dna probes

Summary

Summary: Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA 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 DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.

Top Publications

  1. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
  2. ncbi affy--analysis of Affymetrix GeneChip data at the probe level
    Laurent Gautier
    Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 20:307-15. 2004
  3. pmc Summaries of Affymetrix GeneChip probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Nucleic Acids Res 31:e15. 2003
  4. ncbi Mutation detection and single-molecule counting using isothermal rolling-circle amplification
    P M Lizardi
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Nat Genet 19:225-32. 1998
  5. pmc Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection
    C Li
    Departments of Statistics and Human Genetics, University of California, Los Angeles, CA 90095
    Proc Natl Acad Sci U S A 98:31-6. 2001
  6. ncbi MLPA and MAPH: new techniques for detection of gene deletions
    Loryn N Sellner
    Molecular Genetics Laboratory, Genetic Services of Western Australia, Princess Margaret Hospital, Perth, Australia
    Hum Mutat 23:413-9. 2004
  7. ncbi Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses
    Stefan J White
    Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    Hum Mutat 24:86-92. 2004
  8. ncbi Rolling-circle amplification in DNA diagnostics: the power of simplicity
    Vadim V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Expert Rev Mol Diagn 2:542-8. 2002
  9. ncbi Making ends meet in genetic analysis using padlock probes
    Mats Nilsson
    Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
    Hum Mutat 19:410-5. 2002
  10. ncbi Robust estimators for expression analysis
    Earl Hubbell
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Bioinformatics 18:1585-92. 2002

Detail Information

Publications331 found, 100 shown here

  1. ncbi Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Biostatistics 4:249-64. 2003
    ..We conclude that there is no obvious downside to using RMA and attaching a standard error (SE) to this quantity using a linear model which removes probe-specific affinities...
  2. ncbi affy--analysis of Affymetrix GeneChip data at the probe level
    Laurent Gautier
    Center for Biological Sequence Analysis CBS, Technical University of Denmark, Building 208, 2800 Lyngby, Denmark
    Bioinformatics 20:307-15. 2004
    ..The processing of the Affymetrix GeneChip data has been a recent focus for data analysts. Alternatives to the original procedure have been proposed and some of these new methods are widely used...
  3. pmc Summaries of Affymetrix GeneChip probe level data
    Rafael A Irizarry
    Department of Biostatistics, Johns Hopkins University, Baltimore, MD 21205, USA
    Nucleic Acids Res 31:e15. 2003
    ..In particular, improvements in the ability to detect differentially expressed genes are demonstrated...
  4. ncbi Mutation detection and single-molecule counting using isothermal rolling-circle amplification
    P M Lizardi
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
    Nat Genet 19:225-32. 1998
    ..RCA also shows promise for the detection of padlock probes bound to single-copy genes in cytological preparations...
  5. pmc Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection
    C Li
    Departments of Statistics and Human Genetics, University of California, Los Angeles, CA 90095
    Proc Natl Acad Sci U S A 98:31-6. 2001
    ..We also present model-based methods for identifying and handling cross-hybridizing probes and contaminating array regions. Applications of these results will be presented elsewhere...
  6. ncbi MLPA and MAPH: new techniques for detection of gene deletions
    Loryn N Sellner
    Molecular Genetics Laboratory, Genetic Services of Western Australia, Princess Margaret Hospital, Perth, Australia
    Hum Mutat 23:413-9. 2004
    ..The relative peak heights or band intensities from each target indicate their initial concentration. The two techniques differ in the ease with which probes can be generated in house, and the labor intensity of performing the assay...
  7. ncbi Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses
    Stefan J White
    Center for Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    Hum Mutat 24:86-92. 2004
    ..The approach is especially suited for cases in which the number of patients to be tested is limited, making it financially unattractive to invest in cloning...
  8. ncbi Rolling-circle amplification in DNA diagnostics: the power of simplicity
    Vadim V Demidov
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
    Expert Rev Mol Diagn 2:542-8. 2002
    Due to its robustness and simplicity, the rolling replication of circular DNA probes holds a distinct position in DNA diagnostics among other isothermal methods of target, probe or signal amplification...
  9. ncbi Making ends meet in genetic analysis using padlock probes
    Mats Nilsson
    Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
    Hum Mutat 19:410-5. 2002
    ..We argue that the probes have the potential to render high-throughput genetic analyses precise and affordable...
  10. ncbi Robust estimators for expression analysis
    Earl Hubbell
    Affymetrix, 3380 Central Expressway, Santa Clara, CA 95051, USA
    Bioinformatics 18:1585-92. 2002
    ..Such estimates should linearly track concentration, yield non-negative results, have statistical guarantees of robustness against outliers, and allow estimates of significance and variance...
  11. pmc Molecular mechanism of transcription inhibition by phage T7 gp2 protein
    Vladimir Mekler
    Department of Molecular Biology and Biochemistry, Waksman Institute for Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
    J Mol Biol 413:1016-27. 2011
    ..The inhibition of RNAP interactions with single-stranded segments of the transcription bubble by gp2 is a novel effect, which may occur via allosteric mechanism that is set in motion by the gp2 binding to the β' jaw...
  12. doi A novel multiplex real-time RT-PCR assay with FRET hybridization probes for the detection and quantitation of 13 respiratory viruses
    R Lassauniere
    Department of Medical Virology, Faculty of Health Sciences, University of Pretoria, South Africa
    J Virol Methods 165:254-60. 2010
    ....
  13. ncbi Chromosome painting in Arabidopsis thaliana
    M A Lysak
    Institute of Plant Genetics and Crop Plant Research (IPK, Gatersleben, D-06466, Germany
    Plant J 28:689-97. 2001
    ..segments or whole chromosomes based on fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes is widely used for chromosome studies in mammals, birds, reptiles and insects...
  14. pmc Identification of an aggregative adhesion fimbria (AAF) type III-encoding operon in enteroaggregative Escherichia coli as a sensitive probe for detecting the AAF-encoding operon family
    Christine Bernier
    Unité de Pathogénie Bactérienne des Muqueuses, Groupe d Etude des Infections Diarrhéiques GEID, Institut Pasteur, 75724 Paris Cedex 15, France
    Infect Immun 70:4302-11. 2002
    ..strains in terms of the virulence factors present render detection of these strains difficult with the available DNA probes. Based on comparison of the agg, aaf, and agg-3 operons, we defined an AAF probe internal to the adhesion gene ..
  15. ncbi Identification of deletions and duplications of the DMD gene in affected males and carrier females by multiple ligation probe amplification (MLPA)
    Valentina Gatta
    Department of Biomedical Sciences, G d Annunzio University Foundation, Chieti, Italy
    Hum Genet 117:92-8. 2005
    ....
  16. ncbi A new summarization method for Affymetrix probe level data
    Sepp Hochreiter
    Department of Electrical Engineering and Computer Science, Technische Universitat Berlin, 10587 Berlin, Germany
    Bioinformatics 22:943-9. 2006
    ..In contrast to previous methods our new method called 'Factor Analysis for Robust Microarray Summarization (FARMS)' supplies both P-values indicating interesting information and signal intensity values...
  17. ncbi Design and evaluation of oligonucleotide-microarray method for the detection of human intestinal bacteria in fecal samples
    Rong Fu Wang
    Microbiology Division, National Center for Toxicological Research, US FDA, Jefferson, AR 72079, USA
    FEMS Microbiol Lett 213:175-82. 2002
    ..The hybridization results indicated that the oligo-microarray method developed in this study is a reliable method for the detection of predominant human intestinal bacteria in the fecal samples...
