nucleic acid hybridization

Summary

Summary: Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)

Top Publications

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  2. ncbi DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
    Johan Goris
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Int J Syst Evol Microbiol 57:81-91. 2007
  3. ncbi Molecular beacons: probes that fluoresce upon hybridization
    S Tyagi
    Department of Molecular Genetics, Public Health Research Institute, New York, NY 10016, USA
    Nat Biotechnol 14:303-8. 1996
  4. ncbi Scaling up digital circuit computation with DNA strand displacement cascades
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    Science 332:1196-201. 2011
  5. ncbi A DNA-fuelled molecular machine made of DNA
    B Yurke
    Bell Laboratories, Lucent Technologies, Murray Hill, New Jersey 07974, USA
    Nature 406:605-8. 2000
  6. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
  7. pmc Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    Scott Baskerville
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    RNA 11:241-7. 2005
  8. ncbi Dynamic DNA nanotechnology using strand-displacement reactions
    David Yu Zhang
    Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Room 530, Boston, Massachussetts 02115, USA
    Nat Chem 3:103-13. 2011
  9. pmc Enrichment of sequencing targets from the human genome by solution hybridization
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Genome Biol 10:R116. 2009
  10. pmc Comprehensive human genome amplification using multiple displacement amplification
    Frank B Dean
    Molecular Staging, Inc, 300 George Street, Suite 701, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 99:5261-6. 2002

Detail Information

Publications315 found, 100 shown here

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
  2. ncbi DNA-DNA hybridization values and their relationship to whole-genome sequence similarities
    Johan Goris
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Int J Syst Evol Microbiol 57:81-91. 2007
    ..It is concluded that ANI can accurately replace DDH values for strains for which genome sequences are available...
  3. ncbi Molecular beacons: probes that fluoresce upon hybridization
    S Tyagi
    Department of Molecular Genetics, Public Health Research Institute, New York, NY 10016, USA
    Nat Biotechnol 14:303-8. 1996
    ..When introduced into living cells, these probes should enable the origin, movement, and fate of specific mRNAs to be traced...
  4. ncbi Scaling up digital circuit computation with DNA strand displacement cascades
    Lulu Qian
    Bioengineering, California Institute of Technology, Pasadena, CA 91125, USA
    Science 332:1196-201. 2011
    ..The design naturally incorporates other crucial elements for large-scale circuitry, such as general debugging tools, parallel circuit preparation, and an abstraction hierarchy supported by an automated circuit compiler...
  5. ncbi A DNA-fuelled molecular machine made of DNA
    B Yurke
    Bell Laboratories, Lucent Technologies, Murray Hill, New Jersey 07974, USA
    Nature 406:605-8. 2000
    ..The machine, made from three strands of DNA, has the form of a pair of tweezers. It may be closed and opened by addition of auxiliary strands of 'fuel' DNA; each cycle produces a duplex DNA waste product...
  6. pmc Relative impact of nucleotide and copy number variation on gene expression phenotypes
    Barbara E Stranger
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
    Science 315:848-53. 2007
    ..Interrogation of the genome for both types of variants may be an effective way to elucidate the causes of complex phenotypes and disease in humans...
  7. pmc Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes
    Scott Baskerville
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    RNA 11:241-7. 2005
    ....
  8. ncbi Dynamic DNA nanotechnology using strand-displacement reactions
    David Yu Zhang
    Wyss Institute for Biologically Inspired Engineering, Harvard University, 3 Blackfan Circle, Room 530, Boston, Massachussetts 02115, USA
    Nat Chem 3:103-13. 2011
    ..This mechanism allows for the kinetic control of reaction pathways. Here, we review DNA strand-displacement-based devices, and look at how this relatively simple mechanism can lead to a surprising diversity of dynamic behaviour...
  9. pmc Enrichment of sequencing targets from the human genome by solution hybridization
    Ryan Tewhey
    Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, 3344 N Torrey Pines Court, La Jolla, CA 92037, USA
    Genome Biol 10:R116. 2009
    ..9 Mb of sequence target. We demonstrate that the tiling probe frequency is important for generating sequence data with high uniform coverage of targets. We obtained 93% sensitivity to detect SNPs, with a calling accuracy greater than 99%...
  10. pmc Comprehensive human genome amplification using multiple displacement amplification
    Frank B Dean
    Molecular Staging, Inc, 300 George Street, Suite 701, New Haven, CT 06511, USA
    Proc Natl Acad Sci U S A 99:5261-6. 2002
    ..MDA-based WGA is a simple and reliable method that could have significant implications for genetic studies, forensics, diagnostics, and long-term sample storage...
  11. ncbi Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation
    Eric C Lai
    University of California at Berkeley, Department of Molecular and Cell Biology, 545 Life Sciences Addition 3200, Berkeley, California 94720 3200, USA
    Nat Genet 30:363-4. 2002
    ..These findings suggest a more general role for micro RNAs in gene regulation through the formation of RNA duplexes...
  12. ncbi GenoType MTBDR assays for the diagnosis of multidrug-resistant tuberculosis: a meta-analysis
    D I Ling
    Dept of Epidemiology, Biostatistics and Occupational Health, McGill University, 1020 Pine Avenue West, Montreal, QC H3A 1A2, Canada
    Eur Respir J 32:1165-74. 2008
    ..While specificity is excellent for isoniazid, sensitivity estimates were modest and variable. Together with data from demonstration projects, the meta-analysis provides evidence for policy making and clinical practice...
  13. ncbi Frequent amplification of chromosomal region 20q12-q13 in ovarian cancer
    M M Tanner
    Laboratory of Cancer Genetics, Institute of Medical Technology, Tampere University and University Hospital, Finland
    Clin Cancer Res 6:1833-9. 2000
    ..5% of the sporadic tumors. The high frequency of gene amplification at 20q12-q13.2 suggests that the genes amplified therein may play a central role in the pathogenesis of sporadic and hereditary ovarian carcinoma...
  14. 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...
  15. pmc Optimizing the specificity of nucleic acid hybridization
    David Yu Zhang
    Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, USA
    Nat Chem 4:208-14. 2012
    ..However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature...
  16. ncbi Single-mismatch detection using gold-quenched fluorescent oligonucleotides
    B Dubertret
    Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10021, USA
    Nat Biotechnol 19:365-70. 2001
    ..In competitive hybridization assays, the ability to detect single mismatch is eightfold greater with this probe than with other molecular beacons...
