oligonucleotide probes

Summary

Summary: Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.

Top Publications

  1. pmc Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Manhong Dai
    Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 33:e175. 2005
  2. ncbi MicroRNA expression in zebrafish embryonic development
    Erno Wienholds
    Hubrecht Laboratory, Centre for Biomedical Genetics, 3584 CT Utrecht, The Netherlands
    Science 309:310-1. 2005
  3. pmc Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification
    Jan P Schouten
    MRC Holland, Hudsonstraat 68, 1057SN Amsterdam, The Netherlands
    Nucleic Acids Res 30:e57. 2002
  4. pmc Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells
    Antony K Chen
    Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:e148. 2010
  5. ncbi Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment
    W Manz
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Germany
    Microbiology 142:1097-106. 1996
  6. ncbi GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
    Zhili He
    Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    ISME J 1:67-77. 2007
  7. ncbi Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples
    Sonia M Tiquia
    Oak Ridge National Laboratory, Oak Ridge, TN, USA
    Biotechniques 36:664-70, 672, 674-5. 2004
  8. pmc Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation
    Jesse Salisbury
    Functional Genomics PhD Program, University of Maine, Orono, Maine, United States of America
    PLoS ONE 4:e7479. 2009
  9. ncbi Nanostructured probes for RNA detection in living cells
    Philip Santangelo
    Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
    Ann Biomed Eng 34:39-50. 2006
  10. ncbi DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles
    Huixiang Li
    Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
    Anal Chem 76:5414-7. 2004

Detail Information

Publications313 found, 100 shown here

  1. pmc Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data
    Manhong Dai
    Molecular and Behavioural Neuroscience Institute and Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 33:e175. 2005
    ..It will be beneficial to re-analyze existing GeneChip data with updated probe set definitions...
  2. ncbi MicroRNA expression in zebrafish embryonic development
    Erno Wienholds
    Hubrecht Laboratory, Centre for Biomedical Genetics, 3584 CT Utrecht, The Netherlands
    Science 309:310-1. 2005
    ..in zebrafish embryos by microarrays and by in situ hybridizations, using locked-nucleic acid-modified oligonucleotide probes. Most miRNAs were expressed in a highly tissue-specific manner during segmentation and later stages, but ..
  3. pmc Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification
    Jan P Schouten
    MRC Holland, Hudsonstraat 68, 1057SN Amsterdam, The Netherlands
    Nucleic Acids Res 30:e57. 2002
    ..Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences...
  4. pmc Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells
    Antony K Chen
    Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
    Nucleic Acids Res 38:e148. 2010
    ..Combined, these attributes enabled RBMBs to exhibit an improved sensitivity for RNA detection in living cells...
  5. ncbi Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment
    W Manz
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, Germany
    Microbiology 142:1097-106. 1996
    We designed a panel of four 16S rRNA-targeted oligonucleotide probes specific for bacteria of the phylum cytophaga-flavobacter-bacteroides (CFB)...
  6. ncbi GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes
    Zhili He
    Department of Botany and Microbiology, Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019, USA
    ISME J 1:67-77. 2007
    ..It is particularly useful for providing direct linkages of microbial genes/populations to ecosystem processes and functions...
  7. ncbi Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples
    Sonia M Tiquia
    Oak Ridge National Laboratory, Oak Ridge, TN, USA
    Biotechniques 36:664-70, 672, 674-5. 2004
    ..These results suggest that the 50-mer oligonucleotide array can be used as a specific and quantitative parallel tool for the detection of microbial populations in environmental samples...
  8. pmc Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation
    Jesse Salisbury
    Functional Genomics PhD Program, University of Maine, Orono, Maine, United States of America
    PLoS ONE 4:e7479. 2009
    ..Novel analyses on existing microarray data provide fresh insights and new interpretations into transcriptome-wide changes in expression...
  9. ncbi Nanostructured probes for RNA detection in living cells
    Philip Santangelo
    Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
    Ann Biomed Eng 34:39-50. 2006
    ..Here we review the recent development of nanostructured oligonucleotide probes for living cell RNA detection, and discuss the biological and engineering issues and challenges of ..
  10. ncbi DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles
    Huixiang Li
    Department of Chemistry, University of Rochester, Rochester, New York 14627, USA
    Anal Chem 76:5414-7. 2004
    ..Subfemtomole amounts of untagged target are detected in minutes using commercially available materials. Target sequences in complex mixtures of DNA and single-base mismatches in DNA sequences are easily detected...
  11. pmc Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment
    Alexander Loy
    Lehrstuhl fur Mikrobiologie, Technische Universitat Munchen, D 85350 Freising, Germany
    Appl Environ Microbiol 68:5064-81. 2002
    ..sulfate-reducing prokaryotes (SRPs) an oligonucleotide microarray consisting of 132 16S rRNA gene-targeted oligonucleotide probes (18-mers) having hierarchical and parallel (identical) specificity for the detection of all known lineages ..
  12. pmc probeBase--an online resource for rRNA-targeted oligonucleotide probes: new features 2007
    Alexander Loy
    Department für Mikrobielle Okologie, Universitat Wien, Althanstrasse 14, A 1090 Wien, Austria
    Nucleic Acids Res 35:D800-4. 2007
    probeBase is a curated database of annotated rRNA-targeted oligonucleotide probes and supporting information...
  13. pmc Detection and enumeration of methanotrophs in acidic Sphagnum peat by 16S rRNA fluorescence in situ hybridization, including the use of newly developed oligonucleotide probes for Methylocella palustris
    S N Dedysh
    Institute of Microbiology, Russian Academy of Sciences, Moscow 117811, Russia
    Appl Environ Microbiol 67:4850-7. 2001
    Two 16S rRNA-targeted oligonucleotide probes, Mcell-1026 and Mcell-181, were developed for specific detection of the acidophilic methanotroph Methylocella palustris using fluorescence in situ hybridization (FISH)...
  14. pmc Real-time PCR in virology
    Ian M Mackay
    Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre, Royal Children s Hospital, Brisbane, Australia
    Nucleic Acids Res 30:1292-305. 2002
    ..However, the technology discussed has been applied to other areas of microbiology as well as studies of gene expression and genetic disease...
  15. ncbi The 18S rDNA sequence of Synchytrium endobioticum and its utility in microarrays for the simultaneous detection of fungal and viral pathogens of potato
    Ismail Abdullahi
    Deutsche Sammlung von Mikroorganismen und Zellkulturen, Plant Virus Division, Biologische Bundesanstalt für Land und Forstwirtschaft, Braunschweig, Germany
    Appl Microbiol Biotechnol 68:368-75. 2005
    ..Using this information, specific oligonucleotide probes were designed and arrayed onto glass slides for detection of the pathogen...
  16. pmc Method for multiplex cellular detection of mRNAs using quantum dot fluorescent in situ hybridization
    Pokman Chan
    Department of Neurology, Mount Sinai School of Medicine, One Gustave L Levy Place, NY 10029, USA
    Nucleic Acids Res 33:e161. 2005
    ..We developed a novel method for direct QD labeling of modified oligonucleotide probes through streptavidin and biotin interactions, as well as protocols for their use in multiple-label FISH...