  18. pmc UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/genomic level
    Shu Hwa Chen
    Institute of Information Science, Academia Sinica, Taipei, Taiwan
    BMC Genomics 11:S6. 2010
    ..This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets...
  19. ncbi Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets
    Heiko Kuhn
    Center for Advanced Biotechnology, Department of Biomedical Engineering, Boston University, 36 Cummington Street, Boston, Massachusetts 02215, USA
    J Am Chem Soc 124:1097-103. 2002
    ....
  20. pmc 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order "Rhodocyclales"
    Alexander Loy
    Department of Microbial Ecology, Institute of Ecology and Conservation Biology, University of Vienna, Vienna, Austria
    Appl Environ Microbiol 71:1373-86. 2005
    ....
  21. ncbi The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria
    T Barry
    National Diagnostic Centre, BioResearch Ireland, University College Galway
    PCR Methods Appl 1:51-6. 1991
    Variable regions of the 16s ribosomal RNA have been frequently used as the target for DNA probes to identify microorganisms...
  22. pmc Electrochemical biosensors employing an internal electrode attachment site and achieving reversible, high gain detection of specific nucleic acid sequences
    Aaron A Rowe
    Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
    Anal Chem 83:9462-6. 2011
    ..Moreover, because the hairpin probe is a single, fully covalent strand of DNA, it is robust to the high stringency washes necessary to remove the target, and thus, these devices are fully reusable...
  23. ncbi Evaluation of minor groove binding probe and Taqman probe PCR assays: Influence of mismatches and template complexity on quantification
    Yuanrong Yao
    Department of Neuroscience, Karolinska Institute, Retzius vag 8, S 171 77 Stockholm, Sweden
    Mol Cell Probes 20:311-6. 2006
    ....
  24. ncbi Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins
    S A Kushon
    Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213-3890, USA
    J Am Chem Soc 123:10805-13. 2001
    The binding of a series of PNA and DNA probes to a group of unusually stable DNA hairpins of the tetraloop motif has been observed using absorbance hypochromicity (ABS), circular dichroism (CD), and a colorimetric assay for PNA/DNA duplex ..
  25. doi Single-cell gel electrophoresis (the comet assay): loops or fragments?
    Sergey A Shaposhnikov
    Department of Nutrition, Faculty of Medicine, University of Oslo, Oslo, Norway
    Electrophoresis 29:3005-12. 2008
    ..After alkaline electrophoresis, the appearance of the fluorescent probes suggests that linear DNA has coalesced into a granular form...
  26. pmc Ultrasensitive single-nucleotide polymorphism detection using target-recycled ligation, strand displacement and enzymatic amplification
    Yue Zhang
    School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
    Nanoscale 5:5027-35. 2013
    ..75%. This sensor appears to be well-suited for sensitive SNP detection and a wide range of DNA mutation based diagnostic applications...
  27. pmc Comparative genomic hybridization: DNA labeling, hybridization and detection
    Richard Redon
    Wellcome Trust, Sanger Institute, Cambridge, UK
    Methods Mol Biol 529:267-78. 2009
    ....
  28. doi An inexpensive and simple method for thermally stable immobilization of DNA on an unmodified glass surface: UV linking of poly(T)10-poly(C)10-tagged DNA probes
    Haukur Gudnason
    DTU Nanotech, Department of Micro and Nanotechnology, Technical University of Denmark, Lyngby
    Biotechniques 45:261-71. 2008
    ..of the immobilized probes on the amino-silane surface, indicating a general benefit of adding a TC tag to DNA probes. In conclusion, our results show that using TC-tagged DNA probes immobilized on an unmodified glass surface is a ..
  29. ncbi DNA probes for the rapid identification of medically important Candida species using a multianalyte profiling system
    Sanchita Das
    Mycotic Diseases Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    FEMS Immunol Med Microbiol 46:244-50. 2006
    ..Austin, TX]. DNA probes, directed to the internal transcribed spacer 2 region of ribosomal DNA, were therefore designed to detect and ..
  30. doi DNA microarrays for hybridization detection by surface plasmon resonance spectroscopy
    Alfred Kick
    Professur für Physikalische Chemie, Mess und Sensortechnik, Technische Universitat Dresden, 01062 Dresden, Germany
    Biosens Bioelectron 26:1543-7. 2010
    ..Furthermore, we demonstrate that sequences with possible hairpin structures significantly lower the binding rate, and thus, the SPR signals during hybridization...
  31. pmc A critical role of downstream RNA polymerase-promoter interactions in the formation of initiation complex
    Vladimir Mekler
    Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
    J Biol Chem 286:22600-8. 2011
    ....
  32. ncbi Rapid aggregation of gold nanoparticles induced by non-cross-linking DNA hybridization
    Kae Sato
    Bioengineering Laboratory, RIKEN The Institute of Physical and Chemical Research, Hirosawa 2 1, Wako, Saitama 351 0198, Japan
    J Am Chem Soc 125:8102-3. 2003
    ..This non-cross-linking aggregation system opens up a new possibility of rapid and reliable genetic analysis...
  33. ncbi Peptide-nucleic acid-modified ion-sensitive field-effect transistor-based biosensor for direct detection of DNA hybridization
    Takeshi Uno
    The Institute of Scientific and Industrial Research, Osaka University, 8 1 Mihogaoka, Ibaraki, Osaka 567 0047, Japan
    Anal Chem 79:52-9. 2007
    ..PNA is particularly advantageous for this system because it enables highly specific and selective binding at low ionic strength...
  34. pmc Conjugation polymer nanobelts: a novel fluorescent sensing platform for nucleic acid detection
    Lei Wang
    State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, Jilin, People s Republic of China
    Nucleic Acids Res 39:e37. 2011
    ..This results in desorption of the hybridized complex from PN surface and subsequent recovery of fluorescence. We also show that the sensing platform described herein can be used for multiplexing detection of nucleic acid sequences...
  35. ncbi Combinatorial labelling of DNA probes enables multicolour fluorescence in situ hybridisation in plants
    Robert Hasterok
    Department of Plant Anatomy and Cytology, University of Silesia, Katowice, Poland
    Folia Histochem Cytobiol 40:319-23. 2002
    ..Three different DNA probes were labelled with only two different fluorophores, hybridised to somatic metaphase chromosomes of Secale ..
  36. ncbi Genomic organization and phylogenetic relationships in the genus Dasypyrum analysed by southern and in situ hybridization of total genomic and cloned DNA probes
    I Galasso
    C N R, Istituto del Germoplasma, Via G Amendola 165 A, I 70126 Bari, Italy
    Chromosoma 106:53-61. 1997
    ..Our data support an autotetraploid origin for D. breviaristatum, but its genome and that of D. villosum show extensive differences, so the tetraploid is unlikely to be directly derived from D. villosum...
  37. ncbi Fluorescent DNA hybridization probe preparation using amine modification and reactive dye coupling
    W Gregory Cox
    Molecular Probes, Inc, Eugene, OR, USA
    Biotechniques 36:114-22. 2004
    ..We optimized this latter two-step approach for maximal hybridization signal brightness using DNA probes labeled to varying degrees with different fluorescent dyes...