  17. pmc Detection of bacterial virulence genes by subtractive hybridization: identification of capsular polysaccharide of Burkholderia pseudomallei as a major virulence determinant
    S L Reckseidler
    Department of Microbiology and Infectious Diseases, University of Calgary Health Sciences Center, Calgary, Alberta, Canada T2N 4N1
    Infect Immun 69:34-44. 2001
    ..Thus, the combination of PCR-based subtractive hybridization, insertional inactivation, and animal virulence studies has facilitated the identification of an important virulence determinant in B. pseudomallei...
  18. ncbi A robust DNA mechanical device controlled by hybridization topology
    Hao Yan
    Department of Chemistry, New York University, New York, NY 10003, USA
    Nature 415:62-5. 2002
    ..We expect that a wide range of analogous yet distinct rotary devices can be created by changing the control strands and the device sequences to which they bind...
  19. pmc Strong association of de novo copy number mutations with autism
    Jonathan Sebat
    Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
    Science 316:445-9. 2007
    ..Affected genomic regions were highly heterogeneous and included mutations of single genes. These findings establish de novo germline mutation as a more significant risk factor for ASD than previously recognized...
  20. 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...
  21. 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
    ....
  22. pmc Efficient siRNA selection using hybridization thermodynamics
    Zhi John Lu
    Department of Biochemistry and Biophysics and Department of Biostatistics and Computational Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
    Nucleic Acids Res 36:640-7. 2008
    ..1% by adding equilibrium terms to 25 local sequence features. Prediction of hybridization affinity using partition functions is now available in the RNAstructure software package...
  23. ncbi A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes
    John P Hammond
    Warwick HRI, University of Warwick, Wellesbourne, Warwick CV35 9EF, UK
    New Phytol 170:239-60. 2006
    ..Future functional analyses of genes identified as differentially expressed in the shoots of these closely related species will improve our understanding of the molecular mechanisms of Zn hyperaccumulation...
  24. ncbi Detection of endogenous K-ras mRNA in living cells at a single base resolution by a PNA molecular beacon
    Yossi Kam
    Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, PO Box 12065, Jerusalem 91120, Israel
    Mol Pharm 9:685-93. 2012
    ....
  25. ncbi LNA flow-FISH: a flow cytometry-fluorescence in situ hybridization method to detect messenger RNA using locked nucleic acid probes
    Kelly L Robertson
    Center for Bio Molecular Science and Engineering, U S Naval Research Laboratory, Washington, DC 20375, USA
    Anal Biochem 390:109-14. 2009
    ..This combined method, called LNA flow-FISH, can be used for detection and quantification of other RNA species as well as for telomerase measurement and detection...
  26. ncbi A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures
    Juan M Gonzalez
    Instituto de Recursos Naturales y Agrobiologia, CSIC, P O Box 1052, 41080 Sevilla, Spain
    Extremophiles 9:75-9. 2005
    ..The method proves to be an easy, rapid, and inexpensive alternative to estimate DNA-DNA relatedness between closely related species...
  27. ncbi Sex-dependent gene expression and evolution of the Drosophila transcriptome
    Jose M Ranz
    Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
    Science 300:1742-5. 2003
    ..Our results suggest that sex-dependent selection may drive changes in expression of many of the most rapidly evolving genes in the Drosophila transcriptome...
  28. ncbi Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer
    Anna Bergamaschi
    Department of Genetics, Institute for Cancer Research, Rikshospitalet Radiumhospitalet Medical Center, Oslo, Norway
    Genes Chromosomes Cancer 45:1033-40. 2006
    ..This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat..
  29. pmc Progressive genetic aberrations detected by comparative genomic hybridization in squamous cell cervical cancer
    D G Allen
    Departments of Gynaecological Oncology, Pathology, Mercy Hospital for Women, East Melbourne, Victoria, 3002, Australia
    Br J Cancer 83:1659-63. 2000
    ..The study identifies progressive DNA copy number changes associated with early-stage invasive cervical cancers with and without lymph node metastases, a factor of potential prognostic and therapeutic value...
  30. ncbi High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays
    D Pinkel
    Cancer Genetics Program, UCSF Cancer Center, University of California San Francisco, 94143 0808, USA
    Nat Genet 20:207-11. 1998
    ..We demonstrate its ability to measure copy number with high precision in the human genome, and to analyse clinical specimens by obtaining new information on chromosome 20 aberrations in breast cancer...
  31. pmc Intercalating nucleic acids containing insertions of 1-O-(1-pyrenylmethyl)glycerol: stabilisation of dsDNA and discrimination of DNA over RNA
    Ulf B Christensen
    Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, DK 5230 Odense M, Denmark
    Nucleic Acids Res 30:4918-25. 2002
    ..Fluorescence measurements show a stronger interaction of the pyrene moiety with DNA than with RNA, indicating intercalation as the stabilising factor in DNA/INA duplexes...
  32. pmc A multiplex PCR predictor for aCGH success of FFPE samples
    E H van Beers
    Division of Experimental Therapy, Netherlands Cancer Institute NKI AvL, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands
    Br J Cancer 94:333-7. 2006
    ....
  33. pmc Analysis of microarray data using Z score transformation
    Chris Cheadle
    DNA Array Unit, Research Resources Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21221, USA
    J Mol Diagn 5:73-81. 2003
    ..The results provided by these methods can be as rigorous and are no more arbitrary than other test methods, and, in addition, they have the advantage that they can be easily adapted to standard spreadsheet programs...
  34. pmc Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process
    Emily M LeProust
    Agilent Technologies Inc, LSSU Genomics, 5301 Stevens Creek Blvd, Santa Clara, CA 95051, USA
    Nucleic Acids Res 38:2522-40. 2010
    ..g. targeted resequencing, preparation of shRNA libraries, site-directed mutagenesis), and have the potential to enable even more novel applications (e.g. high-complexity synthetic biology)...
  35. pmc Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing
    Andreas Gnirke
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nat Biotechnol 27:182-9. 2009
    ..One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space...
  36. ncbi Direct selection of human genomic loci by microarray hybridization
    Thomas J Albert
    NimbleGen Systems Inc, 1 Science Court, Madison, Wisconsin 53711, USA
    Nat Methods 4:903-5. 2007
    ..These direct selection methods supersede multiplex PCR for the large-scale analysis of genomic regions...
  37. ncbi 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...
  38. ncbi DNA nanotweezers studied with a coarse-grained model of DNA
    Thomas E Ouldridge
    Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford, OX1 3NP, United Kingdom
    Phys Rev Lett 104:178101. 2010
    ..We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA "tweezers," a simple machine driven by hybridization and strand displacement...
