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Journal articles on the topic 'DNA probe assay'

Author: Grafiati

Published: 4 June 2021

Last updated: 2 February 2022

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1

Carpenter, W. R., T. E. Schutzbank, V. J. Tevere, K. R. Tocyloski, N. Dattagupta, and K. K. Yeung. "A transcriptionally amplified DNA probe assay with ligatable probes and immunochemical detection." Clinical Chemistry 39, no. 9 (1993): 1934–38. http://dx.doi.org/10.1093/clinchem/39.9.1934.

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Abstract Transcriptionally amplified DNA probes are valuable tools in the development of sensitive nucleic acid-based diagnostic assays. Here we describe a model assay using a novel oligonucleotide hairpin probe that encodes a T7 RNA polymerase promoter. The hairpin probe and an adjacently hybridizing biotinylated capture probe were hybridized to target DNA and the duplex was captured onto streptavidin-coated magnetic particles. After ligation of the immobilized probes, which served to maintain specificity, the hairpin probe was transcribed by T7 RNA polymerase. The amplified RNA product was h

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2

Arnold, L. J., P. W. Hammond, W. A. Wiese, and N. C. Nelson. "Assay formats involving acridinium-ester-labeled DNA probes." Clinical Chemistry 35, no. 8 (1989): 1588–94. http://dx.doi.org/10.1093/clinchem/35.8.1588.

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Abstract We describe the development of several hybridization assay formats involving acridinium-ester-labeled DNA probes. The simplest of these is a homogeneous assay procedure that requires only three steps to complete, including a 5-s detection step. Using this format, we have detected target sequences in the 10(-16) to 10(-17) mol range; when rRNA is the target, this translates to 3000 to 300 bacterial organisms. The entire assay can be carried out in less than 30 min. This is the first homogeneous DNA probe assay to be of practical use in the clinical laboratory, and it represents a major

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Chan, S. K., Y. S. Choong, D. Perera, and T. S. Lim. "Dengue serotyping with a label-free DNA sensor." Analytical Methods 10, no. 2 (2018): 214–22. http://dx.doi.org/10.1039/c7ay02131c.

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4

Nitsche, Andreas, Nina Steuer, Christian Andreas Schmidt, Olfert Landt, and Wolfgang Siegert. "Different Real-Time PCR Formats Compared for the Quantitative Detection of Human Cytomegalovirus DNA." Clinical Chemistry 45, no. 11 (1999): 1932–37. http://dx.doi.org/10.1093/clinchem/45.11.1932.

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Abstract Background: The aim of this study was to compare the ABI PRISM 7700 Sequence Detection System and the LightCycler to develop a quantitative real-time PCR assay for the detection of human cytomegalovirus (HCMV) DNA suitable for routine hospital application. Methods: We used one exonuclease probe and five different hybridization probe sets as sequence-specific fluorescence detection formats. For the exonuclease assay and two hybridization probe sets, reproducibility and the detection limit were determined. To keep the total assay time to a minimum, we gradually shortened individual reac

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5

French, Cynthia, Conan Li, Charles Strom, et al. "Detection of the Factor V Leiden Mutation by a Modified Photo-Cross-Linking Oligonucleotide Hybridization Assay." Clinical Chemistry 50, no. 2 (2004): 296–305. http://dx.doi.org/10.1373/clinchem.2003.023556.

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Abstract Background: Our previously developed assay for detection of the factor V Leiden mutation (G1691A) based on a nucleic acid photo-cross-linking technology used two allele-specific capture probes and six fluorescein-modified signal-generating reporter probes. We wished to improve the sensitivity and performance of the method. Methods: We developed new reporter probes with ∼10-fold more fluorescein molecules than the original probes. The single, cross-linker-modified capture probe was replaced by a three-probe system, separating the probe–target cross-linking function and the allelic diff

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6

Okano, K., and H. Kambara. "DNA Probe Assay Based on Exonuclease III Digestion of Probes Hybridized on Target DNA." Analytical Biochemistry 228, no. 1 (1995): 101–8. http://dx.doi.org/10.1006/abio.1995.1320.

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7

Chase, Catherine J., Melanie P. Ulrich, Leonard P. Wasieloski, et al. "Real-Time PCR Assays Targeting a Unique Chromosomal Sequence of Yersinia pestis." Clinical Chemistry 51, no. 10 (2005): 1778–85. http://dx.doi.org/10.1373/clinchem.2005.051839.

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Abstract Background: Yersinia pestis, the causative agent of the zoonotic infection plague, is a major concern as a potential bioweapon. Current real-time PCR assays used for Y. pestis detection are based on plasmid targets, some of which may generate false-positive results. Methods: Using the yp48 gene of Y. pestis, we designed and tested 2 real-time TaqMan® minor groove binder (MGB) assays that allowed us to use chromosomal genes as both confirmatory and differential targets for Y. pestis. We also designed several additional assays using both Simple-Probe® and MGB Eclipse™ probe technologies

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8

Guillot, Emmanuelle, and Christian Mouton. "A PCR-DNA probe assay specific forBacteroides forsythus." Molecular and Cellular Probes 10, no. 6 (1996): 413–21. http://dx.doi.org/10.1006/mcpr.1996.0057.