  17. pmc Simultaneous analysis of microbial identity and function using NanoSIMS
    Tianlun Li
    Cemagref, Unité de Recherche Hydrosystèmes et Bioprocédés, Parc de Tourvoie, BP 44, 92163 Antony cedex, France
    Environ Microbiol 10:580-8. 2008
    ..The applicability of this new technique to the study of in situ ecophysiology of uncultured microorganisms within complex microbial communities is illustrated...
  18. doi Investigation of chicken intestinal bacterial communities by 16S rRNA targeted fluorescence in situ hybridization
    K N Olsen
    Department of Veterinary Pathobiology, Faculty of Life Sciences, University of Copenhagen, Stigbøjlen 4, Frederiksberg C, Denmark
    Antonie Van Leeuwenhoek 94:423-37. 2008
    ....
  19. pmc Multiplex fluorescence melting curve analysis for mutation detection with dual-labeled, self-quenched probes
    Qiuying Huang
    Engineering Research Center of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences, School of Life Sciences, and Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen, Fujian, China
    PLoS ONE 6:e19206. 2011
    ....
  20. ncbi Delineating genetic pathways of disease progression in head and neck squamous cell carcinoma
    Maria J Worsham
    Department of Otolaryngology Head and Neck Surgery, Research Division, Henry Ford Health System, Detroit, MI 48202, USA
    Arch Otolaryngol Head Neck Surg 129:702-8. 2003
    ..Identification of key molecular events may be useful for more accurate distinction of prognostic groups for selection and targeting of therapy...
  21. pmc Gold nanoparticle probe-based gene expression analysis with unamplified total human RNA
    Martin Huber
    Nanosphere Inc, 4088 Commercial Ave, Northbrook, IL 60062, USA
    Nucleic Acids Res 32:e137. 2004
    ..The high sensitivity afforded by the nanoparticle probes allows differential gene expression from as little as 0.5 microg unamplified total human RNA in a 2 h hybridization without the need for elaborate sample labeling steps...
  22. pmc Real-time PCR in clinical microbiology: applications for routine laboratory testing
    M J Espy
    Mayo Clinic, 200 First St SW, Hilton 470, Rochester, MN 55905, USA
    Clin Microbiol Rev 19:165-256. 2006
    ..This review focuses on the application of real-time PCR in the clinical microbiology laboratory...
  23. pmc Rapid universal identification of bacterial pathogens from clinical cultures by using a novel sloppy molecular beacon melting temperature signature technique
    Soumitesh Chakravorty
    Division of Infectious Disease, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, 185 South Orange Avenue, Newark, NJ 07103, USA
    J Clin Microbiol 48:258-67. 2010
    ..This approach enables highly multiplexed target detection using a simple PCR format that can transform infectious disease diagnostics and improve patient outcomes...
  24. doi Carbon nanotube-quenched fluorescent oligonucleotides: probes that fluoresce upon hybridization
    Ronghua Yang
    Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
    J Am Chem Soc 130:8351-8. 2008
    ..Our results show that MB/SWNT probes can be an excellent platform for nucleic acid studies and molecular sensing...
  25. pmc An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues
    Chang Gong Liu
    Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Proc Natl Acad Sci U S A 101:9740-4. 2004
    ..The microchip oligolibrary can be expanded to include an increasing number of miRNAs discovered in various species and is useful for the analysis of normal and disease states...
  26. ncbi What controls the melting properties of DNA-linked gold nanoparticle assemblies?
    Rongchao Jin
    Department of Chemistry and Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
    J Am Chem Soc 125:1643-54. 2003
    ....
  27. doi MicroRNA detection by microarray
    Wei Li
    State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China
    Anal Bioanal Chem 394:1117-24. 2009
    ..This review discusses the main existing microRNA detection technologies, while emphasizing microRNA arrays...
  28. ncbi Fluorescence in situ hybridization of 16S rRNA gene clones (Clone-FISH) for probe validation and screening of clone libraries
    Andreas Schramm
    Department of Civil and Environmental Engineering, University of Washington, Seattle, WA 98195 2700, USA
    Environ Microbiol 4:713-20. 2002
    ..Probe dissociation curves for three oligonucleotide probes were compared for reference cells containing native (FISH) or cloned (Clone-FISH) target sequences...
  29. pmc Diversity of bacteria growing in natural mineral water after bottling
    Alexander Loy
    Abteilung für Mikrobielle Okologie, Institut für Okologie und Naturschutz, Universitat Wien, Althanstr 14, A 1090 Vienna, Austria
    Appl Environ Microbiol 71:3624-32. 2005
    ..For the first time, key genera responsible for bacterial growth in a natural mineral water were identified by applying molecular cultivation-independent techniques...
  30. doi Recent trends in molecular beacon design and applications
    Kewei Huang
    Department of Chemistry, Rice University, 6100 South Main Street, Houston, TX 77005, USA
    Anal Bioanal Chem 402:3091-102. 2012
    ..On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides...
  31. pmc Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification
    X B Zhong
    Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06510, USA
    Proc Natl Acad Sci U S A 98:3940-5. 2001
    ..Allele-discriminating oligonucleotide probes in conjunction with RCA also were used to discriminate wild-type and mutant alleles in the cystic fibrosis ..
  32. doi Detection of single-copy functional genes in prokaryotic cells by two-pass TSA-FISH with polynucleotide probes
    Shuji Kawakami
    Department of Civil and Environmental Engineering, Tohoku University, 6 6 06 Aoba, Aramaki, Aoba ku, Sendai, Miyagi 980 8579, Japan
    J Microbiol Methods 88:218-23. 2012
    ..The developed protocol is useful for identifying single microbial cells based on functional gene sequences...
  33. ncbi Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21
    M Nilsson
    Beijer Laboratory, Department of Medical Genetics, Uppsala, Sweden
    Nat Genet 16:252-5. 1997
    ....
  34. ncbi Microbial community and physicochemical analysis of an industrial waste gas biofilter and design of 16S rRNA-targeting oligonucleotide probes
    Udo Friedrich
    Abteilung Mikrobiologie, Fachbereich Biologie chemie, Universitat Osnabruck, 49069 Osnabruck, Germany
    Environ Microbiol 5:183-201. 2003
    ..Statistical analysis of microbial versus waste gas parameters generally revealed only weak or non-significant correlations between the two. Possible explanations for this finding are discussed...
  35. doi Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridization
    L Safak Yilmaz
    Department of Civil and Environmental Engineering, University of Wisconsin Madison, 1415 Engineering Drive, Madison, WI 53706 1691, USA
    Environ Microbiol 10:2872-85. 2008
    ..The use of DeltaDeltaG degrees (1) and WM in probe design was illustrated as a tool that complements experimental design approaches...
  36. pmc Detection and differentiation of chlamydiae by fluorescence in situ hybridization
    Sven Poppert
    Abteilung für Medizinische Mikrobiologie und Hygiene, Universitat Ulm, Ulm, Germany
    Appl Environ Microbiol 68:4081-9. 2002
    ..Fluorescence in situ hybridization (FISH) using rRNA-targeted oligonucleotide probes is widely used for the investigation of uncultured bacteria in complex microbial communities and has ..
