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Zhao D, Kong Y, Zhao S, Xing H. Engineering Functional DNA–Protein Conjugates for Biosensing, Biomedical, and Nanoassembly Applications. Top Curr Chem (Cham) 2020; 378:41. [DOI: 10.1007/s41061-020-00305-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 05/05/2020] [Indexed: 12/31/2022]
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Vecchioni S, Capece MC, Toomey E, Nguyen L, Ray A, Greenberg A, Fujishima K, Urbina J, Paulino-Lima IG, Pinheiro V, Shih J, Wessel G, Wind SJ, Rothschild L. Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology. Sci Rep 2019; 9:6942. [PMID: 31061396 PMCID: PMC6502794 DOI: 10.1038/s41598-019-43316-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/25/2019] [Indexed: 12/28/2022] Open
Abstract
DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag+ in polycytosine-mismatch oligonucleotides, the resulting C-Ag+-C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag+-mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag+-C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11-50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag+-C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.
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Affiliation(s)
- Simon Vecchioni
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA.
| | - Mark C Capece
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Emily Toomey
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Le Nguyen
- School of Engineering, Brown University, Providence, RI, 02912, USA
| | - Austin Ray
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alissa Greenberg
- Department of History, Stanford University, Stanford, CA, 94305, USA
| | - Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo, 152-8550, Japan
| | - Jesica Urbina
- Geology, Minerals, Energy, & Geophysics Science Center, U.S. Geological Survey, Menlo Park, CA, 94025, USA
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA
| | - Ivan G Paulino-Lima
- Blue Marble Space Institute of Science, NASA Ames Research Center, Planetary Systems Branch, Moffett Field, CA, 94035-0001, USA
| | - Vitor Pinheiro
- Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK
| | - Joseph Shih
- Department of Natural Sciences and Mathematics, University of Saint Mary, Leavenworth, KS, 66048, USA
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA
| | - Shalom J Wind
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, 10027, USA
| | - Lynn Rothschild
- Planetary Science Branch, NASA Ames Research Center, Moffett Field, CA, 94035, USA.
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, 02912, USA.
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3
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Characterization of alkaline phosphatase labeled UidA(Gus) probe and its application in testing of transgenic tritordeum. Mol Biol Rep 2010; 38:3629-34. [DOI: 10.1007/s11033-010-0475-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
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Pfleiderer W, Maier T. Nucleotides Part: LXXVII. New Types of Fluorescence Labeling of 2’-Deoxyguanosine. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)54] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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5
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Vos MJD, Cravador A, Lenders JP, Houard S, Bollen A. Solid Phase Non Isotopic Labelling of Oligodeoxynucleotides Using 5′- Protected Aminoalkyl Phosphoramidites: Application to the Specific Detection of Human Papilloma Virus Dna. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319008045137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Sigmund H, Maier T, Pfleiderer W. A New Type of Fluorescence Labeling of Nucleosides, Nucleotides and Oligonucleotides. ACTA ACUST UNITED AC 2006. [DOI: 10.1080/07328319708002935] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Harald Sigmund
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434, Konstanz , Germany
| | - Thomas Maier
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434, Konstanz , Germany
| | - Wolfgang Pfleiderer
- a Fakultät für Chemie, Universität Konstanz , Postfach 5560, D-78434, Konstanz , Germany
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7
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DNA Immobilization: Silanized Nucleic Acids and Nanoprinting. Top Curr Chem (Cham) 2005. [DOI: 10.1007/b136870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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8
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Jahn-Hofmann K, Engels J. Efficient Solid Phase Synthesis of Cleavable Oligodeoxynucleotides Based on a Novel Strategy for the Synthesis of 5?-S-(4,4?-Dimethoxytrityl)-2?-deoxy-5?-thionucleoside Phosphoramidites. Helv Chim Acta 2004. [DOI: 10.1002/hlca.200490252] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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10
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Evaluation of a 23S rRNA Insertion as Target for the Analysis of Uncultured Frankia Populations in Root Nodules of Alders by Whole Cell Hybridization. Syst Appl Microbiol 1997. [DOI: 10.1016/s0723-2020(97)80056-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Buijsman RC, Kuijpers WHA, Basten JEM, Kuyl-Yeheskiely E, van der Marel GA, van Boeckel CAA, van Boom JH. Synthesis of a Pentasaccharide–Oligonucleotide Conjugate: A Novel Antithrombotic Agent. Chemistry 1996. [DOI: 10.1002/chem.19960021216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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12
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Patil SV, Salunkhe MM. Fluorescent-Labeled Oligonucleotide Probes with Non-Nucleotide Linker: Detection of Hybrid Formation by Fluorescence Anisotropy. ACTA ACUST UNITED AC 1996. [DOI: 10.1080/07328319608002460] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Abstract
The simple use of nonisotopic hybridization probes to detect complementary sequences provides valuable information in a large number of research and commercial applications. In hybridization assays, the four "S's (speed, simplicity, sensitivity, and specificity) are important criteria for determining the choice of probe and label. The direct chemical combination of synthetic oligonucleotide probes and enzyme labels offer advantages unmatched by other approaches, with the oligonucleotide providing rapid hybridization and high specificity, and the direct enzyme label providing simple and sensitive detection. Such oligonucleotide-enzyme conjugates ("oligozymes") can be used in a variety of hybridization and detection formats, including dot blots, Southern/northern blots, in situ, and solution hybridization/capture schemes. The practical synthesis and use of such oligozymes are summarized.