  39. pmc Cross-species hybridization of microarrays for studying tumor transcriptome of brain metastasis
    Eun Sung Park
    Department of Systems Biology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 108:17456-61. 2011
    ..These observations provide proof of principle for competitive cross-species hybridization of microarray experiments to characterize the effect of the microenvironment on tumor cell behavior...
  40. ncbi Recurrent 200-kb deletions of 16p11.2 that include the SH2B1 gene are associated with developmental delay and obesity
    Ruxandra Bachmann-Gagescu
    Division of Genetic Medicine, Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
    Genet Med 12:641-7. 2010
    ..The purpose of this study was to better define the phenotype of this recurrent SH2B1-containing microdeletion in a cohort of phenotypically abnormal patients not selected for obesity...
  41. ncbi Electrochemical detection of microRNAs via gap hybridization assay
    Christopher Pöhlmann
    Laboratorium fur Biochemie, Universitat Bayreuth, Universitatsstrasse 30, 95440 Bayreuth, Germany
    Anal Chem 82:4434-40. 2010
    ..The characteristics of the assay developed in this work could satisfy the need for rapid and easy methods for early cancer marker detection in clinical diagnostics...
  42. ncbi Array-based electrical detection of DNA with nanoparticle probes
    So Jung Park
    Department of Chemistry and Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA
    Science 295:1503-6. 2002
    ..Using this method, we have detected target DNA at concentrations as low as 500 femtomolar with a point mutation selectivity factor of approximately 100,000:1...
  43. ncbi Remote toehold: a mechanism for flexible control of DNA hybridization kinetics
    Anthony J Genot
    Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
    J Am Chem Soc 133:2177-82. 2011
    ..We apply this mechanism to operate displacement reactions in potentially useful kinetic regimes: the kinetic proofreading and concentration-robust regimes...
  44. ncbi Rapid and sensitive detection of infectious hypodermal and hematopoietic necrosis virus by loop-mediated isothermal amplification combined with a lateral flow dipstick
    Narong Arunrut
    National Center for Genetic Engineering and Biotechnology BIOTEC, National Science and Technology Development Agency, Pathumthani, Thailand
    J Virol Methods 171:21-5. 2011
    ....
  45. pmc Accurate and reliable high-throughput detection of copy number variation in the human genome
    Heike Fiegler
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
    Genome Res 16:1566-74. 2006
    ..Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method...
  46. pmc Salt concentration effects on equilibrium melting curves from DNA microarrays
    J Fuchs
    Structure et Propriétés d Architectures Moleculaires UMR 5819, Commissariat à l Énergie Atomique et aux Énergies Alternatives, Centre National de la Recherche Scientifique, Universite Joseph Fourier, and Institute for Nanoscience and Cryogenics, Grenoble, France
    Biophys J 99:1886-95. 2010
    ..Various salt concentrations have been considered and deviations from the commonly used Langmuir adsorption model are experimentally quantified for the first time in agreement with theoretical predictions...
  47. ncbi Identification of genes upregulated by pinewood nematode inoculation in Japanese red pine
    Hanna Shin
    Department of Forest Genetic Resources, Korea Forest Research Institute, Suwon 441 350, Korea
    Tree Physiol 29:411-21. 2009
    ..Our report provides fundamental information on the molecular mechanisms controlling the biochemical and physiological responses of Japanese red pine trees to PWN invasion...
  48. ncbi DNA surface hybridization: comparison of theory and experiment
    Damion Irving
    Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, Brooklyn, New York 11201, USA
    J Phys Chem B 114:7631-40. 2010
    ..By delineating conditions under which specific hybridization behaviors are observed, the results advance fundamental knowledge in support of DNA microarray and biosensor applications...
  49. pmc Chromosomal amplifications, 3q gain and deletions of 2q33-q37 are the frequent genetic changes in cervical carcinoma
    Pulivarthi H Rao
    Texas Children s Cancer Center, Baylor College of Medicine, Houston, TX, USA
    BMC Cancer 4:5. 2004
    ..Therefore, genetic characterization is essential for understanding the biology and clinical heterogeneity in cervical cancer (CC)...
  50. ncbi Microarray-based genomic selection for high-throughput resequencing
    David T Okou
    Department of Human Genetics, Emory University School of Medicine, 615 Michael Street, Suite 301, Atlanta, Georgia 30322, USA
    Nat Methods 4:907-9. 2007
    ..MGS, when combined with a next-generation resequencing technology, can enable large-scale resequencing in single-investigator laboratories...
  51. pmc DINAMelt web server for nucleic acid melting prediction
    Nicholas R Markham
    Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY 12180 3590, USA
    Nucleic Acids Res 33:W577-81. 2005
    ..This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is http://www.bioinfo.rpi.edu/applications/hybrid/...
  52. pmc Identifying differentially methylated genes using mixed effect and generalized least square models
    Shuying Sun
    Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio 44106, USA
    BMC Bioinformatics 10:404. 2009
    ..However, patient samples or cell lines are heterogeneous, so their methylation pattern may be very different. In addition, neighboring probes at each CGI are correlated. How these factors affect the analysis of DMH data is unknown...
  53. pmc Whole genome analysis of genetic alterations in small DNA samples using hyperbranched strand displacement amplification and array-CGH
    José M Lage
    Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
    Genome Res 13:294-307. 2003
    ..Gene-dosage alterations of threefold or more can be observed with high reproducibility with as few as 1000 cells of starting material...
  54. 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
    ....
  55. pmc Colorectal cancer genomics: evidence for multiple genotypes which influence survival
    P H Rooney
    Department of Medicine and Therapeutics, University of Aberdeen, Foresterhill, AB25 2ZD, Aberdeen
    Br J Cancer 85:1492-8. 2001
    ..Although genomic change in CRC is relevant to the survival of patients with Dukes' C CRC, careful analysis is required to identify cell lines which are representative models of CRC genomics...
  56. ncbi The RAB25 small GTPase determines aggressiveness of ovarian and breast cancers
    Kwai Wa Cheng
    Department of Molecular Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas 77054, USA
    Nat Med 10:1251-6. 2004
    ..Overall, these studies implicate RAB25, and thus the RAB family of small G proteins, in aggressiveness of epithelial cancers...
  57. pmc Microarray karyotyping of commercial wine yeast strains reveals shared, as well as unique, genomic signatures
    Barbara Dunn
    Dept of Genetics, Stanford University Medical Ctr, Stanford, CA 94305 5120, USA
    BMC Genomics 6:53. 2005
    ..To investigate this, we have determined genomic differences among several Saccharomyces cerevisiae wine strains by using a "microarray karyotyping" (also known as "array-CGH" or "aCGH") technique...