  38. pmc Novel DNA probes with low background and high hybridization-triggered fluorescence
    Eugeny A Lukhtanov
    Nanogen, Inc, 21720 23rd Drive SE, Suite 150, Bothell, WA 98021, USA
    Nucleic Acids Res 35:e30. 2007
    Novel fluorogenic DNA probes are described. The probes (called Pleiades) have a minor groove binder (MGB) and a fluorophore at the 5'-end and a non-fluorescent quencher at the 3'-end of the DNA sequence...
  39. ncbi Gold nanoparticle-based detection of genomic DNA targets on microarrays using a novel optical detection system
    James J Storhoff
    Nanosphere, Inc, Applied Research, 4088 Commercial Ave, Northbrook, IL 60062, USA
    Biosens Bioelectron 19:875-83. 2004
    ..Furthermore, direct detection of non-amplified genomic DNA from infectious agents is afforded through increased specificity and even identification of single nucleotide polymorphisms (SNP) in human genomic DNA appears feasible...
  40. ncbi The thermodynamics of DNA structural motifs
    John SantaLucia
    Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
    Annu Rev Biophys Biomol Struct 33:415-40. 2004
    ..This review presents the current parameter set available for making accurate DNA structure predictions and also points to future directions for improvement...
  41. ncbi Detecting copy number changes in genomic DNA: MAPH and MLPA
    Stefan J White
    Center for Human and Clinical Genetics, Leiden University Medical Center, 2333 AL Leiden, Nederland
    Methods Cell Biol 75:751-68. 2004
  42. doi On the causes of outliers in Affymetrix GeneChip data
    Graham J G Upton
    University of Essex, Wivenhoe Park, Colchester, Essex CO4 3SQ, UK
    Brief Funct Genomic Proteomic 8:199-212. 2009
    ..In this review we describe a number of causes for why some reported intensities might be misleading on GeneChips...
  43. 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
    ....
  44. ncbi Applications of Luminex xMAP technology for rapid, high-throughput multiplexed nucleic acid detection
    Sherry A Dunbar
    Luminex Corporation, Austin, TX 78727, USA
    Clin Chim Acta 363:71-82. 2006
    ..Multiplexing technologies, which allow for simultaneous detection of multiple nucleic acid sequences in a single reaction, can greatly reduce the time, cost and labor associated with single reaction detection technologies...
  45. pmc Direct identification of mycobacteria from MB/BacT alert 3D bottles: comparative evaluation of two commercial probe assays
    C Scarparo
    Regional Mycobacteria Reference Centre, Laboratory of Clinical Microbiology and Virology, San Bortolo Hospital, Vicenza, Italy
    J Clin Microbiol 39:3222-7. 2001
    ....
  46. doi Nonspecific hybridization scaling of microarray expression estimates: a physicochemical approach for chip-to-chip normalization
    Hans Binder
    Interdisciplinary Centre for Bioinformatics of Leipzig University, D 4107 Leipzig, Haertelstrasse 16 18, Germany
    J Phys Chem B 113:2874-95. 2009
    ..The results emphasize the importance of physicochemical approaches for improving heuristic normalization algorithms to proceed toward quantitative microarray data analysis...
  47. ncbi DNA quality control by conformational readout on the undamaged strand of the double helix
    Tonko Buterin
    Institute of Pharmacology and Toxicology, University of Zurich Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
    Chem Biol 12:913-22. 2005
    Synthetic DNA probes were incubated in human cell extracts to dissect the early step of bulky lesion recognition in the nucleotide excision repair pathway...
  48. pmc Improved in situ hybridization efficiency with locked-nucleic-acid-incorporated DNA probes
    Kengo Kubota
    Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603 1 Kamitomioka, Nagaoka, Niigata 940 2188, Japan
    Appl Environ Microbiol 72:5311-7. 2006
    ..hybridization efficiency by applying locked-nucleic-acid (LNA)-incorporated oligodeoxynucleotide probes (LNA/DNA probes) without compromising specificity...
  49. pmc Nano-flares: probes for transfection and mRNA detection in living cells
    Dwight S Seferos
    Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 3113, USA
    J Am Chem Soc 129:15477-9. 2007
  50. pmc Fluorescent quenching-based quantitative detection of specific DNA/RNA using a BODIPY((R)) FL-labeled probe or primer
    S Kurata
    Kankyo Engineering Corporation, 1 Kimitsu, Kimitsu-shi, Chiba 299-1141, Japan
    Nucleic Acids Res 29:E34. 2001
    ..This widely applicable technique will be used directly with larger samples or in conjunction with the polymerase chain reaction to quantify small DNA samples...
  51. pmc G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration
    Mario Fasold
    Interdisciplinary Centre for Bioinformatics, University Leipzig, Germany
    BMC Bioinformatics 11:207. 2010
    ..Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis...
  52. ncbi Multiplex ligation-dependent probe amplification using a completely synthetic probe set
    Rowena F Stern
    Department of Medical and Molecular Genetics, Guy s, King s and St Thomas School of Medicine, London, UK
    Biotechniques 37:399-405. 2004
    ..We conclude that the use of synthetic probes for MLPA is a rapid, robust, and efficient alternative for research (and potentially diagnostic) deletion and duplication screening of multiple genomic loci...
  53. pmc Mismatch and G-stack modulated probe signals on SNP microarrays
    Hans Binder
    Interdisciplinary Centre for Bioinformatics, Universitat Leipzig, Leipzig, Germany
    PLoS ONE 4:e7862. 2009
    ..This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. We analyze the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe ..
  54. pmc Structure and DNA hybridization properties of mixed nucleic acid/maleimide-ethylene glycol monolayers
    Chi Ying Lee
    National ESCA and Surface Analysis Center for Biomedical Problems, University of Washington, Box 351750, Seattle, Washington 98195 1750, USA
    Anal Chem 79:4390-400. 2007
    ..The amounts of target detected for both ssDNA surfaces were several orders of magnitude poorer in serum than in purified DNA samples due to nonspecific serum protein adsorption onto the sensing surface...
  55. ncbi PROBER: oligonucleotide FISH probe design software
    Nicholas Navin
    Watson School of Biological Sciences, Cold Spring Harbor, NY 11724, USA
    Bioinformatics 22:2437-8. 2006
    ..genomic sequences and delineating essentially unique regions that can be amplified to yield small (100-2000 bp) DNA probes that in aggregate will generate a single, strong fluorescent signal for regions as small as a single gene...
  56. pmc Sequence-based design of single-copy genomic DNA probes for fluorescence in situ hybridization
    P K Rogan
    Section of Medical Genetics and Molecular Medicine, Children s Mercy Hospital and Clinics, University of Missouri Kansas City School of Medicine, Kansas City, Missouri 64108, USA
    Genome Res 11:1086-94. 2001
    ..rearrangements are frequently monitored by fluorescence in situ hybridization (FISH) using large, recombinant DNA probes consisting of contiguous genomic intervals that are often distant from disease loci...
  57. ncbi Strategies in the preparation of DNA oligonucleotide arrays for diagnostic applications
    S L Beaucage
    Division of Therapeutic Proteins, Center for Biologics Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
    Curr Med Chem 8:1213-44. 2001
    ..10(6) sequences per cm(2) on DNA chips...