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9

Rashtchian, A., J. Eldredge, M. Ottaviani, et al. "Immunological capture of nucleic acid hybrids and application to nonradioactive DNA probe assay." Clinical Chemistry 33, no. 9 (1987): 1526–30. http://dx.doi.org/10.1093/clinchem/33.9.1526.

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Abstract Antibodies specific for DNA:RNA hybrids were coated onto polystyrene test tubes and applied to hybridization assays involving DNA and RNA. Synthetic DNA probes complementary to 16S rRNA of Campylobacter were labeled with biotin and hybridized to ribosomal RNA directly in lysates of bacterial cells. After hybridization, DNA:RNA hybrids were captured with immobilized anti-DNA:RNA antibody, and the biotinylated probe was detected with streptavidin-horseradish peroxidase (EC 1.11.1.7) conjugate. The assay was optimized to detect as few as 70,000 Campylobacter cells in a sample. We compare

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Smith, Maria, Kenneth Smith, Alan Olstein, Andrew Oleinikov, and Andrey Ghindilis. "Restriction Endonuclease-Based Assays for DNA Detection and Isothermal Exponential Signal Amplification." Sensors 20, no. 14 (2020): 3873. http://dx.doi.org/10.3390/s20143873.

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Application of restriction endonuclease (REase) enzymes for specific detection of nucleic acids provides for high assay specificity, convenience and low cost. A direct restriction assay format is based on the specific enzymatic cleavage of a target–probe hybrid that is accompanied with the release of a molecular marker into the solution, enabling target quantification. This format has the detection limit in nanomolar range. The assay sensitivity is improved drastically to the attomolar level by implementation of exponential signal amplification that is based on a cascade of self-perpetuating r

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11

Dames, Shale, David C. Pattison, L. Kathryn Bromley, Carl T. Wittwer, and Karl V. Voelkerding. "Unlabeled Probes for the Detection and Typing of Herpes Simplex Virus." Clinical Chemistry 53, no. 10 (2007): 1847–54. http://dx.doi.org/10.1373/clinchem.2007.090761.

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Abstract Background: Unlabeled probe detection with a double-stranded DNA (dsDNA) binding dye is one method to detect and confirm target amplification after PCR. Unlabeled probes and amplicon melting have been used to detect small deletions and single-nucleotide polymorphisms in assays where template is in abundance. Unlabeled probes have not been applied to low-level target detection, however. Methods: Herpes simplex virus (HSV) was chosen as a model to compare the unlabeled probe method to an in-house reference assay using dual-labeled, minor groove binding probes. A saturating dsDNA dye (LC

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12

Gentilomi, G., M. Musiani, M. Zerbini, D. Gibellini, G. Gallinella, and S. Venturoli. "Double in situ hybridization for detection of Herpes simplex virus and cytomegalovirus DNA using non-radioactive probes." Journal of Histochemistry & Cytochemistry 40, no. 3 (1992): 421–25. http://dx.doi.org/10.1177/40.3.1313062.

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We describe a double in situ hybridization assay for the simultaneous detection of Herpes simplex virus (HSV) and cytomegalovirus (CMV) DNA in infected cell cultures using non-radioactive-labeled probes. This work used a biotinylated HSV DNA probe, which can be revealed by an avidin-biotin-peroxidase complex and a digoxigenin-labeled CMV DNA probe, visualized by anti-digoxigenin F(ab) fragments conjugated with alkaline phosphatase. Light microscopy visualization was achieved by the contrasting colors of appropriate peroxidase and alkaline phosphatase reaction products (red and dark blue, respe

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Rapier, J. M., Y. Villamarzo, G. Schochetman, et al. "Nonradioactive, colorimetric microplate hybridization assay for detecting amplified human immunodeficiency virus DNA." Clinical Chemistry 39, no. 2 (1993): 244–47. http://dx.doi.org/10.1093/clinchem/39.2.244.

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Abstract A nonradioactive, colorimetric microplate hybridization procedure was used to assay human immunodeficiency virus (HIV) DNA, amplified by the polymerase chain reaction (PCR). Under the PCR conditions used, four proviral copies per 150,000 cells were detected by amplifying a series of DNA mixtures that contained various copy numbers of HIV. Assays of PCR-amplified DNA from peripheral blood mononuclear cells of seronegative individuals yielded negative results (104 of 104), whereas samples from seropositive individuals yielded &gt; 99% positive results (141 of 142). Similar results w

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Coutlée, François, Patti Gravitt, Harriet Richardson, et al. "Nonisotopic Detection and Typing of Human Papillomavirus DNA in Genital Samples by the Line Blot Assay." Journal of Clinical Microbiology 37, no. 6 (1999): 1852–57. http://dx.doi.org/10.1128/jcm.37.6.1852-1857.1999.