  37. pmc An aminoacylation-dependent nuclear tRNA export pathway in yeast
    H Grosshans
    Biochemie Zentrum Heidelberg BZH, University of Heidelberg, D 69120 Heidelberg, Germany
    Genes Dev 14:830-40. 2000
    ..Our data show that tRNA aminoacylation and eEF-1A are required for efficient nuclear tRNA export in yeast and suggest coordination between the protein translation and the nuclear tRNA processing and transport machineries...
  38. pmc Oligonucleotide probes that detect quantitatively significant groups of butyrate-producing bacteria in human feces
    Georgina L Hold
    Rowett Research Institute, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
    Appl Environ Microbiol 69:4320-4. 2003
    16S rRNA-targeted oligonucleotide probes were designed for butyrate-producing bacteria from human feces...
  39. doi Rapid authentication of Bupleurum species using an array of immobilized sequence-specific oligonucleotide probes
    Wen Yu Lin
    Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan, Republic of China
    Planta Med 74:464-9. 2008
    ..The short duration of the procedure (within 30 h) makes it an especially useful tool in verifying processed plant material...
  40. ncbi Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons
    Kazuhisa Fujimoto
    Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Toyama 930 0194, Japan
    J Org Chem 69:3271-5. 2004
    ..Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones...
  41. ncbi Optical detection of DNA hybridization based on fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles
    Zai Sheng Wu
    State Key Laboratory for Chemo Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, People s Republic of China
    Anal Biochem 353:22-9. 2006
    ..In addition, this is a homogeneous assay that can offer the potential to be monitored in real time, be amenable to automation, eliminate washing steps, and reduce the risk of contamination...
  42. pmc A real-time RT-PCR for detection of clade 1 and 2 H5N1 influenza A virus using locked nucleic acid (LNA) TaqMan probes
    Tran Tan Thanh
    Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, Dist 05, Ho Chi Minh City, Viet Nam
    Virol J 7:46. 2010
    ..The emergence and co-circulation of two different clades (clade 1 and 2) of H5N1 influenza viruses in Vietnam necessitates the availability of a diagnostic assay that can detect both variants...
  43. pmc Design, validation and annotation of transcriptome-wide oligonucleotide probes for the oligochaete annelid Eisenia fetida
    Ping Gong
    Environmental Services, SpecPro Inc, Vicksburg, Mississippi, United States of America
    PLoS ONE 5:e14266. 2010
    ..This approach is particularly applicable to organisms with a wealth of EST sequences but unfinished genome...
  44. pmc High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes
    Yan Fu
    Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
    PLoS ONE 5:e14178. 2010
    ..Approximately 200,000 long oligonucleotide probes were identified as being polymorphic between the inbred parents of a mapping population and used to ..
  45. pmc Molecular beacons with intrinsically fluorescent nucleotides
    Angel A Marti
    Department of Chemistry, Columbia University, New York, NY 10027, USA
    Nucleic Acids Res 34:e50. 2006
    ..The thermal denaturation profile of MB-FB hybridized with its target shows a marked fluorescence reduction at 53 degrees C, consistent with a transition from double stranded helix to random coil DNA...
  46. pmc Phylogenetic group- and species-specific oligonucleotide probes for single-cell detection of lactic acid bacteria in oral biofilms
    Beatrice Quevedo
    Institute of Oral Biology, University of Zurich, Zurich, Switzerland
    BMC Microbiol 11:14. 2011
    ....
  47. pmc Direct profiling of environmental microbial populations by thermal dissociation analysis of native rRNAs hybridized to oligonucleotide microarrays
    Said El Fantroussi
    Department of Civil and Environmental Engineering, University of Washington, Seattle 98195, USA
    Appl Environ Microbiol 69:2377-82. 2003
    ..e., melting profile) for each probe-target duplex provided information on hybridization specificity, which is essential for confirming adequate discrimination between target and nontarget sequences...
  48. pmc Design and validation of an oligonucleotide probe for the detection of protozoa from the order Trichomonadida using chromogenic in situ hybridization
    Meike Marissa Mostegl
    Institute of Pathology and Forensic Veterinary Medicine, Department of Pathobiology, University of Veterinary Medicine, Veterinarplatz 1, 1210 Vienna, Austria
    Vet Parasitol 171:1-6. 2010
    ..The probe presented here can be considered an important tool for diagnosis of all to date described relevant protozoal parasites of the order Trichomonadida in tissue samples...
  49. pmc Unlabeled helper oligonucleotides increase the in situ accessibility to 16S rRNA of fluorescently labeled oligonucleotide probes
    B M Fuchs
    Max Planck Institut für Marine Mikrobiologie, D 28359 Bremen, Germany
    Appl Environ Microbiol 66:3603-7. 2000
    ..represents a significant problem for fluorescence in situ hybridization (FISH) of 16S rRNA with oligonucleotide probes. Here, unlabeled oligonucleotides (helpers) that bind adjacent to the probe target site were evaluated for ..
  50. ncbi Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization
    P Hugenholtz
    Advanced Computational Modeling Centre, Department of Mathematics, University of Queensland, Queensland, Australia
    Methods Mol Biol 179:29-42. 2002
  51. ncbi Microarray assay for detection and discrimination of Orthopoxvirus species
    Vladimir A Ryabinin
    State Research Center of Virology and Biotechnology Vector, Novosibirsk Region, Kol tsovo, Russia
    J Med Virol 78:1325-40. 2006
    ..for 86 and 72 different OPV strains, respectively, were used to design species-specific microarray oligonucleotide probes (oligoprobes)...
  52. pmc Development and application of a novel peptide nucleic acid probe for the specific detection of Cronobacter genomospecies (Enterobacter sakazakii) in powdered infant formula
    C Almeida
    Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, Universidade do Minho, 4710 057 Braga, Portugal
    Appl Environ Microbiol 75:2925-30. 2009
    ..FISH using PNA could detect as few as 1 CFU per 10 g of Cronobacter in PIF after an 8-h enrichment step, even in a mixed population containing bacterial contaminants...
  53. pmc RTPrimerDB: the real-time PCR primer and probe database, major update 2006
    Filip Pattyn
    Center for Medical Genetics Ghent CMGG, Ghent University Hospital, De Pintelaan 185, 9000 Ghent, Belgium
    Nucleic Acids Res 34:D684-8. 2006
    ....
  54. doi MicroRNA detection by northern blotting using locked nucleic acid probes
    Eva Várallyay
    Agricultural Biotechnology Center, Plant Virology Group, Szent Gyorgyi Albert ut 4, Gödöllõ H 2100, Hungary
    Nat Protoc 3:190-6. 2008
    ..The major disadvantages of the northern blot technology using the traditional DNA oligonucleotide probes are its poor sensitivity and the high time consumption...
  55. ncbi Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes
    Mary Katherine Johansson
    Biosearch Technologies, 81 Digital Drive, Novato, California 94949, USA
    J Am Chem Soc 124:6950-6. 2002
    Many genomics assays use profluorescent oligonucleotide probes that are covalently labeled at the 5' end with a fluorophore and at the 3' end with a quencher...
  56. doi GeneFISH--an in situ technique for linking gene presence and cell identity in environmental microorganisms
    Cristina Moraru
    Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, D 28359 Bremen, Germany
    Environ Microbiol 12:3057-73. 2010
    ..It was shown that at least 30%, but potentially the majority of the Crenarchaeota present in these samples harboured the amoA gene and were therefore likely to be catalysing the oxidation of ammonia...