  58. pmc Performance assessment of new multiplex probe assay for identification of mycobacteria
    E Tortoli
    Centro Regionale di Riferimento per la Diagnostica delle Micobatteriosi, Laboratorio di Microbiologia e Virologia, Ospedale di Careggi, Piastra del servizi, Viale Morgagni 85, 50134 Florence, Italy
    J Clin Microbiol 39:1079-84. 2001
    ..The turnaround time of the method is approximately 6 h, including a preliminary PCR amplification...
  59. ncbi Colorimetric detection of eukaryotic gene expression with DNA-derivatized gold nanoparticles
    Pedro Baptista
    CIGMH SABT, Faculdade de Ciencias e Tecnologia, Universidade Nova de Lisboa, 2829 516 Caparica, Portugal
    J Biotechnol 119:111-7. 2005
    ..No temperature control is necessary and color change can be easily detected visually...
  60. doi Effects of probe length, probe geometry, and redox-tag placement on the performance of the electrochemical E-DNA sensor
    Arica A Lubin
    Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, USA
    Anal Chem 81:2150-8. 2009
    ..Finally, we find that sensor response time and selectivity are only minimally affected by probe geometry or length. The results of this comparative study will help guide future designs and applications of these sensors...
  61. ncbi Exploring the new world of the genome with DNA microarrays
    P O Brown
    Department of Biochemistry, Howard Hughes Medical Institute, Stanford University School of Medicine, California 94305, USA
    Nat Genet 21:33-7. 1999
    ..Exploration of the genome using DNA microarrays and other genome-scale technologies should narrow the gap in our knowledge of gene function and molecular biology between the currently-favoured model organisms and other species...
  62. ncbi Nanoscale-controlled spacing provides DNA microarrays with the SNP discrimination efficiency in solution phase
    Bong Jin Hong
    Langmuir 21:4257-61. 2005
    ..In addition, high hybridization yield confirms that DNA probes on the mesospaced surface are sterically unhindered for the hybridization.
  63. ncbi Copy number analysis of survival motor neuron genes by multiplex ligation-dependent probe amplification
    Chien Hao Huang
    Genephile Bioscience Laboratory, Ko s Obstetrics and Gynecology, Taipei, Taiwan
    Genet Med 9:241-8. 2007
    ..To determine the copy number of survival motor genes using multiplex ligation-dependent probe amplification...
  64. ncbi Detection of circovirus infection in pigeons by in situ hybridization using cloned DNA probes
    J A Smyth
    Department of Agriculture and Rural Development for Northern Ireland, Belfast
    J Vet Diagn Invest 13:475-82. 2001
    ..This high prevalence of infection in diseased birds is noteworthy, emphasizing the need for studies to determine the precise role of this virus as a disease-producing agent...
  65. pmc Commercial DNA probes for mycobacteria incorrectly identify a number of less frequently encountered species
    Enrico Tortoli
    Regional Reference Center for Mycobacteria, Piastra dei Servizi, A O U Careggi, Viale Morgagni 85, 50134 Florence, Italy
    J Clin Microbiol 48:307-10. 2010
    Although commercially available DNA probes for identification of mycobacteria have been investigated with large numbers of strains, nothing is known about the ability of these probes to identify less frequently encountered species...
  66. doi An electrochemical alkaline phosphatase biosensor fabricated with two DNA probes coupled with λ exonuclease
    Peng Miao
    Laboratory of Biosensing Technology, School of Life Sciences, Shanghai University, Shanghai, PR China
    Biosens Bioelectron 27:178-82. 2011
    ..a novel electrochemical biosensor for the detection of alkaline phosphatase (AP) by the use of two complementary DNA probes (DNA 1 and DNA 2) coupled with λ exonuclease (λ exo)...
  67. pmc Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments
    Bryan A Baker
    School of Materials Science and Engineering, Georgia Institute of Technology, 771 Ferst Dr NW, Atlanta, GA 30332 0245, USA
    Nucleic Acids Res 39:e99. 2011
    We have investigated the time-dependent strand displacement activity of several targets with double-stranded DNA probes (dsProbes) of varying affinity...
  68. pmc High throughput screening of human subtelomeric DNA for copy number changes using multiplex amplifiable probe hybridisation (MAPH)
    E J Hollox
    Institute of Genetics, Queen s Medical Centre, University of Nottingham, Nottingham, UK
    J Med Genet 39:790-5. 2002
    ..Here we report that a new method, multiplex amplifiable probe hybridisation (MAPH), can be used to screen for copy number at subtelomeric regions...
  69. pmc Single-gene detection and karyotyping using small-target fluorescence in situ hybridization on maize somatic chromosomes
    Jonathan C Lamb
    Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
    Genetics 175:1047-58. 2007
    ..The probes were demonstrated to produce signals in several wild relatives of maize, including Zea luxurians, Z. diploperennis, and Tripsacum dactyloides...
  70. ncbi A thermodynamic investigation into the binding properties of DNA functionalized gold nanoparticle probes and molecular fluorophore probes
    Abigail K R Lytton-Jean
    Department of Chemistry and Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
    J Am Chem Soc 127:12754-5. 2005
    ..This is significant because probe binding strength directly influences detection sensitivity limits...
  71. doi Unlabeled hairpin-DNA probe for the detection of single-nucleotide mismatches by electrochemical impedance spectroscopy
    Ying Wang
    Department of Chemistry, Beijing Normal University, Beijing, China, 100875
    Anal Chem 80:2255-60. 2008
    ..The detection limit was measured, and DeltaR(CT) allows the discrimination of a single-nucleotide mismatch with the concentration of the target strand as low as 10 pM...
  72. pmc Comparison of the benzoyl-DL-arginine-naphthylamide (BANA) test, DNA probes, and immunological reagents for ability to detect anaerobic periodontal infections due to Porphyromonas gingivalis, Treponema denticola, and Bacteroides forsythus
    W J Loesche
    Department of Biological and Materials Sciences, University of Michigan School of Dentistry, Ann Arbor 48109 1078
    J Clin Microbiol 30:427-33. 1992
    ..gingivalis, T. denticola, and B. forsythus; (ii) whole genomic DNA probes to P. gingivalis and T. denticola; and (iii) culturing or microscopic procedures...
  73. pmc Label-free electrochemical detection of the specific oligonucleotide sequence of dengue virus type 1 on pencil graphite electrodes
    Elaine Souza
    Laboratory of Immunopathology Keizo Asami LIKA, Universidade Federal de Pernambuco UFPE, Recife, PE, Brazil
    Sensors (Basel) 11:5616-29. 2011
    ..The target could be quantified in a range from 1 to 40 nM with good linearity and a detection limit of 0.92 nM. The specificity of the electrochemical biosensor was tested using non-complementary sequences of dengue virus 2 and 3...
  74. ncbi PhylArray: phylogenetic probe design algorithm for microarray
    Cécile Militon
    Génomique Intégrée des Interactions Microbiennes, Laboratoire de Biologie des Protistes, UMR CNRS 6023, Blaise Pascal University, 24 avenue des Landais, Campus des Cézeaux, France
    Bioinformatics 23:2550-7. 2007
    ..Finally, hybridizations with environmental targets have shown that the use of the PhylArray strategy can draw attention to even previously unknown bacteria...