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The line blot assay, a gene amplification method that combines PCR with nonisotopic detection of amplified DNA, was evaluated for its ability to detect human papillomavirus (HPV) DNA in genital specimens. Processed samples were amplified with biotin-labeled primers for HPV detection (primers MY09, MY11, and HMB01) and for β-globin detection (primers PC03 and PC04). Amplified DNA products were hybridized by a reverse blot method with oligonucleotide probe mixtures fixed on a strip that allowed the identification of 27 HPV genotypes. The line blot assay was compared to a standard consensus PCR t

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15

HSU, HSIEN-YEH, SAMUEL W. CHAN, DAVID I. SOBELL, DONALD N. HALBERT, and E. PATRICK GROODY. "A Colorimetric DNA Hybridization Method for the Detection of Escherichia coli in Foods." Journal of Food Protection 54, no. 4 (1991): 249–55. http://dx.doi.org/10.4315/0362-028x-54.4.249.

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A colorimetric DNA hybridization assay has been developed for the rapid detection of Escherichia coli in foods. The method employs two oligonucleotide probes which are specific for the 16S ribosomal RNA of E. coli. Probes are added to lysates of test cultures and allowed to hybridize to target rRNA if present. The probe-target complex is captured via hybridization to a polystyrene dipstick. The immobilized target is detected using an antibody-horseradish peroxidase conjugate which binds to the immobilized probe-target complex. The probe-target-antibody complex generates a colorimetric signal w

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STERN, NORMAN J., and MARK A. MOZOLA. "Methods for Selective Enrichment of Campylobacter spp. from Poultry for Use in Conjunction with DNA Hybridization." Journal of Food Protection 55, no. 10 (1992): 767–70. http://dx.doi.org/10.4315/0362-028x-55.10.767.

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A DNA hybridization test was investigated for application to the detection of Campylobacter spp. in poultry samples. The test chemistry involves solution phase hybridization and detection by means of an enzymatically generated colorimetric endpoint. DNA probes used in the test system are targeted to unique sequences of ribosomal RNA and are specific for Campylobacter jejuni, Campylobacter coli, Campylobacter lari, and Campylobacter fetus subsp. fetus. Initial experiments with pure cultures of C. jejuni established the sensitivity limit of the DNA hybridization assay at approximately 106–7 CFU

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Zammatteo, Nathalie, Laurence Lockman, Francis Brasseur, et al. "DNA Microarray to Monitor the Expression of MAGE-A Genes." Clinical Chemistry 48, no. 1 (2002): 25–34. http://dx.doi.org/10.1093/clinchem/48.1.25.

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Abstract Background: The MAGE-A genes encode antigens that are of particular interest for antitumor immunotherapy because they are strictly tumor specific and are shared by many tumors. We developed a rapid method to identify the MAGE-A genes expressed in tumors. Methods: A low-density DNA microarray was designed to discriminate between the 12 MAGE-A cDNAs amplified by PCR with only one pair of consensus primers. The assay involved reverse transcription of total RNA with oligo(dT) primer, followed by PCR amplification and hybridization on a microarray. Amplification in the presence of Biotin-1

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18

Tooley, Paul W., Frank N. Martin, Marie M. Carras, and Reid D. Frederick. "Real-Time Fluorescent Polymerase Chain Reaction Detection of Phytophthora ramorum and Phytophthora pseudosyringae Using Mitochondrial Gene Regions." Phytopathology® 96, no. 4 (2006): 336–45. http://dx.doi.org/10.1094/phyto-96-0336.

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A real-time fluorescent polymerase chain reaction (PCR) detection method for the sudden oak death pathogen Phytophthora ramorum was developed based on mitochondrial DNA sequence with an ABI Prism 7700 (TaqMan) Sequence Detection System. Primers and probes were also developed for detecting P. pseudosyringae, a newly described species that causes symptoms similar to P. ramorum on certain hosts. The species-specific primer-probe systems were combined in a multiplex assay with a plant primer-probe system to allow plant DNA present in extracted samples to serve as a positive control in each reactio

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Johnson, D. W., N. J. Pieniazek, and J. B. Rose. "DNA Probe Hybridization and PCR Detection of Cryptosporidium Compared to Immunofluorescence Assay." Water Science and Technology 27, no. 3-4 (1993): 77–84. http://dx.doi.org/10.2166/wst.1993.0325.

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There is a need for the development of methods for the detection of Cryptosporidium in environmental samples. Two assays which detect the DNA of this parasite were developed and compared to the traditional method of detection, immunofluorescence assay (IFA). Oligonucleotide primers hybridizing to small subunit ribosomal RNA coding sequences were used in the polymerase chain reaction to develop highly specific detection of Cryptosporidium species. The PCR assay could detect about 20-100 oocyst equivalents in clean samples, but the sensitivity was reduced in some environmental samples. Detection

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Lee, Hui Wen, Wellcome W. H. Ho, Raja Thangavel, Jeyaseelan Baskarathevan, and Brett J. R. Alexander. "Validation of qPCR assays for the detection of citrus canker." New Zealand Plant Protection 72 (July 28, 2019): 282. http://dx.doi.org/10.30843/nzpp.2019.72.328.