  57. pmc Comparison of vertical distributions of prokaryotic assemblages in the anoxic Cariaco Basin and Black Sea by use of fluorescence in situ hybridization
    Xueju Lin
    Marine Sciences Research Center, Stony Brook University, Stony Brook, NY 11794 5000, USA
    Appl Environ Microbiol 72:2679-90. 2006
    ..fluorescence in situ hybridization (FISH) with the fluorochrome Cy3 or horseradish peroxidase-modified oligonucleotide probes. For both basins, significant differences in total prokaryotic abundance and phylogenetic composition were ..
  58. ncbi Closely related Prochlorococcus genotypes show remarkably different depth distributions in two oceanic regions as revealed by in situ hybridization using 16S rRNA-targeted oligonucleotides
    N J West
    Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, , Bremen, Germany
    Microbiology 147:1731-44. 2001
    ..assignable to the genus Prochlorococcus using horseradish-peroxidase-labelled 16S rRNA-targeted oligonucleotide probes in combination with tyramide signal amplification (TSA)...
  59. pmc The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters
    J Hooyberghs
    Institute for Theoretical Physics, Katholieke Universiteit Leuven, Leuven, Belgium
    Nucleic Acids Res 37:e53. 2009
    ..These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays...
  60. ncbi Real-time genotyping with oligonucleotide probes containing locked nucleic acids
    Luis A Ugozzoli
    Bio Rad Laboratories, 2000 A Nobel Drive, Hercules, CA 94547, USA
    Anal Biochem 324:143-52. 2004
    b>Oligonucleotide probes containing locked nucleic acid (LNA) hybridize to complementary single-stranded target DNA sequences with an increased affinity compared to oligonucleotide DNA probes...
  61. pmc 18S rRNA gene variation among common airborne fungi, and development of specific oligonucleotide probes for the detection of fungal isolates
    Zhihong Wu
    National Institute for Working Life, SE 907 13 Umeå, Sweden
    Appl Environ Microbiol 69:5389-97. 2003
    ..Based on the 18S rDNA sequence variation, 108 oligonucleotide probes were designed for each genus and species included in this study...
  62. pmc Rapid high resolution single nucleotide polymorphism-comparative genome hybridization mapping in Caenorhabditis elegans
    Stephane Flibotte
    Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
    Genetics 181:33-7. 2009
    ..This method will be particularly powerful when applied to difficult or hard-to-map low-penetrance phenotypes. It should also be possible to map polygenic traits using this method...
  63. ncbi In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes
    Wigard P Kloosterman
    Hubrecht Laboratory, Center for Biomedical Genetics, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
    Nat Methods 3:27-9. 2006
    ..Here we performed a detailed analysis of conditions for in situ detection of miRNAs in the zebrafish embryo using locked nucleic acid (LNA)-modified DNA probes and report expression patterns for 15 miRNAs in the mouse embryo...
  64. ncbi Global identification of human transcribed sequences with genome tiling arrays
    Paul Bertone
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Science 306:2242-6. 2004
    ..A large fraction of these are located in intergenic regions distal from previously annotated genes and exhibit significant homology to other mammalian proteins...
  65. pmc Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) improves signal intensity and increases rRNA accessibility
    Kilian Stoecker
    Department of Microbial Ecology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 76:922-6. 2010
    Fluorescence in situ hybridization (FISH) with singly labeled rRNA-targeted oligonucleotide probes is widely applied for direct identification of microbes in the environment or in clinical specimens...
  66. pmc PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
    Kevin E Ashelford
    Cardiff School of Biosciences, Cardiff University, PO Box 915, Cardiff CF10 3TL, UK
    Nucleic Acids Res 30:3481-9. 2002
    ..PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors...
  67. pmc Fluorescence in situ hybridization and catalyzed reporter deposition for the identification of marine bacteria
    Annelie Pernthaler
    Max Planck Institute for Marine Microbiology, D 28359 Bremen, Germany
    Appl Environ Microbiol 68:3094-101. 2002
    Fluorescence in situ hybridization (FISH) with horseradish peroxidase (HRP)-labeled oligonucleotide probes and tyramide signal amplification, also known as catalyzed reporter deposition (CARD), is currently not generally applicable to ..
  68. pmc Dendrimeric coating of glass slides for sensitive DNA microarrays analysis
    Véronique Le Berre
    Transcriptome Biochips Platform of Genopole Toulouse Midi Pyrénées, Centre de Bioingénierie Gilbert Durand UMR CNRS 5504, UMR INRA 792, Institut National des Sciences Appliquees, F 31077 Toulouse Cedex 04, France
    Nucleic Acids Res 31:e88. 2003
    ..This detection limit was estimated to 0.1 pM of cDNA targets. Altogether, these features make dendrimer-activated slides ideal for manufacturing cost-effective DNA arrays applicable for gene expression and detection of mutations...
  69. pmc Is the in situ accessibility of the 16S rRNA of Escherichia coli for Cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30S ribosomal subunit?
    Sebastian Behrens
    Max Planck Institute of Marine Microbiology, Bremen Max Planck Institute of Molecular Genetics, Berlin, Germany
    Appl Environ Microbiol 69:4935-41. 2003
    ..The presence or absence of the strongly denaturing detergent sodium dodecyl sulfate had a much more pronounced effect than a change of fixative from paraformaldehyde to ethanol...
  70. doi Development of a consensus microarray method for identification of some highly pathogenic viruses
    Kang Xiao-Ping
    State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
    J Med Virol 81:1945-50. 2009
    ..Using this method, one unknown virus isolated from pig brain in Shanxi Province, China was identified. This method may have an important potential application for the diagnosis of virus infection...
  71. pmc Sequence versus structure for the direct detection of 16S rRNA on planar oligonucleotide microarrays
    Darrell P Chandler
    Biochip Technology Center, Argonne National Laboratory, 9700 South Cass Avenue, Building 202, A 249, Argonne, IL 60439, USA
    Appl Environ Microbiol 69:2950-8. 2003
    ....
  72. pmc Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot
    Gurman Singh Pall
    Division of Cancer Sciences and Molecular Pathology, Glasgow University, Western Infirmary, Dumbarton Road, Glasgow, G11 6NT, UK
    Nucleic Acids Res 35:e60. 2007
    ..All types of hybridization probes tested benefited from the new cross-linking procedure. Cross-linking was dependent on a terminal phosphate and so, should be applicable to other related categories of small RNA...
  73. pmc DNA enrichment by allele-specific hybridization (DEASH): a novel method for haplotyping and for detecting low-frequency base substitutional variants and recombinant DNA molecules
    Alec J Jeffreys
    Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
    Genome Res 13:2316-24. 2003
    ..This technique offers a new approach to the analysis of mutation and recombination, and has the potential to detect very rare de novo base substitutions...
  74. ncbi Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission
    Akimitsu Okamoto
    Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University and SORST, Japan Science and Technology Corporation, Kyoto 615 8510, Japan
    J Am Chem Soc 126:8364-5. 2004
    ..This method is useful for the determination of the presence/absence of insertion polymorphisms located at a specific site on the target DNA...
  75. doi The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structure
    Anna Pasternak
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, 60 714 Poznan, Noskowskiego 12 14, Poland
    Biochemistry 47:1249-58. 2008
    ..This is useful for design of hybridization probes to interrogate RNA structure and/or expression by microarray and other methods...