  75. ncbi Rapid and unequivocal differentiation of Candida dubliniensis from other Candida species using species-specific DNA probes: comparison with phenotypic identification methods
    A N B Ellepola
    Mycotic Diseases Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
    Oral Microbiol Immunol 18:379-88. 2003
    ..using universal fungal primers to the internal transcribed spacer 2 (ITS2) region of rDNA and species-specific DNA probes in an enzyme immunoassay format (PCR-EIA). DNA sequencing of the ITS1 rDNA region was also conducted. The C...
  76. ncbi Fluorescent-labeled DNA probes applied to novel biological aspects of B-cell chronic lymphocytic leukemia
    Stephanie R Fink
    Division of Laboratory Genetics, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA
    Leuk Res 29:253-62. 2005
    Fluorescent-labeled DNA probes were used to study 52 chronic lymphocytic leukemia (B-CLL) patients for (1) disease progression, (2) angiogenesis genes, (3) T-cell leukemia 1 gene (TCL1), (4) immunoglobulin heavy chain variable region (..
  77. ncbi Malacosporean-like spores in urine of rainbow trout react with antibody and DNA probes to Tetracapsuloides bryosalmonae
    R P Hedrick
    School of Veterinary Medicine, Department of Medicine and Epidemiology, University of California, Davis, CA 95616, USA
    Parasitol Res 92:81-8. 2004
    ..Despite morphological differences, a relationship between the spores in the urine of rainbow trout and T. bryosalmonae was demonstrated by binding of monoclonal and polyclonal antibodies and DNA probes specific to T. bryosalmonae.
  78. doi Comet-FISH with rDNA probes for the analysis of mutagen-induced DNA damage in plant cells
    Jolanta Kwaśniewska
    Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40 032 Katowice, Poland
    Environ Mol Mutagen 53:369-75. 2012
    ..Moreover, our work suggests that comet-FISH in plants may be a useful tool for environmental monitoring assessment...
  79. ncbi Binding-induced fluorescence turn-on assay using aptamer-functionalized silver nanocluster DNA probes
    Jingjing Li
    State Key Lab of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, People s Republic of China
    Anal Chem 84:5170-4. 2012
    ....
  80. pmc Resolution of discrepant results for Candida species identification by using DNA probes
    Catherine Coignard
    Mycotic Diseases Branch, Division of Bacterial and Mycotic Diseases, National Center for Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA
    J Clin Microbiol 42:858-61. 2004
    ..Such misidentifications could lead to the administration of inappropriate therapy given the propensity of C. glabrata to develop resistance to azole antifungal drugs...
  81. doi Rapid microRNA detection using power-free microfluidic chip: coaxial stacking effect enhances the sandwich hybridization
    Hideyuki Arata
    Bioengineering Laboratory, RIKEN, 2 1 Hirosawa, Wako, Saitama 351 0198, Japan
    Analyst 137:3234-7. 2012
    ..5 μL sample volume at a limit of detection of 0.62 nM. Since microRNAs can act as cancer markers, this method might substantially contribute to future point-of-care cancer diagnosis...
  82. doi Progress and prospects of pyrrole-imidazole polyamide-fluorophore conjugates as sequence-selective DNA probes
    Thangavel Vaijayanthi
    Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa Oiwakecho, Kyoto 606 8502, Japan
    Chembiochem 13:2170-85. 2012
    ....
  83. ncbi Subgingival microbiota in healthy, well-maintained elder and periodontitis subjects
    A D Haffajee
    Department of Periodontology, Forsyth Dental Center, Boston, MA, USA
    J Clin Periodontol 25:346-53. 1998
    ..The presence and levels of 40 subgingival taxa were determined in 5003 plaque samples using whole genomic DNA probes and checkerboard DNA-DNA hybridization...
  84. doi Increasing the physical markers of wheat chromosomes using SSRs as FISH probes
    Angeles Cuadrado
    Department of Cell Biology and Genetics, University of Alcala, 28871 Alcala de Henares Madrid, Spain
    Genome 51:809-15. 2008
    In plants the marker sequences used to identify chromosomes are mainly repetitive DNA probes. Simple sequence repeats (SSRs) are major components of many plant genomes and could be good markers for chromosome identification...
  85. doi Use of centromeric and telomeric DNA probes in in situ hybridization for differentiation of micronuclei induced by lomefloxacin
    Sabry M Attia
    Department of Pharmacology and Toxicology, Faculty of Pharmacy, Al Azhar University, Cairo, Egypt
    Environ Mol Mutagen 50:394-403. 2009
    ..quinolone bactericidal agent, in mouse bone marrow was performed by fluorescence in situ hybridization using DNA probes for the centromere repeated minor satellite DNA and the telomeric hexamer repeat (5'-TTAGGG-3')...
  86. pmc Low density DNA microarray for detection of most frequent TP53 missense point mutations
    Angélica Rangel-López
    Escuela Nacional de Ciencias Biologicas IPN, Mexico, 11340, D F, Mexico, 11340, D F, Mexico
    BMC Biotechnol 5:8. 2005
    ....
  87. ncbi An efficient chemical method to generate repetitive sequences depleted DNA probes
    Joe N Lucas
    ChromoTrax, Inc, Frederick Innovative Technology Center, Federick, Maryland 21701, USA
    Am J Med Genet A 140:2115-20. 2006
    ..FISH analyses using these probes show consistent strong signals with no cross-hybridization, and optimal hybridization results can be obtained relatively quickly...
  88. doi Authentication of Atlantic cod (Gadus morhua) using real time PCR
    Beatriz Herrero
    Area of Molecular Biology and Biotechnology, ANFACO CECOPESCA, Vigo, 36310 Pontevedra, Spain
    J Agric Food Chem 58:4794-9. 2010
    ..The methodology herein developed is useful to check the fulfilment of labeling regulations for seafood products and verify the correct traceability in commercial trade and for fisheries control...
  89. doi Fluorescent silver nanoclusters as DNA probes
    Judy M Obliosca
    Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
    Nanoscale 5:8443-61. 2013
    ..In this review we present the recent discoveries of activatable and color-switchable properties of DNA-templated silver nanoclusters and discuss the strategies to use these new properties in DNA sensing. ..
  90. doi Dimeric gold nanoparticle assembly for detection and discrimination of single nucleotide mutation in Duchenne muscular dystrophy
    Wei Jie Qin
    Department of Chemical and Biomolecular Engineering, Faculty of Engineering, National University of Singapore, Singapore 119260, Singapore
    Biosens Bioelectron 25:2021-5. 2010
    ..Our results show that conjugating the gold nanoparticles with short DNA probes of 18 bases and 70 bases complimentary to target sequences allows specific discrimination between wild-type and ..
  91. pmc A rapid, cost-effective method of assembly and purification of synthetic DNA probes >100 bp
    Michael A Jensen
    Stanford Genome Technology Center, Palo Alto, California, United States of America
    PLoS ONE 7:e34373. 2012
    Here we introduce a rapid, cost-effective method of generating molecular DNA probes in just under 15 minutes without the need for expensive, time-consuming gel-extraction steps...
  92. ncbi Applications and technical challenges of fluorescence in situ hybridization in stem cell research
    Heinz Ulli G Weier
    Life Sciences Division 74 157, University of California, E O Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
    Blood Cells Mol Dis 32:68-76. 2004
    ..these highly relevant issues is based on fluorescence in situ hybridization (FISH) using nonisotopically labeled DNA probes. As a single cell analysis technique, FISH is expected to be applicable to a variety of cells and tissues ..