  58. ncbi OLIGO 7 primer analysis software
    Wojciech Rychlik
    Molecular Biology Insights, Inc, Cascade, CO, USA
    Methods Mol Biol 402:35-60. 2007
    ..OLIGO allows for sequence file batch processing that is essential for automation. This chapter describes the major functions of OLIGO version 7 software...
  59. pmc A fluorescence in situ hybridization system for karyotyping soybean
    Seth D Findley
    Division of Plant Sciences, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri 65211, USA
    Genetics 185:727-44. 2010
    ..The data confirm that this translocation is widespread in G. soja accessions and likely accounts for the semi-sterility found in some G. soja by G. max crosses...
  60. pmc Hybrid selection for sequencing pathogen genomes from clinical samples
    Alexandre Melnikov
    Genome Sequencing and Analysis Program, Broad Institute, Cambridge, MA 02142, USA
    Genome Biol 12:R73. 2011
    ..This approach will enable efficient genome sequencing of pathogens from clinical samples, as well as sequencing of endosymbiotic organisms such as Wolbachia that live inside diverse metazoan phyla...
  61. pmc Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA
    Chunhai Fan
    Institute for Polymers and Organic Solids, University of California, Santa Barbara, CA 93106, USA
    Proc Natl Acad Sci U S A 100:9134-7. 2003
    ..The E-DNA sensor thus offers the promise of convenient, reusable detection of picomolar DNA...
  62. ncbi Acinetobacter ursingii sp. nov. and Acinetobacter schindleri sp. nov., isolated from human clinical specimens
    A Nemec
    National Institute of Public Health, Prague, Czech Republic
    Int J Syst Evol Microbiol 51:1891-9. 2001
    ..Clinical and epidemiological data indicate that A. ursingii has the capacity to cause bloodstream infections in hospitalized patients...
  63. ncbi Tissue-wide expression profiling using cDNA subtraction and microarrays to identify tumor-specific genes
    Stefan Amatschek
    Department of Dermatology, University of Vienna, Vienna, Austria
    Cancer Res 64:844-56. 2004
    ..The gene dendogram clearly separates two groups of genes, those up-regulated such as cyclin B1, TGF-beta 3, B-Myb, Erg2, VCAM-1, and CD44 and those down-regulated such as MIG-6, Esp15, and CAK in patients with short survival time...
  64. pmc Specificity of microRNA target selection in translational repression
    John G Doench
    Center for Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
    Genes Dev 18:504-11. 2004
    ..Thus, predicted miRNA:mRNA interactions must be viewed in the context of other potential interactions and cellular conditions...
  65. pmc Efficient and cost effective population resequencing by pooling and in-solution hybridization
    Vikas Bansal
    Scripps Genomic Medicine, Scripps Translational Science Institute, La Jolla, California, United States of America
    PLoS ONE 6:e18353. 2011
    ..6% of variants below 5% in frequency. Finally, allele frequencies for single nucleotide variants (SNVs) estimated from the pooled data and the HapMap genotype data were tightly correlated (correlation coefficient >  =  0.995)...
  66. pmc Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast
    P James
    Department of Biomolecular Chemistry, University of Wisconsin, Madison 53706, USA
    Genetics 144:1425-36. 1996
    ..Our analysis indicates that the libraries and host strain provide significant improvements in both the number of interacting clones identified and the efficiency of two-hybrid selections...
  67. pmc Comparative isoschizomer profiling of cytosine methylation: the HELP assay
    Batbayar Khulan
    Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
    Genome Res 16:1046-55. 2006
    ..The HELP assay is robust, quantitative, and accurate and is providing new insights into the distribution and dynamic nature of cytosine methylation in the genome...
  68. ncbi Synthesis of cell-permeable peptide nucleic acids and characterization of their hybridization and uptake properties
    Peng Zhou
    Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA
    Bioorg Med Chem Lett 16:4931-5. 2006
    ..Thermal denaturation study showed that GPNA oligomers containing alternate D-backbone configuration bind sequence-specifically to DNA and, when incubated with mammalian cells, localized specifically to the endoplasmic reticulum (ER)...
  69. ncbi Oocyte karyotyping by comparative genomic hybridization [correction of hybrydization] provides a highly reliable method for selecting "competent" embryos, markedly improving in vitro fertilization outcome: a multiphase study
    Geoffrey Sher
    Sher Institute for Reproductive Medicine, Las Vegas, Nevada 89109, USA
    Fertil Steril 87:1033-40. 2007
    ....
  70. ncbi Evolutionary origin and emergence of a highly successful clone of serotype M1 group a Streptococcus involved multiple horizontal gene transfer events
    Paul Sumby
    Laboratory of Human Bacterial Pathogenesis, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
    J Infect Dis 192:771-82. 2005
    ..Multiple horizontal gene transfer events were a crucial factor in the evolutionary origin and emergence of a very abundant contemporary clone of serotype M1 GAS...
  71. ncbi Methods for genomic partitioning
    Emily H Turner
    Department of Genome Sciences, University of Washington, Seattle, Washington 98195 5065, USA
    Annu Rev Genomics Hum Genet 10:263-84. 2009
    ..The successful development of genomic partitioning strategies will be key to taking full advantage of massively parallel sequencing, at least until resequencing of complete mammalian genomes becomes widely affordable...
  72. ncbi Real-time multiplex PCR assays
    C T Wittwer
    Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84132, USA
    Methods 25:430-42. 2001
    ..Instead of physical separation along the X and Y axes, amplification products are identified by different fluorescence spectra and melting characteristics...
  73. ncbi Molecular basis for target RNA recognition and cleavage by human RISC
    Stefan Ludwig Ameres
    Max F Perutz Laboratories, University of Vienna, Vienna, Austria
    Cell 130:101-12. 2007
    ..We therefore provide mechanistic insights by revealing features of RISC and target RNAs that are crucial to achieve efficiency and specificity in RNA interference...
  74. ncbi Guidelines for molecular karyotyping in constitutional genetic diagnosis
    Joris Robert Vermeesch
    Center for Human Genetics, University Hospital Gasthuisberg, Leuven, Belgium
    Eur J Hum Genet 15:1105-14. 2007
    ..Internal and external quality control programmes are urgently needed to evaluate and standardise the test results between laboratories...
  75. pmc The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNA
    Toby J Soper
    Program in Cellular, Molecular, Developmental Biology and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218 2685, USA
    RNA 14:1907-17. 2008
    ..Once base-pairing between DsrA and rpoS mRNA is established, interactions between Hfq and the mRNA may stabilize the RNA complex by removing Hfq from the sRNA...