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Citrus canker, a serious bacterial disease affecting the citrus industry worldwide, is caused by Xanthomonas citri subsp. citri (Xcc) pathotypes A, A* and Aw, and to a lesser extent by X. fuscans subsp. aurantifolii (Xfa). The recent citrus canker outbreak in Australia has emphasised the need to re-evaluate the efficiency of molecular assays used for detecting citrus canker bacteria. Two published probe-based qPCR assays targeting the pth and lrp genes were tested for Xcc, whereas a SYBR Greenbased qPCR assay was tested for Xfa. The Xcc pth gene and Xfa qPCR assays were shown to be specific to

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Newby, D. T., T. L. Hadfield, and F. F. Roberto. "Real-Time PCR Detection of Brucella abortus: a Comparative Study of SYBR Green I, 5′-Exonuclease, and Hybridization Probe Assays." Applied and Environmental Microbiology 69, no. 8 (2003): 4753–59. http://dx.doi.org/10.1128/aem.69.8.4753-4759.2003.

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ABSTRACT Real-time PCR provides a means of detecting and quantifying DNA targets by monitoring PCR product accumulation during cycling as indicated by increased fluorescence. A number of different approaches can be used to generate the fluorescence signal. Three approaches—SYBR Green I (a double-stranded DNA intercalating dye), 5′-exonuclease (enzymatically released fluors), and hybridization probes (fluorescence resonance energy transfer)—were evaluated for use in a real-time PCR assay to detect Brucella abortus. The three assays utilized the same amplification primers to produce an identical

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CERQUEIRA, ALOYSIO M. F., ANITA TIBANA, TANIA A. T. GOMES, and BEATRIZ E. C. GUTH. "Search for LT-II and STb DNA Sequences Among Escherichia coli Isolated from Bovine Meat Products by Colony Hybridization." Journal of Food Protection 57, no. 8 (1994): 734–36. http://dx.doi.org/10.4315/0362-028x-57.8.734.

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A total of 1,066 Escherichia coli colonies isolated from 105 raw bovine meat samples purchased at supermarkets in Rio de Janeiro were submitted to hybridization assays with gene probes for LT-II and STb enterotoxins. Five colonies comprising four different E. coli strains isolated from four pieces of beef, two samples of ground beef (5.7%) and two hamburger patties (5.7%) hybridized with the LT-II probe, while no hybridization occurred with the STb probe. Expression of LT-II enterotoxin using the Y1 adrenal cell assay was verified in two of four E. coli strains. A serotype diversity existed am

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Martin, Cara, David Roberts, Marjo van der Weide, et al. "Development of a PCR-Based Line Probe Assay for Identification of Fungal Pathogens." Journal of Clinical Microbiology 38, no. 10 (2000): 3735–42. http://dx.doi.org/10.1128/jcm.38.10.3735-3742.2000.

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We report on a reverse-hybridization line probe assay (LiPA) which when combined with PCR amplification detects and identifies clinically significant fungal pathogens including Candida,Aspergillus, and Cryptococcus species. DNA probes have been designed from the internal transcribed-spacer (ITS) regions of Candida albicans, Candida parapsilosis, Candida glabrata, Candida tropicalis, Candida krusei, Candida dubliniensis, Cryptococcus neoformans,Aspergillus fumigatus, Aspergillus versicolor,Aspergillus nidulans and Aspergillus flavus. The probes were incorporated into a LiPA for detection of bio

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IZAT, A. L., C. D. DRIGGERS, M. COLBERG, M. A. REIBER, and M. H. ADAMS. "Comparison of the DNA Probe to Culture Methods for the Detection of Salmonella on Poultry Carcasses and Processing Waters1." Journal of Food Protection 52, no. 8 (1989): 564–70. http://dx.doi.org/10.4315/0362-028x-52.8.564.

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In a series of five experiments a total of 269 broiler carcass and chill tank water samples were tested for the presence of Salmonella using the DNA probe and the standard cultural method. Carcasses were sampled using a whole carcass rinse technique. Samples consisted of pre- (48) and post-chill (103) carcasses, and pre-chill (48) and chill (70) tank water. Samples to be evaluated with the DNA probe were subjected to three preenrichment/enrichment procedures to determine the most accurate and reliable enrichment procedure to use with the DNA probe assay. Direct enrichment in Selenite Cystine f

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Howson, Emma L. A., Richard J. Orton, Valerie Mioulet, Tiziana Lembo, Donald P. King, and Veronica L. Fowler. "GoPrime: Development of an In Silico Framework to Predict the Performance of Real-Time PCR Primers and Probes Using Foot-and-Mouth Disease Virus as a Model." Pathogens 9, no. 4 (2020): 303. http://dx.doi.org/10.3390/pathogens9040303.