  93. pmc Uprobe: a genome-wide universal probe resource for comparative physical mapping in vertebrates
    Wendy A Kellner
    Emory University School of Medicine, Department of Human Genetics, Atlanta, Georgia 30322, USA
    Genome Res 15:166-73. 2005
    ..Future implementation of the universal probe design strategy will be used to create an expanded number of whole-genome probe sets that will encompass all vertebrate genomes...
  94. ncbi DNA microarrays with unimolecular hairpin double-stranded DNA probes: fabrication and exploration of sequence-specific DNA/protein interactions
    Jinke Wang
    National Laboratory for Molecular and Biomolecular Electronics, Southeast University, Nanjing 210096 Jiangsu Province, China
    J Biochem Biophys Methods 55:215-32. 2003
    ..The dsDNA microarrays have great potential to provide a high-throughput platform for investigation of sequence-specific DNA/protein interactions involved in gene expression regulation, restriction and so on...
  95. ncbi Identification and mapping of six microdissected genomic DNA probes to the proximal region of mouse chromosome 1
    S M Vidal
    Department of Biochemistry, McGill University, Montreal, Canada
    Genomics 14:32-7. 1992
    Six independent DNA probes, lambda Mm1C-150, lambda Mm1C-153, lambda Mm1C-156, lambda Mm1C-162, lambda Mm1C-163, and lambda Mm1C-165, have been isolated from a library of microdissected fragments from mouse chromosome 1, spanning ..
  96. ncbi Molecular dynamics simulations of end-tethered single-stranded DNA probes on a silica surface
    Zunliang Wang
    The State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China
    J Nanosci Nanotechnol 11:8457-68. 2011
    ..Herein, we investigated the dynamics and interaction of seven DNA probes tethered on a silica surface by a molecular dynamics simulation...
  97. pmc Label-free potentiometry for detecting DNA hybridization using peptide nucleic acid and DNA probes
    Tatsuro Goda
    Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, Chiyoda, Tokyo, Japan
    Sensors (Basel) 13:2267-78. 2013
    ..for potentiometric DNA detection or not, we conducted a comparative study on the hybridization of PNA and DNA probes on the surface of a 10-channel gold electrodes microarray...
  98. ncbi Detection of virulence-associated genes in clinical isolates of bacillus anthracis by multiplex PCR and DNA probes
    Sanjay Kumar
    Division of Microbiology, Defence Research and Development Establishment, Jhansi Road, Gwalior 474 002, Madhya Pradesh
    J Microbiol Biotechnol 19:1475-81. 2009
    ..anthracis isolated from clinical and environmental samples. For this purpose, multiplex PCR and DNA probes were designed to detect protective antigen ( pag), edema factor (cya), lethal factor (lef ), and capsule (cap) ..
  99. pmc Fluorescence, XPS, and TOF-SIMS surface chemical state image analysis of DNA microarrays
    Chi Ying Lee
    National ESCA and Surface Analysis Center for Biomedical Problems, Department of Bioengineering, University of Washington, Seattle, WA 98195 1750, USA
    J Am Chem Soc 129:9429-38. 2007
    ....
  100. pmc FISH in analysis of gamma ray-induced micronuclei formation in barley
    Jolanta Juchimiuk-Kwasniewska
    Department of Plant Anatomy and Cytology, University of Silesia, Jagiellonska 28, 40 032, Katowice, Poland
    J Appl Genet 52:23-9. 2011
    ..FISH with four DNA probes was used to examine the involvement of specific chromosomes or chromosome fragments in gamma ray-induced ..
  101. pmc DNA probes using fluorescence resonance energy transfer (FRET): designs and applications
    V V Didenko
    Baylor College of Medicine, Houston, TX, USA
    Biotechniques 31:1106-16, 1118, 1120-1. 2001
    ..This paper reviews the design and applications of various DNA-based probes that use FRET The approaches used in the design of new DNA FRET probes are discussed...

Research Grants63

  1. Detection of Category A Pathogens by Gold Nanoparticles
    Steven Wolinsky; Fiscal Year: 2007
    ..are substantially more sensitive and selective than conventional assays based on fluorophore-labeled DNA probes. Ultimately, the assay will be as accurate and sensitive as PCR-based assays...
  2. RADIATION-INDUCED THYROID CANCER
    Heinz Ulrich G Weier; Fiscal Year: 2011
    ..Interphase cell preparations from the control groups will be studied with DNA probes specific for candidate loci to detect rearrangements...
  3. Encapsidation of the poxvirus genome
    Paula Traktman; Fiscal Year: 2012
    ..In vitro, the I6 protein binds with great specificity to DNA probes representing the telomeric hairpins of the viral genome...
  4. Accelerating Cancer Research with Single Cell Arrays
    Heinz Ulrich Weier; Fiscal Year: 2009
    ..protocols to enzymatically digest and remove RNAs that interfere with the assay or to block hybridization of DNA probes to residual RNA, while minimizing DNA loss...
  5. Nanoscale Optical Fiber Biosensor Assays for Detection of Category A and B Select
    Thomas J Inzana; Fiscal Year: 2010
    ..specific aims are to: (i) develop a DNA-hybridization assay using nanoscale optical fiber biosensors coupled to DNA probes to detect specific oligonucleotide sequences;(ii) develop an antigen-binding assay using nanoscale optical fiber ..
  6. Nanoparticle-based Antimicrobial Photochemotherapy in Biofilms
    NIKOLAOS SOUKOS; Fiscal Year: 2010
    ..evaluate their photodynamic effects on biofilm species by total viable counts, an species identification using DNA probes and PCR...
  7. Comprehensive transcriptome analysis for Porphyromonas gingivalis
    Tsute Chen; Fiscal Year: 2009
    ..By designing DNA probes based on the genomic sequences, microarray can monitor the expression of tens of thousands of genes or specific ..
  8. QP Expression Benchtop Colony Picking System
    Dara W Frank; Fiscal Year: 2010
    ..of analyses of phenotype, including growth properties, protein production, and recognition by antibody or DNA probes. Through each step, the system tracks the source and destination of each clone, and allows the user to simply ..
  9. Comparison of Morpholino and DNA Technologies for Surface-Based Diagnostics
    Rastislav Levicky; Fiscal Year: 2010
    ..where a markedly enhanced diagnostic response is realized compared to conventional approaches based on DNA probes, and where purely electronic (i.e...
  10. Label-free and simultaneous detection of multiple bacterial pathogens and virulen
    HAO HOWARD XU; Fiscal Year: 2010
    ..this grant proposal, support is requested to design and validate species-specific or virulence factor- specific DNA probes, and to demonstrate proof-of-concept with 20 pathogenic bacterial species and 10 virulence factor genes (..
  11. Rapid Cystic Fibrosis Mutation Screening Test
    Wlodek Mandecki; Fiscal Year: 2010
    ..is composed of photocells, antenna and memory to store information that identifies the sequence of the DNA probes attached to the microtransponder surface...
  12. Nuclease Probe Mediated Sequencing
    Bruce E Seligmann; Fiscal Year: 2011
    ..quantitative Nuclease Protection Assay (qNPA") or ligation/exonuclease generated Padlock probes to generate DNA probes for sequencing by synthesis, combined with gene tagging and experiment tagging methods to permit pooling to ..
  13. CONFERENCE--ISOLATED FETAL CELLS IN MATERNAL BLOOD
    Joe Simpson; Fiscal Year: 1993
    ..We thus are employing fluorescence in situ hybridization (FISH) with chromosome-specific DNA probes. In one of our first successes, a blood sample taken prior to CVS and flow-sorted revealed trisomy 18 cells...
