation.

Northern blot hybridization is one of the most convenient methods of detecting an mRNA. Nonradioactive Northern blotting using digoxigenin (DIG) is becoming widely applied because it is rapid and safe. Previous studies have indicated that DIG-labeled RNA probes are suitable for Northern blot hybridization. Here, the application of PCR-generated double-stranded DNA probes labeled with DIG by nick translation is described. DNA probes were synthesized by PCR, then labeled with DIG by nick translation. Northern blot hybridization was performed using the DIG-labeled DNA probes, and the signals were detected by means of a chemiluminescent reaction. A low amount of DIG-dUTP in the labeling reaction resulted in excellent Northern blots with low background. Densitometric analysis of the blots showed that the mRNA concentrations could be determined by densitometric analysis. The sensitivity of the DIG-Northern system was comparable to Northern blotting using 32P and was sufficiently sensitive to detect low-abundance mRNA.

Animals↗

PubMed1991

A cloned DNA probe identifies Cowdria ruminantium in Amblyomma variegatum ticks.

Heartwater, caused by Cowdria ruminantium and transmitted by ticks of the genus Amblyomma, is a constraint to ruminant animal production in sub-Saharan Africa. This rickettsial disease could spread from endemically infected areas of sub-Saharan Africa and certain Caribbean islands to other countries, including the United States, in which Amblyomma ticks exist. To detect C. ruminantium in tick vectors and animals, we made DNA probes from C. ruminantium DNA isolated from endothelial cell cultures. Two clones were evaluated; pCS20 from Crystal Springs (Zimbabwe) strain DNA had a 1,306-bp insert, and pCR9 from Kiswani (Kenya) strain DNA had a 754-bp insert. Both DNA probes detected 1 ng of Crystal Springs DNA; however, the pCS20 probe had a 10-fold-greater ability to discriminate between C. ruminantium DNA and DNA from other organisms. Also, the pCS20 probe did not hybridize to 400 ng (highest amount tested) of DNA from bovine cells, 3 protozoa, 3 rickettsiae, and 12 bacteria. In all experiments, C. ruminantium DNA was detected in midguts from 99 of 160 Amblyomma variegatum nymphs infected as larvae and in midguts from 38 of 80 adult ticks infected as nymphs but not in midguts from control nymphs and adults. The presence of C. ruminantium in nymphs and adults was confirmed by transmission of heartwater to goats. The DNA sequences of both probes were determined; synthetic oligonucleotides from pCS20 are recommended as DNA probes for C. ruminantium.

Animals↗

PubMedDate not supplied

Evaluation of radiolabeled and colorimetric DNA probes in comparison with an antigen screening assay for the detection of Salmonella from poultry farms.

A total of 48 environmental drag-swab samples from various poultry farms were tested for the presence of Salmonella spp. by culture, an enzyme-linked immunosorbent assay-based Salmonella antigen screening (SAS) assay, and two DNA probes (radiolabeled and colorimetric). The radiolabeled DNA probe was allowed to hybridize with culture-positive samples (n = 8) and was found to detect Salmonella spp. in all cases (100%). Both of the probes, subsequently hybridized with culture-negative samples (n = 8), were observed to yield good agreement (91%) with the culture findings. The remaining samples (n = 32) were tested by the SAS assay, and where there was no agreement between the culture and SAS, samples were further examined by the DNA probes. Results using both probes agreed with those obtained by culturing the samples but did not agree with the SAS assay result when the ratio of samples tested to samples positive (S/P) cutoff value used was 0.5.

Animals↗

PubMed1996

[Evaluation of non radioactive DNA probe (Affirm DP) for detecting periodontopathic bacteria].

The purpose of this investigation was to evaluate the potential of application of non-radioactive DNA probe method (Affirm DP) in clinical diagnosis and evaluation of treatment efficacy. Sensitivity and specificity of two different cut-off levels (10(4), 5 x 10(5)) of the method with bacterial culture in detection of Bacteroides forsythus, Porphyromonas gingivalis, and Actinobacillus actinomycetemcomitans were compared. Those bacteria were obtained from bacterial cultures and clinical samples from healthy subjects and patients with periodontal disease. The results showed that detection percentage of DNA probe method with 10(4) cut-off was equal to or higher than the culture method for Bacteroides forsythus and Porphyromonas gingivalis detection. Therefore, it is suggested to be a useful chairside DNA probe kit as an aid in clinical diagnosis and evaluation of treatment efficacy.

Aggregatibacter actinomycetemcomitans↗

PubMed1994

Directly labeled DNA probes using fluorescent nucleotides with different length linkers.

Directly labeled fluorescent DNA probes have been made by nick translation and PCR using dUTP attached to the fluorescent label, Cy3, with different length linkers. With preparation of probes by PCR we find that linker length affects the efficiency of incorporation of Cy3-dUTP, the yield of labeled probe, and the signal intensity of labeled probes hybridized to chromosome target sequences. For nick translation and PCR, both the level of incorporation and the hybridization fluorescence signal increased in parallel when the length of the linker arm is increased. Under optimal conditions, PCR yielded more densely labeled probes, however, the yield of PCR labeled probe decreased with greater linear density of labeling. By using a Cy3-modified dUTP with the longest linker under optimal conditions it was possible to label up to 28% of the possible substitution sites on the target DNA with reasonable yield by PCR and 18% by nick translation. A mechanism involving steric interactions between the polymerase, cyanine-labeled sites on template and extending chains and the modified dUTP substrate is proposed to explain the inverse correlation between the labeling efficiency and the yield of DNA probe synthesis by PCR.

Carbocyanines↗