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Real-time PCR (rPCR) is a widely accepted diagnostic tool for the detection and quantification of nucleic acid targets. In order for these assays to achieve high sensitivity and specificity, primer and probe-template complementarity is essential; however, mismatches are often unavoidable and can result in false-negative results and errors in quantifying target sequences. Primer and probe sequences therefore require continual evaluation to ensure they remain fit for purpose. This paper describes the development of a linear model and associated computational tool (GoPrime) designed to predict th

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Weller, S. A., J. G. Elphinstone, N. C. Smith, N. Boonham, and D. E. Stead. "Detection of Ralstonia solanacearumStrains with a Quantitative, Multiplex, Real-Time, Fluorogenic PCR (TaqMan) Assay." Applied and Environmental Microbiology 66, no. 7 (2000): 2853–58. http://dx.doi.org/10.1128/aem.66.7.2853-2858.2000.

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ABSTRACT A fluorogenic (TaqMan) PCR assay was developed to detectRalstonia solanacearum strains. Two fluorogenic probes were utilized in a multiplex reaction; one broad-range probe (RS) detected all biovars of R. solanacearum, and a second more specific probe (B2) detected only biovar 2A. Amplification of the target was measured by the 5′ nuclease activity of Taq DNA polymerase on each probe, resulting in emission of fluorescence. TaqMan PCR was performed with DNA extracted from 42 R. solanacearum and genetically or serologically related strains to demonstrate the specificity of the assay. In

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LAHIFF, S., M. GLENNON, J. LYNG, T. SMITH, N. SHILTON, and M. MAHER. "Real-Time Polymerase Chain Reaction Detection of Bovine DNA in Meat and Bone Meal Samples." Journal of Food Protection 65, no. 7 (2002): 1158–65. http://dx.doi.org/10.4315/0362-028x-65.7.1158.

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We describe a real-time polymerase chain reaction (PCR) assay for the detection of bovine DNA extracted from meat and bone meal (MBM) samples. PCR primers were used to amplify a 271-bp region of the mitochondrial ATPase 8–ATPase 6 gene, and a fluorogenic probe (BOV1) labeled with a 5′ FAM reporter and a 3′ TAMRA quencher was designed to specifically detect bovine PCR product. The specificity of the BOV1 probe for the detection of the bovine PCR product was confirmed by Southern blot hybridization analysis of the probe with PCR products generated from ovine, porcine, and bovine genomic DNA extr

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Brock, Kenny V., and Leon N. D. Potgieter. "Rapid Fluorescence Detection of in Situ Hybridization with Biotinylated Bovine Herpesvirus-1 DNA Probes." Journal of Veterinary Diagnostic Investigation 1, no. 1 (1989): 34–38. http://dx.doi.org/10.1177/104063878900100111.

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The use of biotinylated DNA hybridization probes for clinical detection of bovine herpesvirus-1 was investigated. Biotinylated DNA hybridization probes were prepared from bovine herpesvirus-1 DNA purified from infected cell cultures. The viral DNA was nick translated in the presence of biotin-dUTP with DNA polymerase to incorporate biotin into the newly synthesized strand. The probe was tested for specificity in in situ hybridization assays with bovine herpesvirus-1 DNA. Hybridization was detected using avidin-fluorescein single sandwich systems and an avidin-globulin with anti-globulin-fluore

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Saxena, Anurag, Keith Bonham, Evan Neuls, and Oksana Moshynska. "G125A Single Nucleotide Polymorphism (SNP) in 5′-UTR of the Tumor Suppressor Gene Bax Affects Its Transcriptional Regulation." Blood 108, no. 11 (2006): 2250. http://dx.doi.org/10.1182/blood.v108.11.2250.2250.

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Abstract Lower expression of Bax protein in various human malignancies is associated with poor response to treatment and shorter disease-free survival. We (Cancer Lett2002; 187:199–205) and others (J Clin Oncol; 23:1514–21) have shown the association of a single nucleotide polymorphism (SNP) in the BAX promoter (G125A) with reduced protein expression and treatment resistance in chronic lymphocytic leukemia (CLL). Using luciferase reporter gene assay we demonstrated that this SNP significantly reduced BAX promoter activity (Oncogene2005; 24:2042–9). Our aim was to determine the effect of this p

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Muir, Alastair, A. Toby A. Jenkins, Gordon Forrest, John Clarkson, and Alan Wheals. "Rapid electrochemical identification of pathogenic Candida species." Journal of Medical Microbiology 58, no. 9 (2009): 1182–89. http://dx.doi.org/10.1099/jmm.0.009183-0.