  76. ncbi Comparative genomic hybridization of cancer of the gastroesophageal junction: deletion of 14Q31-32.1 discriminates between esophageal (Barrett's) and gastric cardia adenocarcinomas
    H van Dekken
    Department of Pathology, University Hospital Rotterdam, Erasmus University, The Netherlands
    Cancer Res 59:748-52. 1999
    ..Second, genetic divergence was revealed in this poorly understood group of cancers...
  77. ncbi Duplication of the MYB oncogene in T cell acute lymphoblastic leukemia
    Idoya Lahortiga
    Human Genome Laboratory, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie VIB, Leuven, Belgium
    Nat Genet 39:593-5. 2007
    ..Our results identify duplication of MYB as an oncogenic event and suggest that MYB could be a therapeutic target in human T-ALL...
  78. ncbi Novel genomic aberrations in testicular germ cell tumors by array-CGH, and associated gene expression changes
    Rolf I Skotheim
    Department of Cancer Prevention, Institute for Cancer Research, Rikshospitalet Radiumhospitalet Medical Center, Oslo, Norway
    Cell Oncol 28:315-26. 2006
    ..Testicular germ cell tumors of adolescent and young adult men (TGCTs) generally have near triploid and complex karyotypes. The actual genes driving the tumorigenesis remain essentially to be identified...
  79. ncbi MicroRNAs and other tiny endogenous RNAs in C. elegans
    Victor Ambros
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Curr Biol 13:807-18. 2003
    ..We employed cDNA sequencing and comparative genomics to identify additional C. elegans small RNAs with properties similar to miRNAs and siRNAs...
  80. pmc Triggered amplification by hybridization chain reaction
    Robert M Dirks
    Department of Chemistry, California Institute of Technology, Pasadena, CA 91125, USA
    Proc Natl Acad Sci U S A 101:15275-8. 2004
    ..Amplification of more diverse recognition events can be achieved by coupling HCR to aptamer triggers. This functionality allows DNA to act as an amplifying transducer for biosensing applications...
  81. ncbi Genetic differences detected by comparative genomic hybridization in head and neck squamous cell carcinomas from different tumor sites: construction of oncogenetic trees for tumor progression
    Qiang Huang
    Department of Otolaryngology, The New York Eye and Ear Infirmary, New York Medical College, New York, New York 10003, USA
    Genes Chromosomes Cancer 34:224-33. 2002
    ..These results suggest that different chromosomal aberrations may play a role in the initiation and/or progression of different subgroups of HNSCC...
  82. ncbi A male accessory gland peptide that regulates reproductive behavior of female D. melanogaster
    P S Chen
    Institute of Zoology, University of Zurich, Switzerland
    Cell 54:291-8. 1988
    ..The precursor peptide is encoded by a short mRNA that accumulates exclusively in the male accessory gland. The gene has been localized by in situ hybridization to polytene chromosomes at 70A...
  83. ncbi Simpleaffy: a BioConductor package for Affymetrix Quality Control and data analysis
    Claire L Wilson
    Paterson Institute for Cancer Research, Manchester M20 4BX, UK
    Bioinformatics 21:3683-5. 2005
    ..Simpleaffy also offers fast implementations of popular algorithms for generating expression summaries and detection calls...
  84. pmc Knowledge-based analysis of microarray gene expression data by using support vector machines
    M P Brown
    Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
    Proc Natl Acad Sci U S A 97:262-7. 2000
    ..Finally, we use SVMs to predict functional roles for uncharacterized yeast ORFs based on their expression data...
  85. pmc Monitoring the expression pattern of 1300 Arabidopsis genes under drought and cold stresses by using a full-length cDNA microarray
    M Seki
    Plant Mutation Exploration Team, Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 3 1 1 Koyadai, Tsukuba 305 0074, Japan
    Plant Cell 13:61-72. 2001
    ....
  86. ncbi Phenotypic characterization of endometrial stromal sarcoma of the uterus
    Kazumi Yamada
    Department of Pathology, Institute of Basic Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, 1 1 1 Tennodai, Tsukuba shi, Ibaraki 305 8575, Japan
    Cancer Sci 97:106-12. 2006
    ....
  87. ncbi Interlaboratory comparability study of cancer gene expression analysis using oligonucleotide microarrays
    Kevin K Dobbin
    Cancer Diagnosis Program, National Cancer Institute NIH, Bethesda, MD 20894, USA
    Clin Cancer Res 11:565-72. 2005
    ..The findings indicate that under properly controlled conditions it is feasible to perform complete tumor microarray analysis, from tissue processing to hybridization and scanning, at multiple independent laboratories for a single study...
  88. ncbi Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov
    M Drancourt
    Laboratoire de Bacteriologie, Hĵpital de la Timone, Marseille, France
    Int J Syst Evol Microbiol 51:925-32. 2001
    ..The name Raoultella is proposed as a genus name for species of cluster II and emended definitions of Klebsiella species are proposed...
  89. pmc Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles
    Huixiang Li
    Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
    Proc Natl Acad Sci U S A 101:14036-9. 2004
    ..The assay is complete within 5 min, and <100 femtomoles of target produces color changes observable without instrumentation. Single-base-pair mismatches are easily detected...
  90. ncbi Comprehensive molecular cytogenetic characterization of cervical cancer cell lines
    Charles P Harris
    Laboratory of Molecular Cytogenetics, Texas Children s Cancer Center, Baylor College of Medicine, Houston, Texas 77030, USA
    Genes Chromosomes Cancer 36:233-41. 2003
    ..This comprehensive cytogenetic characterization of eight CC cell lines enhances their utility in experimental studies aimed at gene discovery and functional analysis...
  91. ncbi Genetic aberrations defined by comparative genomic hybridization distinguish long-term from typical survivors of glioblastoma
    Eric C Burton
    Department of Neurological Surgery, University of California, San Francisco 94143, USA
    Cancer Res 62:6205-10. 2002
    ..Loss of 19q may be a marker of long-term survival...
  92. pmc Molecular systematics, GISH and the origin of hybrid taxa in Nicotiana (Solanaceae)
    Mark W Chase
    Molecular Systematics Section, Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK
    Ann Bot 92:107-27. 2003
    ....
  93. ncbi Comparative genomic hybridization array analysis and real time PCR reveals genomic alterations in squamous cell carcinomas of the lung
    Yong Woo Choi
    Department of Anesthesiology, St Mary s Hospital, The Catholic University, Seoul, South Korea
    Lung Cancer 55:43-51. 2007
    ..Our results show that array CGH is a useful tool for identification of gene alteration in lung cancer, and that the above-mentioned genes might represent potential candidate genes for pathogenesis and diagnosis of lung cancer...