  76. pmc Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays
    J Small
    Analytical Microbiology, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
    Appl Environ Microbiol 67:4708-16. 2001
    ..5 x 10(6) Geobacter cell equivalents of RNA. These results suggest that it is now possible to apply microarray technology to the direct detection of microorganisms in environmental samples, without using PCR...
  77. ncbi Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays
    Jiang Li
    School of Pharmacy, University of Wisconsin Madison, Madison, Wisconsin 53705 2222, USA
    Physiol Genomics 21:43-58. 2005
    ..Integration of the gene expression profiles from different array platforms may not only help for cross-validation but also provide a more complete view of the transcriptional scenario...
  78. ncbi Development and application of oligonucleotide probes for in situ detection of thermotolerant Campylobacter in chicken faecal and liver samples
    Michael W Schmid
    GSF Forschungszentrum für Umwelt und Gesundheit, Institut für Bodenökologie, Abteilung Rhizosphärenbiologie, Ingolstadter Landstr 1, D 85764 Neuherberg, Germany
    Int J Food Microbiol 105:245-55. 2005
    Based on Campylobacter 16S- and 23S-rRNA sequence data oligonucleotide probes specific for thermotolerant campylobacters and for members of the genus Campylobacter have been developed...
  79. pmc Using triplex-forming oligonucleotide probes for the reagentless, electrochemical detection of double-stranded DNA
    Adriana Patterson
    Interdepartmental Program in Biomolecular Science and Engineering, and Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106, United States, and Dipartimento di Scienze e Tecnologie Chimiche, Universita di Roma Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
    Anal Chem 82:9109-15. 2010
    ..Moreover, to demonstrate real-world applicability of this new sensor platform, we have successfully detected unpurified, double-stranded PCR amplicons containing the relevant conserved HIV-1 sequence...
  80. doi Design of species-specific oligonucleotide probes for the detection of Bacteroides and Parabacteroides by fluorescence in situ hybridization and their application to the analysis of mouse caecal Bacteroides-Parabacteroides microbiota
    Y Momose
    Laboratory of Veterinary Public Health, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo ku, Tokyo, Japan
    J Appl Microbiol 111:176-84. 2011
    ..To develop species-specific monitoring techniques for rapid detection of Bacteroides and Parabacteroides inhabiting the mouse intestine by fluorescence in situ hybridization...
  81. pmc Empirical evaluation of oligonucleotide probe selection for DNA microarrays
    JENNIFER G MULLE
    Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America
    PLoS ONE 5:e9921. 2010
    ..These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications...
  82. pmc Oligonucleotide probes detect splicing variants in situ in Drosophila embryos
    R D Artero
    Department of Genetics, University of Valencia, Burjasot, Spain
    Nucleic Acids Res 20:5687-90. 1992
    ..Variant IVa is only detected in the CNS (ps6) at stages 16 and 17. We also present evidence indicating that the first splicing event is cotranscriptional...
  83. ncbi Real-time PCR in the microbiology laboratory
    I M Mackay
    Clinical Virology Research Unit, Sir Albert Sakzewski Virus Research Centre and Department of Paediatrics, Royal Children s Hospital, Brisbane, Queensland, Australia
    Clin Microbiol Infect 10:190-212. 2004
    ..These include the non-specific DNA-binding fluorophores and the specific, fluorophore-labelled oligonucleotide probes, some of which will be discussed in detail...
  84. pmc Detection of specific polymerase chain reaction product by utilizing the 5'----3' exonuclease activity of Thermus aquaticus DNA polymerase
    P M Holland
    Cetus Corporation, PCR Division, Emeryville, CA 94608
    Proc Natl Acad Sci U S A 88:7276-80. 1991
    ..aquaticus DNA polymerase degrades the probe into smaller fragments that can be differentiated from undegraded probe. The assay is sensitive and specific and is a significant improvement over more cumbersome detection methods...
  85. ncbi Sequence-specific, self-reporting hairpin inversion probes
    Kenneth A Browne
    Gen Probe Incorporated, 10210 Genetic Center Drive, San Diego, CA 92121, USA
    J Am Chem Soc 127:1989-94. 2005
    ....
  86. ncbi Lateral-flow and up-converting phosphor reporters to detect single-stranded nucleic acids in a sandwich-hybridization assay
    Paul L A M Corstjens
    Laboratory for Cytochemistry and Cytometry, Department of Molecular Cell Biology, Leiden University Medical Center, Wassenaarseweg 72, The Netherlands
    Anal Biochem 312:191-200. 2003
    ..With the assay described here as little as 0.1 fmol of a specific single-stranded nucleic acid target was detected in a background of 10 microg fish sperm DNA...
  87. ncbi Copper(II)-quenched oligonucleotide probes for fluorescent DNA sensing
    Jens Brunner
    Anorganisch Chemisches Institut, Universitat Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
    J Am Chem Soc 126:13626-7. 2004
    ..In the presence of complementary DNA, copper(II) and dye are spatially separated in the duplex and fluorescence increases up to 15-fold, with excellent discrimination of single base mismatches...
  88. ncbi Detection of multiple human herpes viruses by DNA microarray technology
    Zeno Földes-Papp
    Clinical Immunology and Jean Dausset Laboratory, Graz University Medical School, Graz, Austria
    Mol Diagn 8:1-9. 2004
    ....
  89. doi New trends in fluorescence in situ hybridization for identification and functional analyses of microbes
    Michael Wagner
    Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
    Curr Opin Biotechnol 23:96-102. 2012
    ....
  90. doi A molecular peptide beacon for the ratiometric sensing of nucleic acids
    Junchen Wu
    Institute for Organic Chemistry, University of Duisburg Essen, 45117 Essen, Germany
    J Am Chem Soc 134:1958-61. 2012
    ..Thus, 1 functions as a molecular peptide beacon, and as it is easily taken up by cells, 1 can also be used for imaging of nucleic acids within cells...
  91. pmc Detection and identification of Mycobacterium species isolates by DNA microarray
    Masao Fukushima
    Genomics Research Institute, SRL, Inc, 5 6 50 Shinmachi, Hino shi, Tokyo 191 0002, Japan
    J Clin Microbiol 41:2605-15. 2003
    ..A set of oligonucleotide probes for specific gyrB gene regions was developed for the identification of 14 Mycobacterium species...
  92. pmc Spotted long oligonucleotide arrays for human gene expression analysis
    Andrea Barczak
    Department of Medicine, University of California, San Francisco, San Francisco, California 94143, USA
    Genome Res 13:1775-85. 2003
    ..8-0.9) between relative gene expression measurements made with spotted long oligonucleotide probes and in situ-synthesized 25-mer probe sets...
  93. doi Loop region-specific oligonucleotide probes for loop-mediated isothermal amplification-enzyme-linked immunosorbent assay truly minimize the instrument needed for detection process
    Hadi Ravan
    Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
    Anal Biochem 439:102-8. 2013
    ..into amplicons during the amplification of the SPA3440 gene, their hybridization to the unique tagged oligonucleotide probes during the LAMP reaction, and finally detection of labeled LAMP amplicons by immunoassay technology...