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Affiliation(s)
- J L Ruth
- US Fish and Wildlife Forensics Laboratory, Ashland, OR 97520, USA
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Bruick RK, Dawson PE, Kent SB, Usman N, Joyce GF. Template-directed ligation of peptides to oligonucleotides. CHEMISTRY & BIOLOGY 1996; 3:49-56. [PMID: 8807828 DOI: 10.1016/s1074-5521(96)90084-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
BACKGROUND Oligonucleotide-peptide conjugates have several applications, including their potential use as therapeutic agents. We developed a strategy for the chemical ligation of unprotected peptides to oligonucleotides in aqueous solution. The two compounds are joined via a stable amide bond in a template-directed reaction. RESULTS Peptides, ending in a carboxy-terminal thioester, were converted to thioester-linked oligonucleotide-peptide intermediates. The oligonucleotide portion of the intermediate binds to a complementary oligonucleotide template, placing the peptide in close proximity to an adjacent template-bound oligonucleotide that terminates in a 3' amine. The ensuing reaction results in the efficient formation of an amide-linked oligonucleotide-peptide conjugate. CONCLUSIONS An oligonucleotide template can be used to direct the ligation of peptides to oligonucleotides via a highly stable amide linkage. The ligation reaction is sequence-specific, allowing the simultaneous ligation of multiple oligonucleotide-peptide pairs.
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Affiliation(s)
- R K Bruick
- The Scripps Research Institute, 10666 North Torrey Pines Road, La Jolla, CA 92037, USA
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15
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Fischer K, Hahn D, Daniel O, Zeyer J, Amann RI. In situ analysis of the bacterial community in the gut of the earthwormLumbricus terrestrisL. by whole-cell hybridization. Can J Microbiol 1995. [DOI: 10.1139/m95-092] [Citation(s) in RCA: 54] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The bacterial community in the gut of the earthworm Lumbricus terrestris was analyzed by whole-cell hybridization with 16S rRNA targeted oligonucleotide probes. Whole-cell hybridization protocols using fluorescence-, peroxidase-, or digoxigenin-labeled oligonucleotide probes facilitated detection of significant fractions of bacterial cells stained with 4′,6-diamidino-2-phenylindole (DAPI) in the fore-, mid-, and hind-gut and cast of the earthworm. The application of peroxidase- and digoxigenin-labeled probes, however, was hampered by several methodological drawbacks: the requirement of enzymatic permeabilization, the diffuse images of stained cells, and the incompatibility with DAPI staining used as control. Quantitative analysis of the bacterial community was also influenced by its considerable variability in different individual earthworms. Though the number of bacteria detected by DAPI staining as well as by whole-cell hybridization with the fluorescent eubacterial probe Eub338 generally showed a significant increase in the number of bacteria towards the end of the gut, a decrease in bacterial numbers could be found in some earthworms. In situ analysis of the bacterial community in the fore-, mid-, and hind-gut of one individual earthworm by whole-cell hybridization with the fluorescent eubacterial probe Eub338 recorded 15, 30, and 25% of DAPI-stained bacteria, respectively. In the cast 37% of the bacteria were detected. Similar to counts obtained by DAPI and by whole-cell hybridization with probe Eub338, the number of bacteria belonging to the α-, β-, and γ-subgroups of proteobacteria increased significantly towards the end of the gut and remained high in the cast. While the most significant difference in the counts of bacteria belonging to the α-subgroup was obtained between the hind-gut and cast, bacterial populations of the β- and γ- subgroups of proteobacteria increased most prominently between the fore- and hind-gut.Key words: digoxigenin, fluorescent probes, in situ detection, Lumbricus terrestris, rRNA, whole-cell hybridization.
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16
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Srivastava SC, Raza SK, Misra R. 1,N6-etheno deoxy and ribo adenosine and 3,N4-etheno deoxy and ribo cytidine phosphoramidites. Strongly fluorescent structures for selective introduction in defined sequence DNA and RNA molecules. Nucleic Acids Res 1994; 22:1296-304. [PMID: 7513082 PMCID: PMC523656 DOI: 10.1093/nar/22.7.1296] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Synthesis of 1,N6-etheno-2'-deoxyadenosine, 3,N4-etheno-2'-deoxycytidine, and further chemistry on both deoxy and ribo series etheno nucleosides produces the corresponding phosphoramidites. These novel phosphoramidites are introduced selectively, quantitatively, and at specific positions at single or multiple sites into DNA or RNA sequences. The purification and chemistry involved in the synthesis of these products has been optimized to achieve the purity in excess of 99%. The resulting phosphoramidites were tested for their ability to couple and produce poly deoxy and ribonucleotides by solid phase chemistry. The coupling efficiency achieved was greater than 99% per step. Due to the instability of these etheno compounds in acidic and basic medium, various criteria to obtain pure oligomers have been established. The selective introduction of these fluorescent nucleosides into defined sequence DNA and RNA molecule will greatly facilitate the structure-function studies of various RNAs, protein-RNA structures, and DNA-RNA based diagnostics applications. The characteristic and high fluorescent intensity (detection below 1 x 10(-9) M for adenosine sites and below 1 x 10(-7) M for cytidine sites) is particularly suited for the biochemical and biological research and product development applications. The usefulness of these etheno containing modified sequences as sequencing and amplification primers is demonstrated by their full participation in polymerase chain reaction experiments.
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17
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Haralambidis J, Lagniton L, Tregear GW. The preparation of enzyme-labelled oligonucleotides by reductive amination. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80671-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Affiliation(s)
- J L Ruth
- US Fish and Wildlife Forensics Laboratory, Ashland, OR
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19
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Yoh M, Miyagi K, Matsumoto Y, Hayashi K, Takarada Y, Yamamoto K, Honda T. Development of an enzyme-labeled oligonucleotide probe for the cholera toxin gene. J Clin Microbiol 1993; 31:1312-4. [PMID: 8501233 PMCID: PMC262925 DOI: 10.1128/jcm.31.5.1312-1314.1993] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
An alkaline phosphatase-conjugated 30-mer oligonucleotide probe was developed to detect the cholera toxin gene (ctx) in Vibrio cholerae O1. For rapid identification, V. cholerae O1 was grown on selective agar (thiosulfate-citrate-bile salts agar) or in alkaline peptone water and organisms were transferred directly to nylon membranes. Lysis of cells, denaturation of DNA, neutralization, and hybridization were carried out on the membrane. These procedures required only 3 h for completion. The results of the hybridization test with 88 clinical and 20 environmental isolates agreed almost exactly with the results of the immunological tests (anti-cholera toxin antibody-sensitized latex agglutination tests). The specificity of the probe was also tested with strains of enterotoxigenic Escherichia coli, V. cholerae non-O1, and Vibrio mimicus.