  94. ncbi Comparative genomics of BCG vaccines by whole-genome DNA microarray
    M A Behr
    Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
    Science 284:1520-3. 1999
    ..A precise understanding of the genetic differences between closely related Mycobacteria suggests rational approaches to the design of improved diagnostics and vaccines...
  95. ncbi Multiplex amplification of large sets of human exons
    Gregory J Porreca
    Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts 02115, USA
    Nat Methods 4:931-6. 2007
    ..We anticipate that highly multiplexed methods for targeted amplification will enable the comprehensive resequencing of human exons at a fraction of the cost of whole-genome resequencing...
  96. ncbi Array comparative genomic hybridization analysis of genomic alterations in breast cancer subtypes
    Lenora W M Loo
    Division of Human Biology, Division of Public Health Sciences, and Genomics Shared Resource, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Cancer Res 64:8541-9. 2004
    ..These results indicate that array comparative genomic hybridization can identify significant differences in the genomic alterations between subtypes of breast cancer...
  97. pmc Relationships of nontypeable Haemophilus influenzae strains to hemolytic and nonhemolytic Haemophilus haemolyticus strains
    Kirk W McCrea
    Department of Epidemiology, University of Michigan School of Public Health Tower, 109 Observatory, Ann Arbor, MI 48109 2029, USA
    J Clin Microbiol 46:406-16. 2008
    ..Future comparative genomic studies identifying common and distinctive genes could be useful in evaluating their role in the commensal or virulent growth, respectively, of H. influenzae...
  98. ncbi 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...
  99. ncbi DNA-templated assembly and electrode attachment of a conducting silver wire
    E Braun
    Department of Physics, Technion Israel Institute of Technology, Haifa
    Nature 391:775-8. 1998
    ..The experiment confirms that the recognition capabilities of DNA can be exploited for the targeted attachment of functional wires...
  100. 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...
  101. ncbi Sequence-specific recognition of DNA oligomer using peptide nucleic acid (PNA)-modified synthetic ion channels: PNA/DNA hybridization in nanoconfined environment
    Mubarak Ali
    Technische Universität Darmstadt, Fachbereich Material u Geowissenschaften, Fachgebiet Materialanalytik, Petersenstrasse 23, D 64287 Darmstadt, Germany
    ACS Nano 4:7267-74. 2010
    ..In this context, we envision that the single conical nanochannels functionalized with a PNA probe will provide a biosensing platform for the detection and discrimination of short single-stranded DNA oligomer of unknown sequence...

Research Grants62

  1. NEUROVIROLOGY-MOLECULAR BIOLOGY
    Donald Gilden; Fiscal Year: 2013
    ..The disciplines currently being used are protein purification and nucleic acid hybridization, molecular genetics, production and characterization of cDNA libraries, DNA sequencing, molecular ..
  2. Bio-imaging with Isothermal DNA Self-Assembly
    David Yu Zhang; Fiscal Year: 2013
    ..The mechanism for ensuring high specificity nucleic acid hybridization has been demonstrated across a variety of temperatures and salinities, and a typical single-base change ..
  3. Bio-imaging with Isothermal DNA Self-Assembly
    David Yu Zhang; Fiscal Year: 2013
    ..The mechanism for ensuring high specificity nucleic acid hybridization has been demonstrated across a variety of temperatures and salinities, and a typical single-base change ..
  4. Water Soluble Nanoarrays for Single Cell Proteomics
    Hao Yan; Fiscal Year: 2013
    ..and also nucleic acid sequences, individual aptamers can bind to a unique position on the array through nucleic acid hybridization and require no printing or lithography...
  5. STUDIES OF NEURONAL AND GLIAL GLUTAMATE DECARBOXYLASES
    Jang Yen Wu; Fiscal Year: 1990
    ..We also plan to use (H3)cDNA probes to localize specific mRNA for GAD in situ by nucleic acid hybridization and GAD by immunocytochemistry...
  6. REGULATION AND FUNCTION OF SPARC IN MALE REPRODUCTION
    Robert Vernon; Fiscal Year: 1991
    ..prepubertal and adult testes, and mature sperm will be determined by immunocytochemistry and in situ nucleic acid hybridization at light and electron microscopic levels...
  7. Rapid Screening of Nucleic Acid Energetics
    GEORGE ERIC PLUM; Fiscal Year: 2010
    ..have presented new and compelling means and objectives to exploit the exquisite specificity of nucleic acid hybridization. Precise knowledge of the temperature dependent stability of nucleic acid (and nucleic acid analog) ..
  8. LATENCY AND LEUKOMOGENICITY OF BOVINE LEUKEMIA VIRUS
    Gary Cockerell; Fiscal Year: 1991
    ..Southern and northern nucleic acid hybridization techniques will be used to detect BLV proviral DNA, and the transcriptional activity of viral and ..
  9. Modified nucleotide cofactors and the interaction of the RNAome with the proteome
    GARY B RUVKUN; Fiscal Year: 2013
    ..We propose to use powerful nucleic acid hybridization and selection techniques to purify the proteins covalently linked to RNA and to use mass spectroscopy to ..
  10. RETROVIRAL ETIOLOGY OF PRIMARY BILIARY CIRRHOSIS
    Andrew Mason; Fiscal Year: 2002
    ..by co-culture with infected hepatic tissue; (3) Assess the prevalence of retroviral infection in PBC patients and controls by nucleic acid hybridization techniques and western blot experiments of recombinant or purified viral proteins.
  11. FUNCTION OF CLATHRIN-COATED MEMBRANES
    Randy Schekman; Fiscal Year: 1990
    ..Structural analogues of clathrin will be sought using sensitive nucleic acid hybridization procedures and by examining alternative associations formed with clathrin light chain in heavy chain ..
  12. MULTI-ANALYTE WAVEGUIDE IMMUNOSENSING
    JAMES HERRON; Fiscal Year: 2002
    ..In particular, the applicants plan to develop nucleic acid hybridization assays (also know as "molecular diagnostics" or "MDx" assays) for use in screening and diagnosis of ..
  13. HORMONAL CONTROL OF UTERINE MUSCLE K-CHANNEL MRNA
    Mary Boyle; Fiscal Year: 1992
    ..expression of the mRNA species encoding the slow K+ channel will be characterized using nucleic acid hybridization methods...
  14. MOLECULAR EVENTS IN BLAST CRISIS OF CML
    Martin Cline; Fiscal Year: 1993
    ..Utilizing nucleic acid hybridization, cytogenetic and immunoblotting techniques, correlations will be sought between structural alterations ..
