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Results for “hybridization chain reaction”

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At least 19 recordsLinked to original sources
PubMed2001

Detection of human papillomavirus on Papanicolaou-stained cervical smears using indirect in situ polymerase chain reaction hybridization.

OBJECTIVE: Polymerase chain reaction (PCR) and indirect in situ hybridization were combined to detect human papillomavirus (HPV) DNA on Papanicolaou (PAP)-stained cervical smears. To our knowledge, this is the first report of an experiment using indirect in situ PCR (IS-PCR) on PAP-stained cervical smears. DESIGN: We collected native cell specimens from cervicovaginal lavage of 162 patients with squamous intraepithelial lesions. Solution-phase PCR (SP-PCR) was performed as the reference method in the detection of HPV DNA. Indirect IS-PCR was carried out for the same patients to detect the HPV DNA types 6/11 and 16/18 after the PAP-stained smears had been decolorized. Low-risk and high-risk HPV DNA types were also detected by both SP-PCR and indirect IS-PCR. RESULTS: In the evaluation by indirect IS-PCR, 48 of 81 PAP-stained cell smears of low-grade squamous intraepithelial lesions were positive for HPV DNA, as compared to 40 positive cell smears determined by indirect SP-PCR (sensitivity of indirect IS-PCR compared to SP-PCR, 98.1%). Forty-two of 42 high-grade squamous intraepithelial lesion samples were positive for HPV DNA, as determined by both methods (sensitivity of IS-PCR, 100%). Cell lines investigated in this study as positive or negative controls for HPV DNA were confirmed by indirect IS-PCR and SP-PCR. CONCLUSIONS: Our data show that in comparison to SP-PCR, indirect IS-PCR is a highly sensitive method to detect HPV DNA in cell smears from the uterine cervix. The advantages of indirect IS-PCR are (a) low numbers of cells needed, (b) the possibility of using PAP-stained specimens, and (c) cytologic details of smears can be preserved.

DNA, Viral↗
PubMed2004

Triggered amplification by hybridization chain reaction.

We introduce the concept of hybridization chain reaction (HCR), in which stable DNA monomers assemble only upon exposure to a target DNA fragment. In the simplest version of this process, two stable species of DNA hairpins coexist in solution until the introduction of initiator strands triggers a cascade of hybridization events that yields nicked double helices analogous to alternating copolymers. The average molecular weight of the HCR products varies inversely with initiator concentration. Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications.

Base Sequence↗
PubMed2001

Detection of Salmonella and simultaneous detection of Salmonella and Shiga-like toxin-producing Escherichia coli using the magnetic capture hybridization polymerase chain reaction.

The magnetic capture hybridization polymerase chain reaction (MCH-PCR) was used to detect Salmonella and also to simultaneously detect Salmonella and Shiga-like toxin-producing Escherichia coli (SLTEC). Fifty-seven Salmonella and 41 SLTEC were included in the study. Salmonella were detected either individually by a single MCH-PCR assay targeting the inv gene or simultaneously with SLTEC by a multiplex MCH-PCR in which SLTEC were detected using primers for the slt genes. Both single and multiplex assays were found to be specific for tested pathogens. The results indicate that MCH-PCR can be used as means of detecting single or multiple bacterial pathogen(s).

Adhesins, Bacterial↗
PubMed1995

Comparison of selective polymerase chain reaction primers and differential probe hybridization of polymerase chain reaction products for determination of relative amounts of codon 215 mutant and wild-type HIV-1 populations.

A mutation at codon 215 of the human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) gene results in decreased sensitivity to zidovudine (ZDV). In order to follow changes in codon 215 mutant (MUT) and wild-type (WT) populations in the plasma of patients during therapy, two polymerase chain reaction (PCR) procedures were investigated. The first was a nested, selective PCR, wherein a first round with viral-specific primers was followed by a second round with allele-specific primers. Although the procedure is relatively sensitive, some samples in the first round of PCR could not be amplified. In mixing experiments, mispriming of the MUT primer made relative determination of quantities subjective and difficult. Differential hybridization of PCR product with probes specific for codon 215 MUT or WT sequences was also investigated. A probe directed to a highly conserved region of the RT gene in the amplified PCR product was used to determine the total amount of PCR product analyzed. Differential hybridization was linear and reproducible over several logs of MUT:WT ratios, and determination of a 1:100 ratio of MUT:WT was readily achieved. When applied to longitudinal samples from three patients, dramatic changes in each population were readily apparent. These changes were evaluated with regard to viral load.