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This study describes the development of a novel assay to detect fungal DNA and identify the most clinically relevant invasive human pathogenic fungi to the species level using oligonucleotide probes, labelled with electrochemically active groups, and solid-state electrodes. A panfungal probe designed against the 18S rRNA gene region, capable of detecting all fungal pathogens tested, and species-specific probes, designed against the ITS2 region for detection of the five Candida species most commonly encountered in the clinical setting (Candida albicans, Candida glabrata, Candida parapsilosis sp

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Vergara, Michelle J., I. P. Shamini Pushparajah, John F. Mackay, and Kerry R. Everett. "Testing new PCR primers and a TaqMan™ probe for detection of Phlyctema vagabunda syn. Neofabraea alba ." New Zealand Plant Protection 72 (July 28, 2019): 278. http://dx.doi.org/10.30843/nzpp.2019.72.309.

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Phlyctema vagabunda syn. Neofabraea alba is a fungal pathogen that causes bull’s eye rot (BER) of apples. Polymerase chain reaction (PCR) primers complementary to the inter-transcribed spacer region of ribosomal DNA (ITS) and the β-tubulin gene region, and a TaqMan™ probe assay were developed to detect this pathogen. These assays were compared in quantitative PCR (qPCR) reactions for amplification of DNA extracted from several fungal species and from apple tissue. Although the ITS and the β-tubulin primers amplified all N. alba isolates, both primers also amplified a few other fungal species.

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Ye, Sujuan, Menglei Wang, Zhenxing Wang, Na Zhang, and Xiliang Luo. "A DNA–linker–DNA bifunctional probe for simultaneous SERS detection of miRNAs via symmetric signal amplification." Chemical Communications 54, no. 56 (2018): 7786–89. http://dx.doi.org/10.1039/c8cc02910e.

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Rubin, Lorry G., and Atqia Rizvi. "PCR-based assays for detection of Streptococcus pneumoniae serotypes 3, 14, 19F and 23F in respiratory specimens." Journal of Medical Microbiology 53, no. 7 (2004): 595–602. http://dx.doi.org/10.1099/jmm.0.45550-0.

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Current culture-based assays are insensitive for detection of simultaneous respiratory tract colonization by more than one pneumococcal serotype. Separate single-tube, nested PCR-based assays have been developed to detect Streptococcus pneumoniae serotypes 3, 14, 19F and 23F by amplifying unique DNA sequences in the capsular polysaccharide gene cluster of each serotype. Pairs of 27–32-base outer primers and 20–21-base inner primers and a 20–22-base probe were designed to amplify and detect a 200–221-base sequence by dot blotting using the labelled probe. Sensitivity of the assays was 0.01–10 f

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El-Yazbi, Amira F., and Glen R. Loppnow. "A selective, inexpensive probe for UV-induced damage in nucleic acids." Canadian Journal of Chemistry 91, no. 5 (2013): 320–25. http://dx.doi.org/10.1139/cjc-2012-0417.

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Absorption of UV light by nucleic acids can result in the formation of molecular lesions in DNA and RNA, leading to mutagenesis, carcinogenesis, and cell death. In this work, hairpin oligonucleotide probes, which have previously been shown to be selective for DNA damage, are used. The hypochromic effect, which arises from the formation of the target–hairpin hybrid when there is no damage, is used to measure the amount of UV damage by measuring the amount of single-stranded DNA oligonucleotides. With accumulated UV exposure, the target–hairpin hybrid concentration decreases and the absorbance i

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Vary, C. P., F. J. McMahon, F. P. Barbone, and S. E. Diamond. "Nonisotopic detection methods for strand displacement assays of nucleic acids." Clinical Chemistry 32, no. 9 (1986): 1696–701. http://dx.doi.org/10.1093/clinchem/32.9.1696.

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Abstract Using the enzymes terminal deoxyribonucleotidyltransferase (EC 2.7.7.31) and polynucleotide phosphorylase (EC 2.7.7.8), we constructed polyriboadenylic acid tracts, approximately 8000 AMP residues long, attached to the 3'-terminus of a synthetic deoxynucleotide. The polyadenylated DNA, termed the "signal strand", was used in a displacement-type nucleic acid probe assay (see pp 1631-6, this issue). A probe-signal strand complex was made by hybridizing the signal strand to a deoxycytidylate-terminal probe DNA. The probe-signal strand complex was immobilized on an oligo (dG)-cellulose su

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Whitcombe, David, Jannine Brownie, Helen L. Gillard, et al. "A homogeneous fluorescence assay for PCR amplicons: its application to real-time, single-tube genotyping." Clinical Chemistry 44, no. 5 (1998): 918–23. http://dx.doi.org/10.1093/clinchem/44.5.918.