  94. pmc Slow non-specific accumulation of 2'-deoxy and 2'-O-methyl oligonucleotide probes at mitochondria in live cells
    Won Jong Rhee
    Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
    Nucleic Acids Res 38:e109. 2010
    ..Here, we show that, when cyanine-dye labeled 2'-deoxy and 2'-O-methyl oligonucleotide probes are inside living cells for >5 h, most of their signals co-localize with mitochondrial staining...
  95. ncbi Fabrication of high quality microarrays
    Martin Dufva
    Microarray Technology Group, Department of Micro and Nanotechnology, Technical University of Denmark, Oersteds Plads, Bld 345 East, DK 2800 Kongens Lyngby, Denmark
    Biomol Eng 22:173-84. 2005
    ....
  96. pmc Slow folding kinetics of RNase P RNA
    P P Zarrinkar
    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139, USA
    RNA 2:564-73. 1996
    ....
  97. ncbi Visualization of mcr mRNA in a methanogen by fluorescence in situ hybridization with an oligonucleotide probe and two-pass tyramide signal amplification (two-pass TSA-FISH)
    Kengo Kubota
    Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603 1 Kamitomioka, Nagaoka, Niigata 940 2188, Japan
    J Microbiol Methods 66:521-8. 2006
    ..Signals from two-pass TSA-FISH were more reliable compared to the weak, spotty signals yielded by TSA-FISH...
  98. ncbi Development of 18S rRNA-targeted oligonucleotide probes for specific detection of Hartmannella and Naegleria in Legionella-positive environmental samples
    D Grimm
    Institut für Molekulare Infektionsbiologie, Universitat Wurzburg, Germany
    Syst Appl Microbiol 24:76-82. 2001
    ..In this study we designed oligonucleotide probes which are complementary to distinct regions of the 18S rRNA of the Legionella host organisms of the genera ..
  99. ncbi A novel, abundant sodium channel expressed in neurons and glia
    K L Schaller
    Department of Cellular and Structural Biology, University of Colorado Health Sciences Center, Denver 80262, USA
    J Neurosci 15:3231-42. 1995
    ..RT-PCR and/or in situ hybridization showed that astrocytes and Schwann cells express NaCh6. Thus, this sodium channel is broadly distributed throughout the nervous system and is shown to be expressed in both neurons and glial cells...
  100. pmc Estimating the proportion of microarray probes expressed in an RNA sample
    Wei Shi
    The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
    Nucleic Acids Res 38:2168-76. 2010
    ..Furthermore, hematopoietic stem cells were found to have a larger transcriptome than progenitor cells. Aire knockout medullary thymic epithelial cells were shown to have significantly less expressed probes than matched wild-type cells...
  101. pmc Dynamics of filamentous viral RNPs prior to egress
    Philip J Santangelo
    Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 313 Ferst Drive, Atlanta, GA 30332, USA
    Nucleic Acids Res 35:3602-11. 2007
    ....

Research Grants62

  1. Transgenesis and Xenotransplantation
    Jorge A Piedrahita; Fiscal Year: 2013
    ..T cells using a T cell receptor excision circle assay (TREC), antibody receptor diversity by using oligonucleotide probes, proliferative responses using mixed leukocyte cultures, and examining novel T- cell specificities by ..
  2. Mechanisms of Altered Gastrointestinal Dysfunction
    QiQi Zhou; Fiscal Year: 2013
    ..These methods combine unique miRNA recognition properties of locked nucleic acid (LNA) modified oligonucleotide probes with fluorescence in situ hybridization (FISH) using tyramide signal amplification (TSA) technology...
  3. Dengue diagnostics using a novel peroxidase chain reaction (PxCR)
    PETER PETER ZASSENHAUS; Fiscal Year: 2013
    ..The Specific Aims are to: (1) Develop pan and serotype specific PxCR assays for dengue viral RNA using oligonucleotide probes. (2) Develop serotype specific PxCR assays for the detection of dengue viral particles using antibodies to ..
  4. Ultrananocrystalline Diamond Microarray Biosensor for Neurochemical Detection
    Prabhu U Arumugam; Fiscal Year: 2012
    ..for "nanotechnologies'in general;and 4) UNCD can be easily modified with enzymes, antibodies and oligonucleotide probes through photochemical or electrochemical means for "biosensors"...
  5. New Technologies to Identify Novel Periodontal Pathogens
    FLAVIA ROCHA TELES; Fiscal Year: 2012
    ..It is based on 16s rRNA targeted oligonucleotide probes and it will determine which of 140 uncultivated/unrecognized species/taxa/ clones are common and numerous ..
  6. A highly multiplexed, scalable ultrananocrystalline diamond microarray sensor for
    Donato M Ceres; Fiscal Year: 2013
    ..Finally, UNCD electrode surfaces modified with SAMs, enzymes, antibodies and oligonucleotide probes can detect a wider range of chemical analytes than any other electrode material...
  7. NIH SBIR Phase I: Development of a Novel Boron-doped Ultrananocrystalline Diamond
    Prabhu U Arumugam; Fiscal Year: 2011
    ..in which probes are fabricated;and 4) for "biosensors"- UNCD can be easily modified with antibodies and oligonucleotide probes through photochemical or electrochemical means...
  8. Genetics of MRSA Infection
    George M Weinstock; Fiscal Year: 2010
    ..1. Development of a capture system for host defense genes. a. Selection of candidate genes and oligonucleotide probes;b. Development of solution capture strategy: WUCap or other state-of-the-art methods will be employed;c...
  9. Nuclease-Activated Probes for Imaging Staphylococcus aureus Infections
    JAMES O apos CONNELL MCNAMARA; Fiscal Year: 2013
    ..aureus. Preliminary studies provide examples of chemically modified oligonucleotide probes that can differentiate between MN and mammalian serum nucleases...
  10. CELLULAR REGULATION OF BLOOD CLOTTING
    Marc Shuman; Fiscal Year: 1992
    ..and fibrinolytic systems into rats and analysis of mRNA from hepatic tissue by Northern hybridization with oligonucleotide probes. Similar studies will be done in vitro with cultured rat hepatocyte and human U937 cells...
  11. INTESTINAL AND COLONIC CYTOCHROME P450 GENE EXPRESSION
    Peter Traber; Fiscal Year: 1993
    ..will be studied in intestinalesinal and colonic mucosa by measuring specific P450 mRNA with cDNA and oligonucleotide probes and P450 apoproteins using immunoblots...
  12. IMMUNE-LIKE PROTEINS OF INVERTEBRATES
    JOHN MARCHALONIS; Fiscal Year: 1993
    ..facilitate detailed comparisons with known recognition molecules and enable the synthesis of synthetic oligonucleotide probes to be used in isolation of relevant genes...
  13. BETA-ENDORPHIN RECEPTOR AND DYNORPHIN RECEPTOR:
    Nancy Lee; Fiscal Year: 1993
    ..will be achieved by classical procedures, including (a) N-terminal microsequencing; (b) synthesis of oligonucleotide probes corresponding to these sequences; (c) use of these probes to identify opioid peptide binding proteins ..
  14. NEUROCHEMICAL CORRELATES OF CEREBELLAR DEVELOPMENT
    Andrej Rotter; Fiscal Year: 1992
    ..receptor alpha and beta subunit mRNAs will be detected by in situ hybridization of complementary [35S]oligonucleotide probes. These techniques will also be used to study the expression of GABA/BZ binding sites, GABA/BZ receptor ..