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Affiliation(s)
- M Yoh
- Research Institute for Microbial Diseases, Osaka University, Japan
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20
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Gudibande SR, Kenten JH, Link J, Friedman K, Massey RJ. Rapid, non-separation electrochemiluminescent DNA hybridization assays for PCR products, using 3'-labelled oligonucleotide probes. Mol Cell Probes 1992; 6:495-503. [PMID: 1480189 DOI: 10.1016/0890-8508(92)90046-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Described are rapid assays for the analysis of PCR products in a one step, non-separation assay based on the use of electrochemiluminescence generated from a tris-bipyridine ruthenium (II) label. The assay uses PCR incorporation of a biotinylated oligonucleotide as a primer, with the inclusion of a labelled oligonucleotide. Oligonucleotides were labelled with an N-hydroxy succinimide ester of tris-bipyridine ruthenium (II) dihexafluorophosphate (Origen-label) by modifying the 3' and 3' 5' ends of the oligonucleotide probes. The assay makes use of the inherent thermal stability and absence of polymerase activity on such probes to allow the PCR and probe hybridization to be completed automatically on the thermocycler. The assay is concluded by the addition of PCR samples to streptavidin beads on an electrochemiluminescence analyser for binding and analysis. Target genes evaluated were the HIV-1 gag gene, and cystic fibrosis delta F-508 deletion mutation. The results obtained from these assays demonstrated the detection of 10 copies of the HIV-1 gag gene, and cystic fibrosis delta F-508 mutation in 1 ng of human DNA within 15 min. This assay format allows a rapid and simple determination of specific amplified DNA sequences, reducing the contamination risks due to washes and multiple pipetting.
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Affiliation(s)
- S R Gudibande
- Department of Molecular Biology, IGEN Inc., Rockville, MD 20852
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21
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Amann RI, Zarda B, Stahl DA, Schleifer KH. Identification of individual prokaryotic cells by using enzyme-labeled, rRNA-targeted oligonucleotide probes. Appl Environ Microbiol 1992; 58:3007-11. [PMID: 1444414 PMCID: PMC183040 DOI: 10.1128/aem.58.9.3007-3011.1992] [Citation(s) in RCA: 107] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A method to microscopically detect and identify individual cells of members of the domains Bacteria and Archaea is presented. rRNA-targeted oligonucleotides were 5' end labeled with the enzyme horseradish peroxidase and used for whole-cell hybridization. Specifically bound probe was visualized by the enzymatic formation of an intracellular precipitate from the substrate diaminobenzidine. Permeation of the enzyme-labeled probe into whole fixed cells of gram-negative bacteria required their pretreatment with lysozyme-EDTA, whereas permeability of some archaebacterial cells was improved by addition of detergent to the hybridization buffer. Hitherto we had not achieved penetration of enzyme-labeled probe into gram-positive bacteria and yeast cells. This method should be a valuable tool for identification of suitable prokaryotic cells in environments with elevated background fluorescence or in situations in which an epifluorescence microscope is not available.
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Affiliation(s)
- R I Amann
- Lehrstuhl für Mikrobiologie, Technische Universität München, Germany
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22
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Begaud E, Germani Y. Detection of enterotoxigenic Escherichia coli in faecal specimens by acetylaminofluorene-labelled DNA probes. Res Microbiol 1992; 143:315-25. [PMID: 1448616 DOI: 10.1016/0923-2508(92)90023-h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The present study describes acetylaminofluorene(AAF)-modified DNA probes for the identification of heat-labile (LT) and heat-stable (porcine STp and human STh) toxins from enterotoxigenic Escherichia coli (ETEC). AAF probes were compared with established biotinylated probes and bioassays. Ultracentrifugation was not necessary in the preparation of AAF-labelled probes, and the procedures, i.e. chemical modification of probes, hybridization and immunodetection steps, were optimized to detect ETEC by colony hybridization or direct dot blot techniques. The method combines chemical labelling (covalent attachment of AAF group to guanosine is achieved by treatment of DNA with N-acetoxy-2-acetylaminofluorene) and detection of the hybridized target DNA by means of anti-AAF monoclonal antibodies and alkaline phosphatase-labelled second antibodies.
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Affiliation(s)
- E Begaud
- Institut Pasteur de Nouvelle Calédonie, Laboratoire des Bactéries Entéropathogènes, Nouméa
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23
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Tamatsukuri S, Yamamoto K, Shibata S, Leaño F, Honda T, Miwatani T. Detection of a heat-labile enterotoxin gene in enterotoxigenic Escherichia coli by densitometric evaluation using highly specific enzyme-linked oligonucleotide probes. Eur J Clin Microbiol Infect Dis 1991; 10:1048-55. [PMID: 1802695 DOI: 10.1007/bf01984927] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Two alkaline phosphatase-conjugated 24-mer oligonucleotide probes were developed to detect the heat-labile enterotoxin gene in enterotoxigenic Escherichia coli. Probes were antisense codon sequences, which are transcribed into mRNA, of the heat-labile enterotoxin gene of enterotoxigenic Escherichia coli of human origin. Using dot-blot hybridization, probes were tested with 100 clinical isolates and evaluated by a reflectance-type densitometer. Results agreed very well with those of an immunological test, the Biken test, and a 32P-labelled recombinant DNA probe. The oligonucleotide probes did not react with nucleic acids prepared from other diarrhoeagenic bacterial pathogens. Thus, the alkaline phosphatase-conjugated oligonucleotide probes seem to be highly sensitive and specific for detection of heat-labile enterotoxin-producing enterotoxigenic Escherichia coli. Moreover, the results indicate a potential usefulness for densitometric evaluation of DNA hybridization.