  15. HIV INFECTION OF NEURAL TISSUE--AN ORGANOTYPIC MODEL
    William Lyman; Fiscal Year: 1991
    ..its genome, or parts thereof, may be incorporated into host cell DNA, Southern Blot analysis and in situ nucleic acid hybridization will be used to examine this point...
  16. Nanowire DNA hybridization sensor
    R Daniels; Fiscal Year: 2004
    ..enabled sensor described in this proposal will be capable of highly selective and sensitive detection of nucleic acid hybridization in an array based format without the need for sample labeling or amplification...
  17. MULTI PARAMETER ANALYSIS OF MRNA LEVELS IN LUNG TISSUE
    Michael Hogan; Fiscal Year: 2001
    This Program Project will develop a novel set of integrated nucleic acid hybridization technologies: oligonucleotide, surface and dye chemistry, fluidic methods for high speed microarry fabrication, a new microarry format for ..
  18. MONOCYTE HIV 1 INFECTION AND NEUROLOGICAL FUNCTION
    ROGER ROSSEN; Fiscal Year: 1993
    ..RNA will also be analyzed by nucleic acid hybridization and the polymerase chain reaction (PCR) will be applied to DNA extracts of these cells to amplify and ..
  19. COMPLEMENTATION ASSAY FOR FUNCTIONAL GENOMICS
    PYARE KHANNA; Fiscal Year: 2001
    ..detection of nucleases; which can be used for drug discovery of nuclease inhibitors and for detection of nucleic acid hybridization. This method uses complementation of inactive enzyme fragments of E...
  20. INFECTIOUS ETIOLOGY OF CONNECTIVE TISSUE DISEASES
    Charles Smith; Fiscal Year: 1980
    ..Another technique is the use of radiolabelled viral nucleic acid probes in nucleic acid hybridization studies with DNA extracted from SLE or RA tissues...
  21. HUMAN CDNAS/GENES FOR IMMUNOSUPPRESSANT BINDING PROTEINS
    ARLENE SEMERJIAN; Fiscal Year: 1993
    ..The aims of this work draw strongly upon techniques of nucleic acid hybridization, DNA sequencing and PCR analysis and are to (i) search for additional classes of human FKBP transcripts, ..
  22. High through-put detection of fungal pathogens
    JACK FELL; Fiscal Year: 2004
    ..The detection method will combine the specificity and reliability of nucleic acid hybridization analysis with the speed and sensitivity of LabMap, a new flow cytometric technique by Luminex Corp...
  23. QUANTITATIVE WAY TO DETECT NUCLEIC ACID HYBRIDS
    NEWTON FAWCETT; Fiscal Year: 1991
    The technique of nucleic acid hybridization, in which target and probe strands of DNA or RNA are duplexed as a means of identifying the target, has the potential to become one of the most widely used ways of identifying pathogenic virus ..
  24. REGULATION OF NEURO-HORMONE RECEPTORS
    Stuart Sealfon; Fiscal Year: 1992
    ..Cloned probes will further the investigation of receptor regulation. In situ nucleic acid hybridization and S1 nuclease assay studies of pituitary AVP and CRF receptor modulation will be performed...
  25. ORGANIZATION OF ANIMAL CELL NUCLEI
    Joseph Gall; Fiscal Year: 1999
    ..Studies will also be conducted on the transcription of the 5S gene sequences on LBCs by in situ nucleic acid hybridization. Finally studies will be carried out on a novel selfcleaving RNA transcribed from a short, repeated ..
  26. DETECTION OF HYBRIDIZATION WITHOUT RADIOACTIVE LABEL
    Qiang Li; Fiscal Year: 1993
    A novel surface phenomenon will be explored for the quantitative detection of nucleic acid hybridization. We will construct a relatively inexpensive instrument, which can attain a sensitivity limit comparable to the existing methodologies,..
  27. EFFECT OF CYTOMEGALOVIRUS ON EMBRYONIC DEVELOPMENT
    JOHN BASKAR; Fiscal Year: 1990
    ..microscopy, conventional histopathology and many other techniques, such as cocultivation assays, nucleic acid hybridization, indirect immunoflurorescence assays and transmission electron microscopy...
  28. INPUT/OUTPUT ANALYSIS OF CELLULAR CIRCADIAN RHYTHMS
    Carl Johnson; Fiscal Year: 1992
    ..For example, rhythmic proteins and mRNAs will be assayed by electrophoresis and nucleic acid hybridization. "Second messenger" output will be assayed by microelectrode recording, calcium-sensitive photoproteins, ..
  29. Rapid NAT System for Point-of-care SARS Diagnosis
    Zihua Wang; Fiscal Year: 2004
    ..Viral RNA isolation using silica magneti6 beads or nucleic acid hybridization methodologies will be integrated into the lab-in-a-tube testing platform...
  30. STRUCTURE AND DIFFERENTIATION OF IMMUNOGLOBULIN GENES
    Janet Stavnezer; Fiscal Year: 1980
    ..Specifically, I plan to continue my studies using nucleic acid hybridization to determine the number of genes for the variable regions of immunoglobulin kappa chain in the mouse in ..
  31. MEMBRANE SUBSTRUCTURE AND CELL DIVISION IN E. COLI
    Kevin Young; Fiscal Year: 1992
    ..of penicillin-binding proteins; genetic characterization using the X174 lysis protein E; and nucleic acid hybridization to detect DNA- vesicle associations, using oriC and mini-F plasmids as experimental probes...
  32. Chemiluminescent Labeling and Detection in Gels
    Hashem Akhavan Tafti; Fiscal Year: 2002
    ..labeled polypeptide and nucleic acid size markers, 2D protein analysis, electrophoretic mobility shift analysis of transcriptional factors, nucleic acid hybridization assays and analysis of gene expression levels.
  33. MOLECULAR PROFILES OF SMALL CELL LUNG CARCINOMA ANTIGENS
    John Harper; Fiscal Year: 1991
    ..clones isolated by immunostaining of phage plaques will be used to screen an Okayama-Berg library by nucleic acid hybridization. From the cDNA clones, RNA will be transcribed in vitro, by way of transcription vector system, that ..
  34. Flow-Chamber Hybridization Rate Enhancement for Distributed Viral Load Measuremen
    DANIEL LASER; Fiscal Year: 2007
    ..thermal cycling and minimally susceptible to contamination, the branched DNA (bDNA) HIV RNA sandwich nucleic acid hybridization/signal amplification assay is a good candidate for viral load measurement in resource-limited settings...
  35. DEVELOPMENT OF HIGH-SPEED NUCLEIC ACID HYBRIDIZATION
    Matthew Winkler; Fiscal Year: 1993
    b>Nucleic acid hybridization reactions are at the heart of a number of powerful assays used in molecular biology research and increasingly in diagnostic applications. Hybridization reactions typically require long incubation times, i.e...