  15. IMMUNOGENETICS OF MARROW ALLOGRAFTING
    John Hansen; Fiscal Year: 1992
    ..The cDNA encoding these variants are sequenced and new oligonucleotide probes developed for prospective typing...
  16. BIOSYNTHESIS NAD STRUCTURE OF THE FIBRINOGEN RECEPTOR
    Paul Bray; Fiscal Year: 1990
    ..These clones are being analyzed on Southern blots with oligonucleotide probes synthesized form known amino acid sequence of GPIIb and GPIIIa...
  17. Point of Care CARD Device for Rapid Molecular Diagnostics
    Peng Zhou; Fiscal Year: 2012
    ..immobilized within the microfluidic channels of the CARD(tm) by use of magnetic beads conjugated to other oligonucleotide probes that are complementary to another region of the target sequences...
  18. IMMUNOREGULATORY EFFECTS OF THE INTERFERONS
    Howard Ozer; Fiscal Year: 1992
    ..of the purified receptor and of isolated tryptic peptides will be determined and used to construct several oligonucleotide probes that will be used to screen a genomic human DNA library contained in lambda phage...
  19. VACUOLE FUNCTION IN NEUROSPORA
    Richard Weiss; Fiscal Year: 1993
    ..The amino acid sequence will be used to synthesize gene-specific oligonucleotide probes and polyclonal antibodies to be used to isolate the structural gene...
  20. REGULATION OF TRACHEA MUCIN SYNTHESIS AND GLYCOSYLATION
    Joseph Mendicino; Fiscal Year: 1990
    ..Suitable sequences will be used to prepare synthetic oligonucleotide probes in order to screen cDNA libraries for recombinant which contain inserts coding for deglycosylated mucin ..
  21. CLONING OF THE HUMAN RECEPTOR FOR ALPHA-2-INTERFERON
    LINVILLE MEADOWS; Fiscal Year: 1990
    ..Amino acid sequence analysis of the N- terminus and of tryptic peptides will be used to prepare oligonucleotide probes predicated on that sequence...
  22. Hybridization of Oligonucleotide Probes with Duplex DNA
    Maxim Frank Kamenetskii; Fiscal Year: 2005
    ..The implementation of the project will open totally new opportunities for DNA diagnostics of pathogens and for isolation and analysis of genes in an intact form. ..
  23. PROBES FOR MULTIPLEXING SINGLE RNA MOLECULE DETECTIION IN LIVING CELLS
    Robert H Singer; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): The goal: To prepare oligonucleotide probes that are coupled to fluorochromes to enter the cell and detect intracellular mRNAs in living cells with single copy sensitivity...
  24. MEMBRANE TOPOLOGY AND BIOSYNTHESIS OF GLYCOSAMINOGLYCANS
    CARLOS HIRSCHBERG; Fiscal Year: 2002
    ..Peptide sequence of the purified PAPS transporter will be used to obtain, via PCR, oligonucleotide probes to screen cDNA libraries to yield a full-length clone of this transporter...
  25. REGULATION OF PARATHYROID FUNCTION
    Jeremiah Morrissey; Fiscal Year: 1992
    ..Synthetic oligonucleotide probes will be used to select for DNA sequences in a normal bovine parathyroid expression library constructed in ..
  26. MOLECULAR BIOLOGY OF BRAIN PROTEIN PHOSPHORYLATION
    James Sikela; Fiscal Year: 1993
    ..In this approach brain cDNA libraries will be screened with two sets of degenerate oligonucleotide probes derived from conserved regions of the catalytic domain of known protein-serine kinase...
  27. HOST DEFENSES IN SYSTEMIC LUPUS ERYTHEMATOSUS
    H Perez; Fiscal Year: 1991
    ..Partial (and known) sequences of DBP and Bp will be used to generate synthetic oligonucleotide probes containing all possible substitutions at each codon...
  28. CALCIUM INDEPENDENT PLA2 AND ISCHEMIC CELL INJURY
    Didier Portilla; Fiscal Year: 2000
    ..Using oligonucleotide probes derived from partial amino acid sequence obtained from this novel protein, we isolated a full length cDNA ..
  29. RECOVERY OF DAMAGE TO THE VESTIBULAR-AUDITORY SYSTEM
    NEAL BARMACK; Fiscal Year: 2003
    ..Second, we will use oligonucleotide probes identified by DD-PCR to reveal the tissue distribution and the time course of changes in tissue ..
  30. LYMPHOCYTE GPL115--STRUCTURE-FUNCTION-DEFECT
    EILEEN REMOLD O DONNELL; Fiscal Year: 1990
    ..Polypeptide fragments will be generated and partial amino acid sequence determined so that oligonucleotide probes can be synthesized...
  31. CLONING OF PO-B: A PRO-OPIOMELANOCORTIN ACTIVATING FACTO
    Anna Riegel; Fiscal Year: 1993
    ..Best-guess' oligonucleotide probes will be designed from these sequences...
  32. GLUCOCORTICOID REGULATION OF GENETIC OBESITY
    David York; Fiscal Year: 1999
    ..b>Oligonucleotide probes based upon N-terminal protein sequence information will be used to identify and sequence the genes for the ..
  33. Mammalian Lactoferrin Receptors: Structure and Function
    Bo Lonnerdal; Fiscal Year: 2007
    ..Peptides binding to the LfR will be generated by combinatorial chemistry. Oligonucleotide probes will be used for in situ hybridization and an LfR antibody will be used for immunostaining of human and ..
  34. Use of nanotechnology to rapidly detect human pathogens
    RICHARD MONTAGNA; Fiscal Year: 2005
    ..Two types of oligonucleotide probes will be designed and utilized...
  35. AUTOIMMUNE ANTIGENS AND SYSTEMIC SCLEROSIS
    SALLIE HOCH; Fiscal Year: 1993
    ..Included in their characterization will be the determination of polypeptide sequences to design oligonucleotide probes to facilitate cDNA cloning...
  36. MOLECULAR CHARACTERIZATION OF A NEURAL PROTEIN
    SUSANNAH CHANG; Fiscal Year: 1993
    ..b>Oligonucleotide probes designed from the amino acid analysis have identified five clones from an E19 chick brain CDNA library...
  37. CHARACTERIZATION OF NUCLEAR PORE COMPLEX PROTEINS
    Howard Worman; Fiscal Year: 1991
    ..Polyclonal antibodies will be raised against these purified proteins and oligonucleotide probes will be synthesized complementary to the determined amino acid sequences of fragments if these proteins...
  38. BIOSYNTHESIS OF A PLATELET--GRANULE MEMBRANE PROTEIN
    RODGER MCEVER; Fiscal Year: 1990
    ..Cyanogen bromide cleavage products of GMP-140 will be sequenced and used to prepare synthetic 16-mer oligonucleotide probes from segments of limited codon degeneracy...
  39. PYRENE-CONTAINING PROBES FOR MUTATION DETECTION
    DAVID PHELPS; Fiscal Year: 2001
    ..b>Oligonucleotide probes can be designed such that two pyrenes, positioned on the adjacent ends of two oligonucleotides, come into ..