Base Sequence↗
PubMed1998

Localization of hepatitis B virus DNA in hepatocellular carcinoma by polymerase chain reaction in situ hybridization.

The polymerase chain reaction in situ hybridization (PCR-ISH) is a new technique that combines the sensitivity of PCR with the localizing ability of ISH. To investigate the expression pattern of hepatitis B virus (HBV) in the tissue of hepatocellular carcinoma (HCC), we detected HBV-DNA with PCR-ISH in paraffin-embedded tumor and corresponding non-tumor tissues from 11 HCC patients. HBV-DNA was detected in 4 of 11 tumor tissues and in 7 of 10 non-tumor tissues. In tumor tissues, positive signals were scattered in the tissue with occasional clustering, and were found mainly in the cytoplasm of HCC cells rather than in the nucleus. In non-tumor tissues, the number of positive signals was higher than in tumor tissues and they were found in regenerating nodules with differing patterns and intensities. When we compared the detection rate of PCR-ISH with nested PCR among 10 tissue samples, HBV-DNA was detected in 5 tissue samples by PCR-ISH, but the S gene was detected in 10, precore gene in 9 and X gene in 8 by nested PCR. The findings suggest that PCR-ISH is a sensitive technique for localizing HBV in tissue sections and that the low level of HBV replication persists in HCC cells.

Carcinoma, Hepatocellular↗
PubMed1997

The mechanism of Epstein-Barr virus infection in nasopharyngeal carcinoma cells.

To investigate the relationship between Epstein-Barr virus (EBV) and nasopharyngeal carcinoma (NPC) cells, we examined the pathway of EBV infection in NPC cell lines. We used immunolocalization to investigate the EBV receptor (C3d-R) and polymeric immunoglobulin receptor [secretory component (SC) protein]. We incubated IgA anti-EBV and EBV particles with NPC cells and observed the EBV DNA signal by in situ polymerase chain reaction hybridization and polymerase chain reaction plus Southern blotting. We also colocalized SC protein and EBV RNA in NPC biopsy specimens. Results showed that: 1) NPC cells did not express the EBV receptor but did express SC protein in each line; 2) SC protein was also expressed in some tumor cells but not in untransformed squamous metaplastic epithelia in NPC biopsy specimens; 3) EBV could infect NPC cells through an EBV-IgA and SC complex and retained an EBV viral genome in their nuclei; SC expression could be down-regulated by EBV proteins; and 4) in biopsy specimens, a fraction of tumor cells showed SC protein expression; only a portion of tumor cells contained EBV, and of these cells only a few expressed SC protein. These findings indicate that EBV cannot infect untransformed nasopharyngeal squamous metaplastic epithelia but can enter NPC cells through IgA-mediated endocytosis.

Carcinoma↗
PubMed2003

A sensitive and specific detection of Human herpesvirus 8 by polymerase chain reaction and dot blot hybridization.

Polymerase chain reaction (PCR) is a powerful technique of detecting Human herpesvirus 8 (HHV-8), but has a limited sensitivity and specificity. A new assay of HHV-8 based on combination of PCR with dot blot hybridization (DBH) was developed and evaluated for its sensitivity and specificity. An HHV-8-specific primer pair, ORF26out was used for amplification of target DNA. When the PCR product was detected visually the limit of detection was 0.1 ng DNA isolated from HHV-8-infected BC-3 cells. For DBH, the DNA amplified with the primer pair ORF26in specific for HHV-8 was labeled with digoxigenin (DIG). This DIG-labeled probe was capable of detecting 1.0 ng of DNA isolated from HHV-8-infected BC-3 cells. On the other hand, PCR combined with DBH (PCR/DBH) was more sensitive than PCR or DBH alone and also very specific. The sensitivity of PCR/DBH was higher than that of PCR and DBH alone. The PCR/DBH assay can be applied efficiently to confirm the presence of HHV-8 in clinical samples and to differentiate specifically HHV-8 infection from other viral infections.

DNA, Viral↗
PubMed1993

Direct detection of Mycobacterium tuberculosis in sputum by polymerase chain reaction and DNA hybridization.