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Abstract We have developed a method whereby a single TaqMan™ probe can be used for many PCR reactions. We demonstrate its application as an integrated system for the direct measurement of allele-specific amplicon generation coupled to the suppression of primer-dimer accumulation in PCR. The system uses a 5′-exonuclease assay of amplicon annealed fluorogenic probes that operates in conjunction with the Amplification Refractory Mutation System, whereby relative changes in reporter fluorescent emission are monitored in real-time using an analytical thermal cycler. We have called this system Three

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Faltin, Bernd, Simon Wadle, Günter Roth, Roland Zengerle, and Felix von Stetten. "Mediator Probe PCR: A Novel Approach for Detection of Real-Time PCR Based on Label-Free Primary Probes and Standardized Secondary Universal Fluorogenic Reporters." Clinical Chemistry 58, no. 11 (2012): 1546–56. http://dx.doi.org/10.1373/clinchem.2012.186734.

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BACKGROUND The majority of established techniques for monitoring real-time PCR amplification involve individual target-specific fluorogenic probes. For analysis of numerous different targets the synthesis of these probes contributes to the overall cost during assay development. Sequence-dependent universal detection techniques overcome this drawback but are prone to detection of unspecific amplification products. We developed the mediator probe PCR as a solution to these problems. METHODS A set of label-free sequence-specific primary probes (mediator probes), each comprising a target-specific

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Fong, Whalley K., Zora Modrusan, John P. Mcnevin, Johanna Marostenmaki, Ben Zin, and Faouzi Bekkaoui. "Rapid Solid-Phase Immunoassay for Detection of Methicillin-Resistant Staphylococcus aureus Using Cycling Probe Technology." Journal of Clinical Microbiology 38, no. 7 (2000): 2525–29. http://dx.doi.org/10.1128/jcm.38.7.2525-2529.2000.

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A Cycling Probe Technology (CPT) assay with a lateral-flow device (strip) was developed for the detection of the mecA gene from methicillin-resistant Staphylococcus aureus (MRSA) cultures. The assay uses a mecA probe (DNA-RNA-DNA) labeled with fluorescein at the 5′ terminus and biotin at the 3′ terminus. The CPT reaction occurs at a constant temperature, which allows the probe to anneal to the target DNA. RNase H cuts the RNA portion of the probe, allowing the cleaved fragments to dissociate from the target DNA, making the target available for further cycling. The strip detection step uses a n

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Sjöroos, Minna, Jorma Ilonen, Helena Reijonen, and Timo Lövgren. "Time-Resolved Fluorometry Based Sandwich Hybridisation Assay for HLA-DQA1 Typing." Disease Markers 14, no. 1 (1998): 9–19. http://dx.doi.org/10.1155/1998/350145.

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A microtitration plate based time-resolved fluorescence (TRF) hybridisation assay was developed for HLA typing utilising biotinylated sequence-specific catching probes and europium (Eu) labelled gene locus-specific detection probe to allow time-resolved fluorometer reading of the reaction. In an application for HLA-DQA typing a 228 base pair long region of the polymorphic exon 2 of DQA1 gene was amplified and the denatured PCR product distributed into streptavidin-coated microtitration wells together with the detection probe and one of the catching probes. After incubation and washes, the enha

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Gomes, Tânia A. T., Mônica A. M. Vieira, Cecilia M. Abe, Daleth Rodrigues, Patricia M. Griffin, and Sônia R. T. S. Ramos. "Adherence Patterns and Adherence-Related DNA Sequences in Escherichia coli Isolates from Children with and without Diarrhea in São Paulo City, Brazil." Journal of Clinical Microbiology 36, no. 12 (1998): 3609–13. http://dx.doi.org/10.1128/jcm.36.12.3609-3613.1998.

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The correlation between various adherence patterns and adherence-related DNA sequences in Escherichia coliisolates from 1- to 4-year-old children with and without diarrhea in São Paulo, Brazil, was evaluated. A total of 1,801 isolates obtained from 200 patients and 200 age-matched controls were studied. The adherence patterns found were classified as diffuse, aggregative, aggregative in a 6-h assay, aggregative predominantly in coverslips, localized, localized-like, and noncharacteristic. In general, the DNA sequences used as probes showed excellent specificities (>93%), but their sensitiv

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Wu, Zhan, Zhen-Kun Wu, Hao Tang, Li-Juan Tang, and Jian-Hui Jiang. "Activity-Based DNA-Gold Nanoparticle Probe as Colorimetric Biosensor for DNA Methyltransferase/Glycosylase Assay." Analytical Chemistry 85, no. 9 (2013): 4376–83. http://dx.doi.org/10.1021/ac303575f.

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Fan, Hao, Fu Sheng Liao, Guo Bing Wei, and Nian Hong. "An Electrochemical Mercuric Ion Sensor Based on CdS Nanparticle Label." Advanced Materials Research 945-949 (June 2014): 2009–12. http://dx.doi.org/10.4028/www.scientific.net/amr.945-949.2009.

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In the present study, we describe an electrochemical sensor for Hg2+ detection by using the DNA probe. Two specific sequence for the probes, one has to ensure that the probe A hybridized with probe B modified on CdS nanoparticle to form stable DNA duplexes only in the presence of Hg2+ at a given operating temperature. After dissolving the CdS particles from the electrode, a mercury-film electrode was used for electrochemical detection of these Cd2+ ions which offered sensitive electrochemical signal transduction.The limit of detection of this assay in buffer is 12 nM. The detection was also sp

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Weiss, J. B. "DNA probes and PCR for diagnosis of parasitic infections." Clinical Microbiology Reviews 8, no. 1 (1995): 113–30. http://dx.doi.org/10.1128/cmr.8.1.113.