  40. CATECHOL-O-METHYLTRANSFERASE: BIOCHEMISTRY AND GENETICS
    Mark Grossman; Fiscal Year: 1991
    ..rat cDNA libraries with a labelled cDNA probe made from immunopurified COMT mRNA already on hand, or with oligonucleotide probes made according to COMT-peptide amino acid sequences (which have yet to be determined)...
  41. CHARACTERIZATION OF TRANSVERSE TUBULE MG2+-ATPASE
    TERENCE KIRLEY; Fiscal Year: 1993
    ..From the protein sequence obtained, oligonucleotide probes will be made to allow the identification of the cDNA coding for the Mg2+ -ATPase and the entire amino acid ..
  42. Studies of RNA modifications on the genomic scale
    Tao Pan; Fiscal Year: 2006
    ..We will synthesize new oligonucleotide probes that are sensitive to individual types of modifications...
  43. RHEUMATIC DISEASE--CORE CENTER
    Peter Schur; Fiscal Year: 1992
    ..for analysis of cell surface markers and cell sorting capability; a Molecular Biology Core to provide oligonucleotide probes; a Morphology Core for enhanced characterization of cellular event; a Laboratory Core for specific ..
  44. Development of DNA Chip with Hairpin Oligonucleotides
    Nanibhushan Dattagupta; Fiscal Year: 2002
    ..We propose a method that is aimed at addressing these drawbacks by use of 'snap-back' oligonucleotide probes and novel detection methods...
  45. Development of ThermoBLAST: Improving the Specificity of Probes and Primers
    Donald Hicks; Fiscal Year: 2007
    unreadable] DESCRIPTION (provided by applicant): Oligonucleotide probes and primers are a crucial component of most diagnostic assays used for detection and quantification of genomic material...
  46. Universal Fingerprinting Chips
    Kenneth Beattie; Fiscal Year: 2006
    ..by applicant): The proposed Universal Fingerprinting Chips (UFCs) are microarrays of thousands of oligonucleotide probes designed to interrogate the "sequence space" occupied by essentially any genome or transcriptome...
  47. GENETICS OF HUMAN T CELL RESPONSE TO CYTOMEGALOVIRUS
    PENELOPE MOREL; Fiscal Year: 1993
    ..the molecular techniques of the polymerase chain reaction (PCR) and dot blot analysis with allele specific oligonucleotide probes. Responsiveness to purified HCMV proteins will be assessed in these individuals...
  48. GENOTYPING WITH MINOR-GROOVE-BINDER-CONTAINING PROBES.
    Michael Reed; Fiscal Year: 2003
    ..A minor groove binder (MGB) has been developed that greatly enhances the ability of oligonucleotide probes to discriminate single nucleotide polymorphisms (SNPs) in the 5' nuclease (Taqman (registered), real time ..
  49. CELL PHYSIOLOGY OF CALCIUM EFFECTS ON PROTEIN SYNTHESIS
    H Palfrey; Fiscal Year: 1993
    ..Microsequencing of enzyme subunits will be performed in order to derive oligonucleotide probes that will be used in probing cDNA libraries for CaM-PK III cDNA's...
  50. GROWTH FACTORS EFFECT ON ASPECTS OF BONE FORMATION
    Ernesto Canalis; Fiscal Year: 2001
    ..a specific radioimmunoassay, and on PDGF A mRNA expression using a rat PDGF A cDNA clone and specific oligonucleotide probes. We also plan to determine, in a more definitive fashion, whether PDGF B mRNA can be detected or induced ..
  51. A METHIONINASE FOR METHIONINE DEPENDENT CHEMOTHERAPY
    Valeryi Lishko; Fiscal Year: 1991
    ..be carried out by sequencing the protein and using the sequence information to design and synthesize mixed oligonucleotide probes that will either be used to prime the polymerase chain reaction and synthesize mixed oligonucleotide ..
  52. CLONING OF A PHOSPHATIDYLINOSITOL KINASE
    Linda Pike; Fiscal Year: 1993
    ..which will permit screening of the library with antibodies to the PI kinase as well as with synthetic oligonucleotide probes. Following cDNA sequencing, clone identification will be carried out by epitope selection as well as by ..
  53. IN SEARCH OF THE UNIVERSAL NUCLEIC ACID BASE
    Donald Bergstrom; Fiscal Year: 1993
    ..to function as universal nucleic acid bases will be synthesized and their suitability as constituents of oligonucleotide probes determined in physicochemical and molecular biological studies...
  54. DNA PROBES TO DETECT PREDISPOSITION TO TYPE I DIABETES
    NICOLAAS VERMEULEN; Fiscal Year: 1992
    ..2 gene. DNA oligonucleotide probes have been used in Southern blots with genomic DNA to identify the DQ3...
  55. DEVELOPMENT OF SALIVARY GLAND SECRETORY FUNCTION
    LESLIE CUTLER; Fiscal Year: 1990
    ..library from total SMG secretory cell poly(A)+ mRNA, 3) screen the library with antibodies or synthetic oligonucleotide probes to the beta AR to identify clones containing the cDNA for the receptor, 4) if necessary, use ..
  56. GENETIC STUDIES OF PREGNANCY SPECIFIC B1 GLYCOPROTEIN
    Wai Yee Chan; Fiscal Year: 1992
    ..Initially, the nucleotide sequence of the different SP1 CDNAs will be determined. Gene-specific oligonucleotide probes will be synthesized basing on the structural differences among these cDNAs...
  57. A-GLOBIN PROMOTOR BINDING FACTORS: STRUCTURE & CLONING
    MICHAEL SHEFFERY; Fiscal Year: 1991
    ..These data will be used to prepare oligonucleotide probes that will be used to screen MEL cell cDNA libraries...
  58. REGULATION OF RETINAL PIGMENTED EPITHELIAL ECMS
    Ted Acott; Fiscal Year: 1993
    ..Direct biochemical analysis, supplemented by studies with protein and anti- peptide antibodies and oligonucleotide probes, will be used to characterize RPE proteoglycan core proteins and their glycosaminoglycan sidechains...
  59. MULTIPLEX DIAGNOSTIC ASSAY BASED ON MICROTRANSPONDERS
    Wlodek Mandecki; Fiscal Year: 2000
    ..During Phase II we will prepare synthetic oligonucleotide probes complementary to viral gene nucleic acid sequences...
  60. Highly Sensitive and Rapid Mix-and-Measure Detection Method for microRNAs in a Ce
    Sapna Deo; Fiscal Year: 2007
    ..of the application is that the formation of an active enzyme from the split enzyme fragments conjugated to oligonucleotide probes upon hybridization provides for the development of mix-and-measure assay, and the use of bioluminescent ..
  61. Reagents for Preparing Structure-Free DNA and RNA
    Howard Gamper; Fiscal Year: 2007
    ..structure in single-stranded ONA and RNA is a significant barrier to the efficient hybridization of short oligonucleotide probes. While some probes to a given target hybridize efficiently, other probes to the same target may not ..
  62. RETINOBLASTOMA DIAGNOSIS USING OLIGONUCLEOTIDE PROBES
    David Yandell; Fiscal Year: 1992
    ..Such treatments may be particularly harmful to individuals that carry a hereditary predisposition to malignancy...