A polymerase chain reaction (PCR) assay for the rapid diagnosis of pulmonary tuberculosis was developed by using oligonucleotide primers to amplify a fragment of IS6110, an insertion sequence repeated multiple times in the chromosome of Mycobacterium tuberculosis. Sediment obtained from sputa processed by the N-acetyl-L-cysteine-NaOH method was suspended in a simple lysis buffer and was heated at 100 degrees C for 30 min prior to amplification. A dUTP-uracil N-glycosylase PCR protocol was used to prevent false-positive test results because of the carryover of products from previous amplification reactions. The 317-bp amplicon was detected by direct gel analysis and Southern blotting and then hybridization with a biotin-labeled internal probe. Hybrid molecules were detected by using a commercially available avidin-alkaline phosphatase-chemiluminescent substrate system (Tropix, Inc., Bedford, Mass.). The analytical sensitivity of the assay was 10 fg of purified mycobacterial DNA. The limits of detection by culture (Middlebrook 7H11 agar and Lowenstein-Jensen medium) and by PCR were equivalent in terminal dilution experiments for organism suspensions and positive sputa. An internal control was used to detect the presence of amplification inhibitors in each negative reaction mixture. DNA was purified from inhibitory specimens by phenol-chloroform extraction and ethanol precipitation. PCR results were compared with results of microscopy and conventional culture for the detection of M. tuberculosis in 313 sputum specimens. There were 124 specimens that were positive for M. tuberculosis by conventional methods and 113 (91%) that were positive by PCR. PCR detected 105 of 110 (95%) of the smear-positive and 8 of 14 (57%) of the smear-negative specimens. There were no false-positive results by PCR (specificity, 100%). This PCR assay innovations that make application of this new technology feasible in clinical microbiology laboratories.

Bacteriological Techniques↗
PubMed1993

Comparison of Virapap filter hybridization with polymerase chain reaction and Southern blot hybridization methods for detection of human papillomavirus in tonsillar and pharyngeal cancers.

A method using a commercial dot filter hybridization kit, Virapap, was compared with Southern blot hybridization and polymerase chain reaction (PCR) for the detection of human papillomavirus (HPV) types 16 and 18 in pharyngeal and tonsillar cancers of 12 patients as well as tonsillar biopsies from 28 patients with chronic tonsillitis. Concordant results between Virapap and PCR, Virapap and Southern hybridization, and PCR and Southern hybridization methods were obtained respectively in 41.7%, 58.3% and 83.3% of the cancer cases, and 67.9%, 67.9% and 85.7% of the control (tonsillitis) cases. Virapap false-positive results were found in 5 cancer cases and 5 control cases. Although the Virapap method is reported to be useful for detecting HPV in gynecological tissues, this method cannot be recommended for the detection of HPV in pharyngeal and tonsillar cancers.

Adolescent↗
PubMed1993

Detection of naturally occurring enteroviruses in waters by reverse transcription, polymerase chain reaction, and hybridization.

Comparison in virus-seeded mineral water of three detection methods for enteroviruses, direct hybridization, cell culture, and reverse transcription into cDNA followed by polymerase chain reaction and hybridization, showed that the last procedure was 10 to 1,000 times more sensitive than detection by cell culture and 10(5) to 10(7) times more sensitive than direct hybridization. The presence of naturally occurring enteroviruses was also demonstrated in activated sludge and in concentrated and non-concentrated surface water samples by reverse transcription-polymerase chain reaction-hybridization. However, in activated sludge and in concentrated surface waters, enzymatic amplification was sometimes inhibited by contaminants.

Animals↗
PubMed1996

Detection of human herpes virus 6 in AIDS-associated retinitis by means of in situ hybridization, polymerase chain reaction and immunohistochemistry.

The ubiquitous nature of HHV-6 and its genomic relationship with cytomegalovirus led us to evaluate an etiological link between HHV-6 and AIDS-associated retinitis in a prospective study. HHV-6 infection was studied in patients with AIDS-associated retinitis and in two control populations. Eye pairs were obtained at necropsy from nine patients with AIDS-associated retinitis, four human immunodeficiency virus (HIV)-sero-positive patients with normal fundus examination and three HIV-seronegative patients. HHV-6 infection was detected by polymerase chain reaction (PCR), in situ hybridization and immunohistochemistry. Human cytomegalovirus (CMV) and HIV-1 infections were detected in parallel by the same methods. HHV-6 infection was detected in three cases of AIDS-associated retinitis. In two of these patients, HHV-6 infection was detected both by immunohistochemistry and PCR while in the third case it was detected by in situ hybridization and PCR. In the three patients, fundus examination showed bilateral retinitis in two of them and unilateral retinitis in one of them. HHV-6 infection was not detected in the retina of the two control groups. CMV was also detected in the three cases positive for HHV-6 by all three methods. HIV DNA was detected by PCR in two of three cases and was confirmed in one of these cases by in situ hybridization. These results confirm that HHV-6 infects the retina but suggests that HHV-6 does not have an exclusive causative role in AIDS-associated retinitis, since CMV coinfection of the retina was detected in all three of the patients positive for HHV-6.