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Affiliation(s)
- S Tamatsukuri
- Department of Bacteriology and Serology, Research Institute for Microbial Diseases, Osaka University, Japan
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24
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Lewis TL, Ridpath JF, Bolin SR, Berry ES. Detection of BVD viruses using synthetic oligonucleotides. Arch Virol 1991; 117:269-78. [PMID: 1850232 DOI: 10.1007/bf01310770] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
This study examined synthetic oligonucleotide probes as potential diagnostic tools for bovine viral diarrhea virus (BVDV). Six 20-base sequences from across the genome were selected by homology analysis of the published genomic sequences of the NADL and Osloss isolates of BVDV. RNA was extracted from 22 BVDV isolates propagated in bovine turbinate (BT) cells, blotted, and probed with 32P end-labeled oligonucleotides. The stringency conditions used were such that more than a single base mismatch would result in no hybridization. The probe originating nearest the 5' end of the viral RNA, ND001, detected 86% of the viral isolates while the other probes detected from 19% to 57%. Both cytopathic and noncytopathic isolates were detected by these synthetic probes. A cocktail of these probes were used to specifically detect BVDV RNA extracted directly from tissues of cattle either persistently or acutely infected.
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Affiliation(s)
- T L Lewis
- Department of Veterinary Science, North Dakota State University, Fargo
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25
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Synthesis of oligodeoxyribonucleotides containing 4-N-(ω-aminohexyl)-5-methyldeoxycytidine. Chem Nat Compd 1991. [DOI: 10.1007/bf00630367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Sato M, Kiyama H, Yoshida S, Saika T, Tohyama M. Postnatal ontogeny of cells expressing prepro-neurotensin/neuromedin N mRNA in the rat forebrain and midbrain: a hybridization histochemical study involving isotope-labeled and enzyme-labeled probes. J Comp Neurol 1991; 310:300-15. [PMID: 1787175 DOI: 10.1002/cne.903100303] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The postnatal ontogeny of cells expressing prepro-neurotensin/neuromedin N messenger RNA (prepro-NT/NN mRNA) in the rat forebrain and midbrain was investigated by in situ hybridization histochemistry. According to the pattern of expression during development, the cells which express prepro-NT/NN mRNA can be roughly divided into 2 groups. In type I cells, prepro-NT/NN mRNA expression reaches a maximum in terms of content during the postnatal period. After this early peak, cells of this type express the same or less prepro-NT/NN mRNA, reaching a plateau at an adult level that still contains a high level of expression. In type II cells, prepro-NT/NN mRNA appears during the postnatal period, and the expression decreases dramatically after the first postnatal week, being almost undetectable by a few weeks after birth. Type I cells were observed in the following areas: the piriform cortex, field CA1 of Ammon's horn, subiculum, vertical, and horizontal limbs of the diagonal band of Broca, intermediate part of the lateral septal nucleus, bed nucleus of the stria terminalis, medial preoptic area, lateral hypothalamus, caudal part of the caudate putamen, medial, cortical, and central amygdaloid nuclei, ventral tegmental area, deep mesencephalic nucleus, cuneiform nucleus, dorsal raphe nucleus, laterodorsal tegmental nucleus, parabrachial nucleus, and oral part of the pontine reticular nucleus. Cells of type II were observed in the following areas: the mitral cell layer of the olfactory bulb, rostral part of the caudate putamen, (anterior) cingulate cortex, and retrosplenial cortex (posterior cingulate cortex).
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Affiliation(s)
- M Sato
- Department of Anatomy and Neuroscience, University Medical School, Osaka, Japan
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27
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Murakami A, Nakaura M, Nakatsuji Y, Nagahara S, Tran-Cong Q, Makino K. Fluorescent-labeled oligonucleotide probes: detection of hybrid formation in solution by fluorescence polarization spectroscopy. Nucleic Acids Res 1991; 19:4097-102. [PMID: 1870966 PMCID: PMC328546 DOI: 10.1093/nar/19.15.4097] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Fluorescein-labeled oligonucleotides as DNA-probes were synthesized and used to monitor hybrid formation, namely to detect DNA or oligonucleotide sequence in solution. The introduction of fluorescein to oligonucleotides was carried out by oxidation of a hydrogen phosphonate linkage with ethylenediamine or hexamethylenediamine as a tether and by a subsequent labeling of the primary amine moiety by FITC. Fluorescence anisotropy, r, was adopted as an index to monitor the behavior of F-probe in solution. An increase in the anisotropy was observed upon an increase in the chain-length of F-probe. When F-Probe formed a hybrid with its complementary oligonucleotide in solution, the r value increased compared to that of F-Probe itself. These observations clearly indicate that measurements of r in solution will readily lead to the monitoring of the presence of a hybrid in solution. Consequently, it is promising to detect a certain nucleic acid sequence in solution using fluorescent-labeled oligonucleotides.
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Affiliation(s)
- A Murakami
- Department of Polymer Science and Engineering, Kyoto Institute of Technology, Japan
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28
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Wasteson Y, Olsvik O. Specific DNA fragments coding for ST1 and LT1 toxins, and K88 (F4) adhesin in enterotoxigenic Escherichia coli. ZENTRALBLATT FUR VETERINARMEDIZIN. REIHE B. JOURNAL OF VETERINARY MEDICINE. SERIES B 1991; 38:445-52. [PMID: 1950252 DOI: 10.1111/j.1439-0450.1991.tb00894.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Ten porcine strains of enterotoxigenic Escherichia coli possessing the K88 (F4) adhesion fimbriae, were selected for study of enterotoxin- and fimbriae-encoding plasmids. Plasmid DNA, separated according to size by gel electrophoresis was transferred to nylon membranes by Southern blotting, and hybridized with enzyme-labelled oligonucleotide probes for ST1 and LT1 enterotoxins, and a 32P-labelled probe for the F4 fimbriae. Plasmids possessing the enterotoxin genes ranged from 50 MDa to 78 MDa in size. The ST1 genes were located on a common 8-MDa EcoR1 restriction endonuclease fragment, while the LT1 genes were located on a 4.5-MDa EcoR1 fragment from the different plasmids. Plasmids with the F4 genes ranged from 50 MDa to 118 MDa in size, but the F4 encoding genes were located on a common 3-MDa HindIII restriction endonuclease fragment. ST1 and LT1 genes were found on the same plasmid in only one strain, LT1 and F4 genes on the same plasmids in 5 strains, while no plasmid contained genes for both ST1 and F4.