  14. SPECIES-SPECIFIC DNA PROBES FOR BANCROFTIAN FILARIASIS
    Steven Williams; Fiscal Year: 1990
    ..The use of cloned species- specific DNA probes to detect parasites in humans and in mosquitoes would provide a valuable tool for studying the epidemiology of ..
  15. Templated Chemistry for RNA Analysis
    Eric T Kool; Fiscal Year: 2013
    ..Moreover, as with most DNA probes, the issue of probe delivery needs to be addressed (for whole-cell applications) by taking advantage of recently ..
  16. MAPPING AND CLONING TRANSLOCATION BREAKPOINTS
    Janet Rowley; Fiscal Year: 2004
    ..b>DNA probes appropriate for the genes will be used to determine whether these "new" genes are involved in other ..
  17. AUTOMATED DETECTION OF GENE DUPLICATIONS OR DELETIONS
    Fatima Merchant; Fiscal Year: 2005
    ..Our approach is to use readily available DNA probes, followed by automated genetic screening to detect duplications/deletions...
  18. DNA Probes for Acanthamoeba Genomics and Epidemiology
    Paul Fuerst; Fiscal Year: 2007
    ..Preliminary results show that this region can be amplified in disparate genotypes. Further, these results may provide potential targets for future treatment, since products of these genes may be antibiotic targets. ..
  19. MOLECULAR CLONING AND ANALYSIS OF HUMAN GENOMIC REGIONS
    Donald Moir; Fiscal Year: 1990
    ..of reliable diagnostic tests for inheritance of these diseases based on the use of tightly linked polymorphic DNA probes. Identification of the gene for an inherited disease offers an opportunity to understand the molecular defect ..
  20. CULTIVABLE & UNCULTIVABLE PERIODONTAL SPIROCHETES
    Floyd Dewhirst; Fiscal Year: 2003
    ..We have developed 16S rRNA based DNA probes that allow identification of cultivable and uncultivable treponemes in clinical samples...
  21. Sequence Based FISH Analysis of Philadelphia Chromosomes
    JOAN KNOLL; Fiscal Year: 2003
    ..can be refined with high- resolution fluorescence in situ studies (scFISH), which uses short single copy (sc) DNA probes designed from the draft genome sequence...
  22. COMPLEMENTARY DNA PROBES TO A STEROID RECEPTOR GENE
    J Pike; Fiscal Year: 1992
    ..We believe that these goals can be met most efficiently utilizing current molecular biologic approaches...
  23. Hybridization of Oligonucleotide Probes with Duplex DNA
    Maxim Frank Kamenetskii; Fiscal Year: 2005
    ..Tris-PNA constructs will also be tried as PNA openers advantageous for extended PD-loops. Enhanced-affinity DNA probes and more stable PNA probes will be involved for this purpose, too...
  24. RHEUMATOID ARTHRITIS
    C Kwoh; Fiscal Year: 1993
    ..e, HLA-A, B, C,and DR specificities), and allele-specific oligonucleotide c-DNA probes (e.g., DR beta I and DQ beta alleles)...
  25. GENETIC DISSECTION OF OCULAR CONNECTIVE TISSUE
    Robert Church; Fiscal Year: 1990
    ..Monoclonal antibody and specific recombinant DNA probes will be used to determine whether certain antigens are being expressed in various human-mouse somatic cell ..
  26. NATIONAL CHIMPANZEE BREEDING AND RESEARCH PROGRAM
    Michale Keeling; Fiscal Year: 1999
    ..continue to collaborate with Trinity University to maintain a comprehensive genetic management program using DNA probes and other techniques to establish positive paternity, determine population heterozygosity and identify genetic ..
  27. VIRAL INTERFERENCE IN CARRIER CULTURES
    Richard Crowell; Fiscal Year: 1992
    ..We will also attempt to use human DNA probes for identification of mouse cDNA clones...
  28. CHEMILUMINESCENT MULTIPLEX GENOME MAPPING
    John Fox; Fiscal Year: 1992
    ..The "down-up" approach of multiplex genome mapping involves hybridization of radiolabeled end- specific DNA probes or oligonucleotides to cloned DNA from YAC, cosmid, lambda, or M13 libraries "dot-blotted" onto nylon or ..
  29. AUTOMATED PRENATAL SCREENING USING MATERNAL BLOOD
    Fatima Merchant; Fiscal Year: 2000
    ..blood, can now be enriched to one per few thousand, and aneuploidies can be detected with chromosome specific DNA probes via fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR)...
  30. PUSHMI-PULLYU HYBRID MAPPING OF THE HUMAN X CHROMOSOME
    HUNTINGTON WILLARD; Fiscal Year: 1992
    ..of markers can be deduced from the linear deletion map generated from hybridization patterns of a number of DNA probes against the Pushmi-pullyu hybrid panel...
  31. CLONING AND CHARACTERIZATION OF THE RETINOBLASTOMA GENE
    YUEN FUNG; Fiscal Year: 1991
    ..The approach of chromosomal walking with DNA probes in the vicinity of the Rb gene will be used for its isolation...
  32. Rapid Cystic Fibrosis DNA Mutation Screening Test
    Wlodek Mandecki; Fiscal Year: 2003
    ..ten important cystic fibrosis (CF) mutations in Caucasians, Black Americans and Hispanics and prepare synthetic DNA probes to these mutations; 2) Prepare primers for all CFTR mutations tested for use in multiplex PCR reaction; 3) ..
  33. MOLECULAR BIOLOGY OF DIABETOGENIC HAPLOTYPES DIABETES
    David Owerbach; Fiscal Year: 1991
    ..A, B, C, and DR, complement BF, C2 and C4 alleles and glyoxylase I alleles will be typed using cDNA and genomic DNA probes for HLA-DQ, DR, and DR alpha and beta DNA sequences...
  34. VIRULENCE OF VANCOMYCIN RESISTANT AND OTHER E FAECIUM
    Barbara Murray; Fiscal Year: 2003
    ..faecalis research. The E. faecium libraries will also be screened with DNA probes from high interest E. faecalis genes, using low stringency hybridization, to look for possible homologs...
  35. GLYCOLYTIC & PEROXISOMAL GENES ON CHROMOSOME 11 AND 12
    GAIL BRUNS; Fiscal Year: 1993
    ..8 megabases of DNA, has been developed with pulse field gel electrophoresis and 24 new DNA probes for the WAGR deletion regions, together with 3 reference loci (catalase, beta subunit of follicle stimulating ..
  36. REPETITIVE SEQUENCE-DEPLETE LIBRARIES OF DNA PROBES
    Xin Yuan Guan; Fiscal Year: 2000
    ..Our new method will simplify the protocol for research scientists using DNA probes in FISH. it will meet the demands of advanced FISH techniques...
  37. MOLECULAR GENETICS OF BIPOLAR AFFECTIVE DISORDER
    Charles Richard; Fiscal Year: 1993
    ..The general strategy of this project involves identifying DNA probes that physically flank the BAD disease gene, cloning all the DNA between the flanking probes, and identifying the ..