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DNA probe and PCR-based assays to identify and detect parasites are technically complex; however, they have high sensitivity, directly detect parasites independent of the immunocompetence or previous clinical history of the patient, and can distinguish between organisms that are morphologically similar. Diagnosis of parasites is often based on direct detection by microscopy, which is insensitive and laborious and can lack specificity. Most PCR-based assays were more sensitive than DNA probe assays. The development of PCR-based diagnostic assays requires multiple steps following the initial sel

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Riggin, A., V. T. Luu, J. K. Lobdell, and M. K. Wind. "A non-isotopic probe-hybridization assay for residual DNA in biopharmaceuticals." Journal of Pharmaceutical and Biomedical Analysis 16, no. 4 (1997): 561–72. http://dx.doi.org/10.1016/s0731-7085(97)00152-0.

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Ankireddy, S. R., and Jongsung Kim. "A Microfluidic Microbeads Fluorescence Assay with Quantum Dots-Bead-DNA Probe." Journal of Nanoscience and Nanotechnology 16, no. 3 (2016): 2897–99. http://dx.doi.org/10.1166/jnn.2016.11072.

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Tenover, F. C., L. Carlson, S. Barbagallo, and I. Nachamkin. "DNA probe culture confirmation assay for identification of thermophilic Campylobacter species." Journal of Clinical Microbiology 28, no. 6 (1990): 1284–87. http://dx.doi.org/10.1128/jcm.28.6.1284-1287.1990.

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Wang, Xiaofang, Beelee Chua, and Ahjeong Son. "The Implications of Fragmented Genomic DNA Size Range on the Hybridization Efficiency in NanoGene Assay." Sensors 18, no. 8 (2018): 2646. http://dx.doi.org/10.3390/s18082646.

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DNA hybridization-based assays are well known for their ability to detect and quantify specific bacteria. Assays that employ DNA hybridization include a NanoGene assay, fluorescence in situ hybridization, and microarrays. Involved in DNA hybridization, fragmentation of genomic DNA (gDNA) is necessary to increase the accessibility of the probe DNA to the target gDNA. However, there has been no thorough and systematic characterization of different fragmented gDNA sizes and their effects on hybridization efficiency. An optimum fragmented size range of gDNA for the NanoGene assay is hypothesized i

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Jothikumar, Narayanan, Theresa L. Cromeans, Vincent R. Hill, Xiaoyan Lu, Mark D. Sobsey, and Dean D. Erdman. "Quantitative Real-Time PCR Assays for Detection of Human Adenoviruses and Identification of Serotypes 40 and 41." Applied and Environmental Microbiology 71, no. 6 (2005): 3131–36. http://dx.doi.org/10.1128/aem.71.6.3131-3136.2005.

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ABSTRACT A quantitative real-time TaqMan PCR assay for detection of human adenoviruses (HAdV) was developed using broadly reactive consensus primers and a TaqMan probe targeting a conserved region of the hexon gene. The TaqMan assay correctly identified 56 representative adenovirus prototype strains and field isolates from all six adenovirus species (A to F). Based on infectious units, the TaqMan assay was able to detect as few as 0.4 and 0.004 infectious units of adenovirus serotype 2 (AdV2) and AdV41, respectively, with results obtained in less than 90 min. Using genomic equivalents, the bro

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Ryncarz, Alexander J., James Goddard, Anna Wald, Meei-Li Huang, Bernard Roizman, and Lawrence Corey. "Development of a High-Throughput Quantitative Assay for Detecting Herpes Simplex Virus DNA in Clinical Samples." Journal of Clinical Microbiology 37, no. 6 (1999): 1941–47. http://dx.doi.org/10.1128/jcm.37.6.1941-1947.1999.

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We have developed a high-throughput, semiautomated, quantitative fluorescence-based PCR assay to detect and type herpes simplex virus (HSV) DNA in clinical samples. The detection assay, which uses primers to the type-common region of HSV glycoprotein B (gB), was linear from <10 to 108 copies of HSV DNA/20 μl of sample. Among duplicate samples in reproducibility runs, the assay showed less than 5% variability. We compared the fluorescence-based PCR assay with culture and gel-based liquid hybridization system with 335 genital tract specimens from HSV type 2 (HSV-2)-seropositive persons attend

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ARAKAWA, Hidetoshi, Masako MAEDA, and Akio TSUJI. "Chemiluminescent and Bioluminescent Assays for Polyadenylic Acid and Applications to DNA Probe Assay and Immunoassay." Analytical Sciences 8, no. 4 (1992): 481–85. http://dx.doi.org/10.2116/analsci.8.481.

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