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Affiliation(s)
- Y Wasteson
- Department of Microbiology and Immunology, Norwegian College of Veterinary Medicine, Oslo
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29
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Englisch U, Gauss DH. Chemisch modifizierte Oligonucleotide als Sonden und Agentien. Angew Chem Int Ed Engl 1991. [DOI: 10.1002/ange.19911030604] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Kessler C. The digoxigenin:anti-digoxigenin (DIG) technology--a survey on the concept and realization of a novel bioanalytical indicator system. Mol Cell Probes 1991; 5:161-205. [PMID: 1870582 DOI: 10.1016/0890-8508(91)90041-h] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A review is given on the novel non-radioactive digoxigenin:anti-digoxigenin (DIG) bioanalytical indicator system. After a general introduction on direct and indirect indicator systems based on previous non-radioactive indicator reactions as well as in vitro and in vivo amplification procedures the principle of the new digoxigenin:anti-digoxigenin technology is demonstrated. The novel system is based on the specific high-affinity interaction between the cardenolide digoxigenin from Digitalis plants and a digoxigenin-specific antibody coupled with a reporter group. A variety of methods for digoxigenin modification of nucleic acids, proteins and glycans are presented. In addition, various applications of the novel non-radioactive indicator system in a variety of direct or indirect detection approaches with either insoluble or soluble substrates are described. It is also shown that with these applications alternative reaction formats are used which are partly characterized by additional amplification steps.
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Affiliation(s)
- C Kessler
- Boehringer Mannheim GmbH, Biochemical Research Center, Department of Genetics, Penzberg, F.R.G
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31
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Nevinny-Stickel C, Bettinotti MD, Andreas A, Hinzpeter M, Mühlegger K, Schmitz G, Albert ED. Nonradioactive HLA class II typing using polymerase chain reaction and digoxigenin-11-2'-3'-dideoxy-uridinetriphosphate-labeled oligonucleotide probes. Hum Immunol 1991; 31:7-13. [PMID: 1679054 DOI: 10.1016/0198-8859(91)90042-8] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We describe a new, simple, rapid, and sensitive nonradioactive technique for the analysis of genetic variations. Genomic DNA was amplified using polymerase chain reaction and amplified DNA was hybridized, with digoxigenin (DIG)-labeled sequence-specific oligonucleotides. High specificity and sensitivity was achieved when labeling the sequence-specific oligonucleotide at the 3' end with only one DIG using digoxigenin-11-2',3'-dideoxy-uridine-5'-triphosphate and DNA deoxynucleotidylexotransferase. The hybridized probes were detected using antidigoxigenin alkaline phosphatase, fab fragments, and X-phosphate/NBT for visualization. This method was applied to the analysis of HLA-DR4-DRB1 alleles in polymerase chain reaction-amplified genomic DNA and resulted in highly specific and sensitive hybridization signals discriminating even in cases of a one-base-pair mismatch. This technique is particularly suited for HLA oligotyping because it allows the use of tetramethylammonium chloride for the simplification of hybridization and washing conditions.
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32
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Abstract
Non-radioactively labelled probes potentially have several advantages over radioactively labelled ones, such as increased stability and reduced hazard. As yet, no non-radioactive methods of labelling are as robust or produce as sensitive a probe as 32P. However, there are many options, some of which use approaches familiar to 32P users (nick translation, random priming, tailing). The majority of methods, whether enzymatic or chemical, direct or indirect, ultimately require the detection of an enzyme by a colourimetric or chemiluminescent substrate. Such detection can be achieved variously by direct visualisation (e.g. of a colourimetrically stained blot), by film, by microtitre plate reader or by CCD camera, depending on the choice of assay format and the degree of quantification required.
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Affiliation(s)
- M R Harris
- Amersham International plc, White Lion Road, Amersham, Buckinghamshire, UK
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33
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Kiyama H, Emson PC, Tohyama M. Recent progress in the use of the technique of non-radioactive in situ hybridization histochemistry: new tools for molecular neurobiology. Neurosci Res 1990; 9:1-21. [PMID: 1702197 DOI: 10.1016/0168-0102(90)90041-c] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent developments in DNA and oligonucleotide chemistry have made it possible to modify nucleotides and link quite complex molecules to the modified nucleotides. These advancements in DNA chemistry provide a number of possibilities for labelling oligonucleotide probes for DNA or RNA detection by non-radioactive methods. Over the years a number of non-radioactive detection systems for mRNA or chromosomal DNA have been developed. As reporter molecules, biotin, acetylaminofluorene, dinitrophenol, digoxigenin, sulfonized nucleotides, and mercury have been used and may be detected with a variety of high-affinity detectors, e.g. avidin (in the case of biotin) or antibodies specific to digoxigenin. These various 'indirect methods' of detection have used a number of chemical amplification procedures in attempts to improve their sensitivity. However, the sensitivity of these methods is often less than that of conventional radioactive methods. A sensitive non-radioactive technique would have a number of advantages over the complex and specialized radioactive in situ hybridization methods. In our laboratory we have recently found that simple enzyme-labelled probes provide excellent sensitivity (equivalent to that found with radioactive methods) and substantially improved cellular resolution. In this article, we describe the principle of the method and illustrate some applications of this novel non-radioactive in situ method.