  38. TARGETING NATIVE DOUBLE HELIX STRUCTURES AND FUNCTIONS
    DAVID ZARLING; Fiscal Year: 1999
    ..coli RecA protein which catalyze the hybridization of pairs of complementary single-stranded (css) DNA probes to homologous dsDNA targets in the presence of very large excesses of heterologous DNA...
  39. GASTROINTESTINAL-LIVER ALKALINE PHOSPHATASES
    WING KAM; Fiscal Year: 1993
    ..Characterization of these two putative forms at the DNA level will provide specific DNA probes to carry out clinical studies to evaluate their potential applications as tumor and disease markers...
  40. GENETICS OF HLA-D AND T-CELL RECEPTOR HAPLOTYPES
    Hugh McDevitt; Fiscal Year: 1991
    ..Using this probe, as well as DNA probes for the V beta and C beta genes from the human beta-chain receptor gene complex, restriction fragment length ..
  41. MECHANISM OF STEROID SPECIFIC GENE ACTIVATION
    DIANE ROBINS; Fiscal Year: 2003
    ..generate probes of protein-protein interaction by expressing these receptor domains in bacteria, and generate DNA probes by greater definition of nonreceptor protein-DNA interaction; III) isolate accessory factor cDNA clones from ..
  42. PHYSICAL MAP FOR HUMAN GENOMIC REGION
    Robert Gemmill; Fiscal Year: 1990
    ..This map should provide a foundation upon which a comprehensive map of the entirety of chromosome 3 can be built...
  43. CHARACTERIZATION OF CORONARY PRONE PEDIGREES
    Roger Williams; Fiscal Year: 1990
    ..coronary disease using a genetic segregation and linkage study of lipids, lipoproteins, apolipoproteins, and DNA probes in 36 large Utah pedigrees (11 previously studied pedigrees and 20 new ones)...
  44. STRUCTURES OF NEURECTODERM TUMOR GLYCOPROTEINS
    MARY GLICK; Fiscal Year: 1992
    ..The DNA probes will be used to address biological questions relating to human neuroblastoma including the mechanisms ..
  45. MOLECULAR GENETIC ANALYSIS OF PNEUMOCYSTIS
    James Stringer; Fiscal Year: 1991
    ..propose here is to use cloned pc DNA fragments to characterize gene structure and organization, and to isolate DNA probes with which to explore the relationship between pneumocystis of rats and man...
  46. MOLECULAR GENETICS OF ENTEROPATHOGENIC E COLI ADHESION
    JAMES KAPER; Fiscal Year: 1991
    ..objectives of this project are to study the pathogenesis of disease due to this organism and to develop DNA probes for diagnosis and vaccine candidates for prevention...
  47. Molecular Typing of Taste Cells Using Microarrays
    Liquan Huang; Fiscal Year: 2004
    ..The specific goals of this application are: 1. To generate DNA probes from taste buds, filiform papillae and 100 individual taste cells using both an aRNA amplification method and a ..
  48. BIOMEDICAL RESEARCH SUPPORT
    Elizabeth Hammond; Fiscal Year: 1990
    ..To enhance the imaging of very weak fluorescence signals (and thus to facilitate the use of small DNA probes) the microscope will be equipped with a cooled CCD camera (Hamamatsu) and the existing inefficient confocal ..
  49. Development of a Multi-State Decoding Framework
    Semyon Kruglyak; Fiscal Year: 2003
    ..b>DNA probes attached to microbeads are randomly loaded onto fiber optic bundles...
  50. GENETIC ASPECTS OF IMMUNODEFICIENCIES
    Mary Conley; Fiscal Year: 2007
    ..specific aim, the PI will use pulse field electrophoresis,[unreadable] yeast artificial chromosomes (YACs), new DNA probes and linkage[unreadable] analysis to further refine the DNA segment within which the XLA gene[unreadable] must ..
  51. INTERPHASE CYTOGENETICS: CHROMOSOME-SPECIFIC DNA PROBES
    Katherine Klinger; Fiscal Year: 1990
    ..Interphase cytogenetics using in situ hybridization of fluorescent labeled DNa probes is potentially rapid, relatively inexpensive, and lends itself to automation...
  52. NIR FLUORESCENT LABELS FOR RNA SCREENING IN MICROARRAYS
    RICHARD TULLIS; Fiscal Year: 1999
    Sensitive fluorescent detection of DNA probes is required for applications such as DNA sequencing, in situ hybridization and multi-component arrays for detecting mRNA expression...
  53. DNA PROBES TO DETECT PREDISPOSITION TO TYPE I DIABETES
    NICOLAAS VERMEULEN; Fiscal Year: 1992
    ..The long-term objectives are development of a product for the detection of genetic predisposition to Type I diabetes, and of a rapid and sensitive nylon bead sandwich assay technology for the detection of additional genetic markers...
  54. High Performance Lanthanide DNA Probes
    Ronald Cook; Fiscal Year: 2002
    ..As a result the practical and economic synthesis of lanthanide oligo probes will become possible, and their application to genomic assays can begin. ..
  55. Multifunctional Dendritic Tethers for Biosensor Devices
    CHARLES SPANGLER; Fiscal Year: 2002
    ..a robust, flexible bioactive signal transduction system, based on the attachment of specific antibodies or DNA probes to a biosensor surface, in a microarray or chromatographic formats...
  56. Development of Clinically Useful Single Copy FISH Probes
    PETER ROGAN; Fiscal Year: 2005
    ..Commercially available DNA probes, which detect the most common abnormalities, bind to chromosomal targets of 40-1000 kb in length, making them ..
  57. Snap-To-It Probes
    John Zebala; Fiscal Year: 2009
    ..We propose to develop a novel Snap-To-It array technology that consists of arrayed PNA and DNA probes that are conformationally constrained by an intra-molecular chelate...
  58. MULTISPECTRAL BACTERIAL IDENTIFICATION
    William Coleman; Fiscal Year: 1999
    ..abstract_text> ..
  59. MICROVASCULAR PERICYTES--CONTROL OF CEREBRAL BLOOD FLOW
    Ira Herman; Fiscal Year: 1992
    ..Morphologic, biochemical and molecular studies using specific antibody and recombinant DNA probes will be implemented in model systems to determine whether extracellular matrix-cytoskeletal interactions ..
  60. MOLECULAR ANALYSIS OF HUMAN CHROMOSOME 17
    Lisa Shaffer; Fiscal Year: 1993
    ..while the other half have recently been shown by us to have submicroscopic deletions detected by anonymous DNA probes. MDS thus offers a model system for the reverse genetics cloning of genes involved in the pathogenesis of a ..
  61. MICROFLUIDIC DETECTION OF ORAL BACTERIA USING DNA PROBES
    PAUL HAYDOCK; Fiscal Year: 2000
    ..The use of DNA probes offers unparalleled specificity but technical requirements have as yet brought DNA probes to the dental ..
  62. Rapid FISH Assay for Disease-Related Nuclear RNA Transcripts
    JOAN AURICH COSTA; Fiscal Year: 2006
    ..This is typically accomplished using DNA probes several hundreds of kilobases (kb) in size, targeting similarly sized DNA regions...
  63. THE MOLECULAR GENETICS OF CYSTIC FIBROSIS
    HAIG KAZAZIAN; Fiscal Year: 1990
    ..or rearrangement involving the CF gene using macro- restriction mapping using the tightly linked, flanking DNA probes Met and D7S8 (J3.11). Any area of rearranged DNA will be explored for the gene which causes CF. 2)...