AIDS-Related Opportunistic Infections↗
PubMed1994

Combined polymerase chain reaction-hybridization microplate assay used to detect bovine leukemia virus and Salmonella.

Here we describe the use of an assay that integrates the polymerase chain reaction (PCR) with hybridization of the amplified product for detection in the same microwell. Traditional PCR requires transportation of the amplified product to another system for characterization of samples. Transportation means time-consuming manipulation and risk of contaminating the laboratory with amplified product. Integration of amplification and specific product detection greatly reduces sample manipulations and the risk of contamination. We used the assay for detection of bovine leukemia virus and Salmonella. The results were identical with those produced by two traditional PCR methods. This assay could easily be adapted for other organisms, simply by using other primers and probes.

Base Sequence↗
PubMed1994

Detection of cytomegalovirus in formalin-fixed paraffin-embedded donor, native and allograft liver tissue using a multiplex polymerase chain reaction-liquid hybridization assay.

A multiplex polymerase chain reaction (PCR)-liquid hybridization assay detecting a minimum 10 fg of cytomegaloviral (CMV) DNA has been developed. This assay successfully detected viral nucleic acids in 25/26 (96.2%) routinely embedded allograft liver biopsies with CMV hepatitis. No CMV DNA was detected in 15 native and 12 donor liver tissues sampled at the time of liver transplantation. These results indicate that archived formalin-fixed, paraffin-embedded liver tissues obtained from patients with significant liver disease can be successfully analyzed for CMV by PCR, retrospectively. Failure to detect CMV in native and donor livers implies that any latent virus present within these tissues is very focally distributed, or is below the threshold of detection applicable to PCR.

Base Sequence↗
PubMed1996

Rapid detection and identification of mycobacteria by combined method of polymerase chain reaction and hybridization protection assay.

A new method for the rapid detection and identification of mycobacteria, combining polymerase chain reaction (PCR) with DNA probe, was developed. The mycobacterial 16S rRNA encoding gene was amplified by nested PCR, and the PCR product was identified by hybridization protection assay using acridinium ester labelled DNA probe. The optimum temperature for hybridization of PCR product and DNA probe was estimated as 55 degrees C. The specificity of the combined method was excellent in the detection and identification of Mycobacterium tuberculosis and Mycobacterium avium-intracellulare complex (MAC). The detection limit was 10 fg DNA for M. tuberculosis, and 100 fg DNA for MAC. Results of preliminary clinical investigation of this method using 207 clinical specimens demonstrated an efficient detection and identification of M. tuberculosis and MAC. These results indicate that the new combined method may be a useful test for the rapid detection and identification of M. tuberculosis and MAC in clinical specimens.

Humans↗
PubMed1996

Detection of herpes simplex virus DNA in cerebrospinal fluid samples using the polymerase chain reaction and microplate hybridization.

As conventional polymerase chain reaction (PCR) procedures are time-consuming and laborious, we developed and evaluated a rapid semi-automatic microplate method to detect the amplified PCR products. The use of PCR, with subsequent hybridization in microplates, is described for the detection of herpes simplex virus (HSV) DNA in cerebrospinal fluid samples. The principle of the method is based on two phases. Firstly, the amplification of the viral DNA in the sample is undertaken using a pair of primers of which one is biotinylated. Secondly, the amplified viral genomic sequences are bound to the wells of streptavidin-coated microplates and hybridized with digoxigenin-labeled oligonucleotide probes which are then detected using anti-digoxigenin antibody enzyme conjugates and either a photometric, fluorometric or luminometric substrate and microplate reader. The method is highly sensitive allowing the detection of as few as five purified DNA molecules. Compared to conventional gel electrophoresis followed by Southern blotting the established microplate hybridization is also much less time-consuming and involves less manual work. The applicability of the method is described for use as a routine diagnostic procedure for detection of early central nervous system infections caused by HSV-1 and HSV-2.

Animals↗