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Affiliation(s)
- H Kiyama
- MRC Group, Institute of Animal Physiology and Genetics Research, Babraham, Cambridge, U.K
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34
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Day PJ, Bevan IS, Gurney SJ, Young LS, Walker MR. Synthesis in vitro and application of biotinylated DNA probes for human papilloma virus type 16 by utilizing the polymerase chain reaction. Biochem J 1990; 267:119-23. [PMID: 2158305 PMCID: PMC1131253 DOI: 10.1042/bj2670119] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The polymerase chain reaction (PCR) has been used to incorporate biotinylated deoxynucleotide triphosphate analogues into a 120 bp sequence from the E6 region of human papilloma virus type 16 (HPV 16). No loss of amplification efficiency is observed utilizing concentrations of up to 200 microM-biotin-11-dUTP, or 180 microM-biotin-7-dATP and -biotin-16-dUTP (where the numbers refer to the number of carbon atoms in the spacer arms). Internally biotinylated PCR products can be detected following slot-blot or vacuum transfer to mitrocellulose or nylon filters without prior electrophoretic separation of the reactants, since unincorporated biotinylated analogues pass through the filter. Internally biotinylated PCR products can also be applied as hybridization probes in Southern blot analysis or in situ hybridization. This system enables detection of PCR products or target sequences at levels below that for 5'-biotinylated probes and can be applied in an 'open sandwich assay' without the need for a separate labelled probe currently required in conventional sandwich assays. However, as hybridization probes, sensitivity may be limited by the steric hindrance of strand hybridization possibly due to the spacer arms linking the nucleotides to the biotin molecule.
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Affiliation(s)
- P J Day
- Department of Clinical Chemistry, University of Birmingham, Edgbaston, U.K
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35
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Haralambidis J, Duncan L, Angus K, Tregear GW. The synthesis of polyamide-oligonucleotide conjugate molecules. Nucleic Acids Res 1990; 18:493-9. [PMID: 2308843 PMCID: PMC333453 DOI: 10.1093/nar/18.3.493] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have developed methods for the synthesis of peptide-oligodeoxyribonucleotide conjugate molecules in particular, and polyamide-oligonucleotide conjugates in general. Synthesis is carried out by a solid-phase procedure and involves the assembly of a polyamide on the solid support, conversion of the terminal amino group to a protected primary aliphatic hydroxy group by reaction with alpha, omega-hydroxycarboxylic acid derivatives, and finally oligonucleotide synthesis using phosphoramidite chemistry. The conjugate molecules can be used as DNA probes, with the polyamide component carrying one or more non-radioactive markers. These conjugates also have the potential to be used as anti-sense inhibitors of gene expression, with the peptide segment acting as a targeting moiety.
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Affiliation(s)
- J Haralambidis
- Howard Florey Institute of Experimental Physiology and Medicine, University of Melbourne, Parkville, Victoria, Australia
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36
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37
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Chu P, Waterhouse P, Martin R, Gerlach W. New Approaches to the Detection of Microbial Plant Pathogens. Biotechnol Genet Eng Rev 1989. [DOI: 10.1080/02648725.1989.10647856] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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38
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Geiger R, Hauber R, Miska W. New, bioluminescence-enhanced detection systems for use in enzyme activity tests, enzyme immunoassays, protein blotting and nucleic acid hybridization. Mol Cell Probes 1989; 3:309-28. [PMID: 2693952 DOI: 10.1016/0890-8508(89)90012-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- R Geiger
- Abteilung für Klinische Chemie, Universität München, FRG
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39
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Roget A, Bazin H, Teoule R. Synthesis and use of labelled nucleoside phosphoramidite building blocks bearing a reporter group: biotinyl, dinitrophenyl, pyrenyl and dansyl. Nucleic Acids Res 1989; 17:7643-51. [PMID: 2798121 PMCID: PMC334873 DOI: 10.1093/nar/17.19.7643] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The synthesis of protected nucleoside phosphoramidites bearing various markers such as biotinyl, dinitrophenyl, dansyl and pyrenyl groups are reported. These labelled deoxynucleosides phosphoramidites were used for solid phase oligonucleotide synthesis in the same way than the usual protected phosphoramidities without any change in the synthetic cycle and the deprotection step. The new labelled building blocks described herein have been used in conjunction with the labile base protected phosphoramidites ('PAC phosphoramidites') which allowed mild ammonia deprotection, especially recommended for the dinitrophenyl-labelled oligonucleotides. Multiple labelling (i.e. 10 to 20 biotins) can be efficiently and easily performed, on the same oligonucleotide which results in an increase of sensitivity. The polylabelled oligonucleotides are chemically well defined and gave increased signal and low background coloration for in situ hybridisation. The modified oligonucleotides can still be kinased in the normal way as the reporter groups are on the heterocycles.
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Affiliation(s)
- A Roget
- CIS Bioindustries, Gif-sur-Yvette, France
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40
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Nishibuchi M, Murakami A, Arita M, Jikuya H, Takano J, Honda T, Miwatani T. Detection with synthetic oligonucleotide probes of nucleotide sequence variations in the genes encoding enterotoxins of Escherichia coli. J Clin Microbiol 1989; 27:2272-6. [PMID: 2685027 PMCID: PMC267009 DOI: 10.1128/jcm.27.10.2272-2276.1989] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
We examined variations in the genes encoding heat-stable enterotoxin (ST) and heat-labile enterotoxin (LT) in 88 strains of Escherichia coli isolated from individuals with traveler's diarrhea to find suitable sequences for use as oligonucleotide probes. Four oligonucleotide probes of the gene encoding ST of human origin (STIb or STh), one oligonucleotide probe of the gene encoding ST of porcine origin (STIa or STp), and three oligonucleotide probes of the gene encoding LT of human origin (LTIh) were used in DNA colony hybridization tests. In 15 of 22 strains possessing the STh gene and 28 of 42 strains producing LT, the sequences of all regions tested were identical to the published sequences. One region in the STh gene examined with a 18-mer probe was relatively well conserved and was shown to be closely associated with the enterotoxicity of the E. coli strains in suckling mice. This oligonucleotide, however, hybridized with strains of Vibrio cholerae O1, V. parahaemolyticus, and Yersinia enterocolitica that gave negative results in the suckling mouse assay.
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Affiliation(s)
- M Nishibuchi
- Research Institute for Microbial Diseases, Osaka University, Japan
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41
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Nelson PS, Sherman-Gold R, Leon R. A new and versatile reagent for incorporating multiple primary aliphatic amines into synthetic oligonucleotides. Nucleic Acids Res 1989; 17:7179-86. [PMID: 2798089 PMCID: PMC334797 DOI: 10.1093/nar/17.18.7179] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A novel and versatile phosphoramidite, N-Fmoc-O1-DMT-O2-cyanoethoxydiisopropylamino-phosphinyl-3-am ino-1,2-propanediol (1, Fig. 1), has been synthesized and used to incorporate primary aliphatic amines into synthetic oligonucleotides. Its convenient preparation and use in solid phase oligonucleotide synthesis is described. Using phosphoramidite 1, an amino-modified oligonucleotide probe complementary to M13mp18 DNA was constructed with five primary amines attached to the 5'-terminus. The amino-modified oligonucleotide was subsequently labeled with biotin and employed in a dot-blot hybridization assay. As little as 0.5 ng of M13mp18 target DNA was colorimetrically detected.
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Affiliation(s)
- P S Nelson
- Organic Chemistry Division, Clontech Laboratories, Inc., Palo Alto, CA 94303
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42
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Nelson PS, Frye RA, Liu E. Bifunctional oligonucleotide probes synthesized using a novel CPG support are able to detect single base pair mutations. Nucleic Acids Res 1989; 17:7187-94. [PMID: 2677994 PMCID: PMC334798 DOI: 10.1093/nar/17.18.7187] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A novel multifunctional controlled pore glass, MF-CPG (Fig. 1), has been synthesized and used to incorporate 3' terminal primary aliphatic amines into synthetic oligonucleotides. MF-CPG consists of a unique succinic acid linking arm which possesses both a masked primary amine for label attachment and a dimethoxytrityl protected hydroxyl for nucleotide chain elongation. Using MF-CPG, we have devised a simple and convenient technique to attach non-radioactive labels to the 3' terminus of oligonucleotides. Bifunctional probes can then be constructed by 32P labeling the 5' terminus with T4 kinase and gamma 32P-ATP. Using such bifunctional oligonucleotide probes in conjunction with polymerase chain reaction (PCR) amplification, we were able to detect single base substitutions in a target segment of the human H-ras protooncogene employing either functionality. Our technique thus expands the potential applications for oligonucleotides as hybridization probes.
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Affiliation(s)
- P S Nelson
- Diagnostic Chemistry Division, Clontech Laboratories, Inc., Palo Alto, CA 94303
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43
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Walker J, Dougan G. DNA probes: a new role in diagnostic microbiology. THE JOURNAL OF APPLIED BACTERIOLOGY 1989; 67:229-38. [PMID: 2482287 DOI: 10.1111/j.1365-2672.1989.tb02490.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- J Walker
- Department of Molecular Biology, Wellcome Research Laboratories, Beckenham, Kent
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44
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Murakami A, Tada J, Yamagata K, Takano J. Highly sensitive detection of DNA using enzyme-linked DNA-probe. 1. Colorimetric and fluorometric detection. Nucleic Acids Res 1989; 17:5587-95. [PMID: 2762149 PMCID: PMC318181 DOI: 10.1093/nar/17.14.5587] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In order to develop non-radioactive oligonucleotide derivatives and to examine their utility as a diagnostic tool, namely as DNA-probe, an enzyme-linked oligonucleotide was synthesized. Oligonucleotide complementary to M13mp8 phage DNA was linked to alkaline phosphatase via a crosslinker and a spacer. M13mp8 phage DNA (single strand) immobilized on the nitrocellulose membrane was hybridized with the enzyme-linked oligonucleotide. The hybrid was detected with three detection methods; (1)colorimetric detection in solution, (2)colorimetric one on membranes, and (3)fluorometric one in solution. Methods(2) and (3) gave high sensitivities to detect as low as several to several tens attomoles of DNA and it was found that those methods with enzyme-linked oligonucleotides are potent for DNA-probe methodology from the viewpoint of automation.
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Affiliation(s)
- A Murakami
- Central Research Laboratory, Shimadzu Corporation, Nakagyoku, Japan
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45
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Sáez-Llorens X, Guzman-Verduzco LM, Shelton S, Nelson JD, Kupersztoch YM. Simultaneous detection of Escherichia coli heat-stable and heat-labile enterotoxin genes with a single RNA probe. J Clin Microbiol 1989; 27:1684-8. [PMID: 2671025 PMCID: PMC267644 DOI: 10.1128/jcm.27.7.1684-1688.1989] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A single RNA probe was synthesized and used to detect simultaneously the methanol-soluble heat-stable enterotoxin and heat-labile enterotoxin genes in Escherichia coli strains. The results with the biotinylated or radioactive probe correlated 100% with the biological assay results for both toxins. The RNA probe detected the three known heat-stable enterotoxin A alleles.
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Affiliation(s)
- X Sáez-Llorens
- Department of Microbiology, University of Texas Southwestern Medical Center, Dallas 75235
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46
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Hauber R, Miska W, Schleinkofer L, Geiger R. New, sensitive, radioactive-free bioluminescence-enhanced detection system in protein blotting and nucleic acid hybridization. JOURNAL OF BIOLUMINESCENCE AND CHEMILUMINESCENCE 1989; 4:367-72. [PMID: 2801223 DOI: 10.1002/bio.1170040150] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A relatively simple, very sensitive bioluminescence-enhanced detection system for protein blotting and nucleic acid hybridization is described. The method utilizes antibodies conjugated with alkaline phosphatase or nucleotide probes complexed with alkaline phosphatase. Then the alkaline phosphatase takes part in a reaction by releasing D-luciferin (Photinus pyralis) from D-luciferin-O-phosphate. Liberated D-luciferin reacts with luciferase, ATP and oxygen under light emission. Light is measured using the Argus-100 a photon counting camera system or photographic films. Bound alkaline phosphatase conjugated antibodies or hybridized nucleotide probes can be visualized. The limit of detection is at present 5 to 50 fg of protein (IgG), corresponding, for example to 30 to 300 x 10(-21) mol. This means a much higher sensitivity of the detection system in comparison to systems used at present. Experiments concerning nucleic acid hybridization and visualization of the emitted light by a photon counting camera (Argus-100) are under investigation.
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Affiliation(s)
- R Hauber
- Abteilung für Klinische Chemie, Universität München, FRG
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47
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Balaguer P, Térouanne B, Eliaou JF, Humbert M, Boussioux AM, Nicolas JC. Use of glucose-6-phosphate dehydrogenase as a new label for nucleic acid hybridization reactions. Anal Biochem 1989; 180:50-4. [PMID: 2530915 DOI: 10.1016/0003-2697(89)90085-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe here a sensitive new procedure for detecting DNA hybridization by dot blots. The method utilizes DNA or oligonucleotide probes labeled with biotin, sulfone, or haptens that can be detected by glucose-6-phosphate dehydrogenase (G6PDH) conjugates. Biotin labeling of DNA gave the best sensitivity. G6PDH activity was revealed by staining or by bioluminescence using an FMN oxidoreductase and a luciferase from Beneckea harveyi. Bioluminescent detection offered better sensitivity and faster revelation than the colorimetric assay and was found to be very useful in visualizing single mutations in human DNA after hybridization with an allele-specific biotinylated oligonucleotide probe. Revelation can be performed using a luminometer, photographic films, or a very sensitive video camera. The detection is limited by the nonspecific binding of the labeled reagent (streptavidin or antibodies). This limit is similar to that obtained with other nonisotopic labeling procedures, but our method is faster and several hybridization reactions can be performed on the same support.
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48
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Ghosh SS, Kao PM, Kwoh DY. Synthesis of 5'-oligonucleotide hydrazide derivatives and their use in preparation of enzyme-nucleic acid hybridization probes. Anal Biochem 1989; 178:43-51. [PMID: 2729579 DOI: 10.1016/0003-2697(89)90354-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A hydrazone-based method for conjugating synthetic nucleic acids and reporter molecules for use as nonradioactive hybridization probes is presented. Oligonucleotides complementary to the hepatitis B virus were derivatized at their 5' ends with hydrazine or homobifunctional acyl hydrazides. These derivatives reacted facilely with aldehydes to give hydrazones, which were characterized by uv spectroscopy and HPLC. Coupling of aldehyde-modified alkaline phosphatase with carbohydrazide-oligonucleotide derivatives provided a mixture of two enzyme-nucleic acid conjugates in 80-85% yield. The conjugates had a 1:1 and a 2:1 oligonucleotide/enzyme ratio, respectively, and were separated by ion-exchange chromatography. Both conjugates were able to detect 7 amol of target DNA in 1 h, using a colorimetric assay. In contrast, oligonucleotide-horseradish peroxidase conjugates were 40-fold lower in sensitivity of detection.
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Affiliation(s)
- S S Ghosh
- SISKA Diagnostics, Inc., La Jolla, California
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49
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Le Brun S, Duchange N, Namane A, Zakin MM, Huynh-Dinh T, Igolen J. Simple chemical synthesis and hybridization properties of non-radioactive DNA probes. Biochimie 1989; 71:319-24. [PMID: 2500982 DOI: 10.1016/0300-9084(89)90003-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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.
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Affiliation(s)
- S Le Brun
- Unité de Chimie Organique, CNRS UA487, Paris, France
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50
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Sommerfelt H, Kalland KH, Raj P, Moseley SL, Bhan MK, Bjorvatn B. Cloned polynucleotide and synthetic oligonucleotide probes used in colony hybridization are equally efficient in the identification of enterotoxigenic Escherichia coli. J Clin Microbiol 1988; 26:2275-8. [PMID: 3069860 PMCID: PMC266875 DOI: 10.1128/jcm.26.11.2275-2278.1988] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Restriction endonuclease-generated polynucleotide and synthetically produced oligonucleotide gene probes used in colony hybridization assays proved to be efficient for the detection and differentiation of enterotoxigenic Escherichia coli. To compare their relative efficiencies, these two sets of probes were radiolabeled with 32P and were applied to 74 strains of E. coli with known enterotoxin profiles and to 156 previously unexamined E. coli isolates. The enterotoxigenic bacteria Vibrio cholerae O1, Vibrio cholerae non-O1 (NAG), Yersinia enterocolitica, and E. coli harboring the plasmid vectors of the polynucleotide gene probes were examined for further evaluation of probe specificity. The two classes of probes showed a perfect concordance in their specific detection and differentiation of enterotoxigenic E. coli. In the analysis of six strains, the signal strength on autoradiography after hybridization with oligonucleotides was weaker than that obtained after hybridization with polynucleotide probes. The probes did not hybridize with DNA from V. cholerae O1, V. cholerae non-O1 (NAG), or Y. enterocolitica. The strains of E. coli harboring the plasmid vectors of the polynucleotide gene probes were, likewise, negative in the hybridization assays.
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Affiliation(s)
- H Sommerfelt
- Institute of International Health, University of Bergen, Norway
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