  36. HIGHLY SENSITIVE RAPID NUCLEIC ACID HYBRIDIZATION
    DAVID KOHNE; Fiscal Year: 1980
    ..develop rapid, specific, extremely sensitive methods for the detection and analysis of nucleic acids by nucleic acid hybridization. This will involve a major effort to develop and refine two recently discovered rapid nucleic acid ..
  37. ACCESSORY CELL ACTIVATION IN THE IMMUNE RESPONSE
    PHILIP AURON; Fiscal Year: 1993
    ..of the monocyte response to chemical and biological induction agents using antibodies and nucleic acid hybridization probes along with subcellular fractionation, in order to determine the events involved in monocyte ..
  38. Amersham Biosciences Typhoon 9410
    Herbert Samuels; Fiscal Year: 2006
    ..only provide improved fluorimetric measurements but also will enable quantitative imaging of Western and nucleic acid hybridization blots labeled with fluorescent probes, replace X-ray film for detection of blots using enhanced ..
  39. B LYMPHOCYTE ACTIVATION
    Subbarao Bondada; Fiscal Year: 1992
    ..be determined by quantitating the expression of the murine heavy chain variable region gene families by nucleic acid hybridization techniques...
  40. PARVOVIRUS INFECTION
    Robert Jacoby; Fiscal Year: 1991
    ..These studies will require a variety of techniques including: virus re-isolation and quantification., nucleic acid hybridization in vitro and in situ, serology and immunohistochemistry.
  41. Metagenomic analysis of the human virome
    Eric L Delwart; Fiscal Year: 2010
    ..in vitro and the limitations of traditional methods requiring antigenic/serological cross-reactivity or nucleic acid hybridization. We postulate, based on our recent study of viral capsid-protected nucleic acids in symptomatic humans, ..
  42. Rapid Screening of Nucleic Acid Energetics
    GEORGE PLUM; Fiscal Year: 2006
    ..have presented new and compelling means and objectives to exploit the exquisite specificity of nucleic acid hybridization. Precise knowledge of the temperature dependent stability of nucleic acid (and nucleic acid analog) ..
  43. Fluorescent Polymer Nanoparticle Gene Expression System
    LAWRENCE HANCOCK; Fiscal Year: 2004
    ..proposes to use amplifying fluorescent polymer (AFP) nanoparticles to improve the sensitivity of nucleic acid hybridization assays by up to 5 orders of magnitude...
  44. Polymer Amplified Nucleic Acid Detection
    LAWRENCE HANCOCK; Fiscal Year: 2003
    ..Combining this inherent signal amplification with the unique specificity exhibited by nucleic acid hybridization events will enable a new generation of solid-state, nucleic acid sensors that do not rely on target ..
  45. RECEPTOR INDUCED ACTIVATION IN LYMPHOID CELLS
    David Shapiro; Fiscal Year: 1991
    ..These objectives will be accomplished by the techniques of differential nucleic acid hybridization in order to isolate genes that are transcriptionally active as a result of antigen receptor-induced ..
  46. PHOTOCHEMICAL MODIFICATION OF HYBRIDIZATION MEMBRANES
    LISE DURAN; Fiscal Year: 1992
    ..It is proposed to apply this technology to modify the surface of membranes used in nucleic acid hybridization assays...
  47. Identification and characterization of the ALS4 gene
    PHILLIP CHANCE; Fiscal Year: 2006
    ..genetic approaches and to determine the expression pattern of the ALS4 gene and the ALS protein by nucleic acid hybridization and immunohistochemical methods using specific probes and/or antibodies...
  48. PATHOBIOLOGICAL DETERMINANTS OF ATHEROSCLEROSIS IN YOUTH
    ABEL ROBERTSON; Fiscal Year: 1992
    ..3) detection of viral antigens at lesion sites by immunohistological methods as well as in situ nucleic acid hybridization technology will be used to evaluate the potential role of viruses and/or their genomes known to produce ..
  49. PROCESS FOR CLONING DIFFERENTIALLY EXPRESSED GENES
    ROBERT MIERENDORF; Fiscal Year: 1992
    ..I studies will focus on steps in the process that currently limit the widespread use of substractive nucleic acid hybridization as a means of isolating the target genes...
  50. Three Periodontal Therapies in Current & Non-Smokers
    Anne Haffajee; Fiscal Year: 2007
    ..The proposed investigation should provide a model to examine methods that could be useful in treating compromised patients whether compromised by harmful habits such as smoking, systemic disease, or genetic background. ..
  51. EFFECT OF ANTIBIOTICS ON ORAL BIOFILMS IN VIVO
    Anne Haffajee; Fiscal Year: 2001
    ..abstract_text> ..
  52. MICROBIAL ASSOCIATIONS IN PERIODONTAL HEALTH AND DISEASE
    Anne Haffajee; Fiscal Year: 2006
    ..These data will provide a basis for understanding microbial community structure, ecological relationships and define desired microbiological end-point of therapy. ..
  53. Identification of Uncultivated and Unrecognized Pathogens of Periodontitis
    ANNE DENISE HAFFAJEE; Fiscal Year: 2010
    ..The identification of such pathogens should, over time, lead to better diagnosis of disease, optimal treatment strategies for the individual patient, new therapeutic approaches and carefully targeted approaches to prevention. ..
  54. NATURAL CORRECTION OF GENE DEFICIENCIES
    AGNES HARFORD; Fiscal Year: 1980
    ..A combination of genetic and biochemical approaches are envisioned. Techniques to be used include sucrose gradient sedimentation, gel electrophoresis, nucleic acid hybridization, fluorescence, and specific enzyme digestion.
  55. Intrabody Therapy in Drosophila for Huntington's Disease
    WILLIAM WOLFGANG; Fiscal Year: 2006
    ..If successful this will provide validation of intrabodies as disease therapeutics and impetus to proceed to preclinical testing in vertebrate models of HD. ..
  56. DNA-Silver Cluster Complexes for Fluorescent Diagnostics
    JEFFREY PETTY; Fiscal Year: 2008
    ..Their favorable photostability, bright fluorescence, and distinctive spectra indicate the promise of this new class of fluorescence labels. [unreadable] [unreadable] [unreadable]..
  57. The Effect of Water on Sequence Specific DNA Recognition
    JEFFREY PETTY; Fiscal Year: 2004
    ..These studies determine the involvement of water exchange in the mechanism, thus complementing the thermodynamic studies. ..
  58. The Role of Mitochondrial DNA Alterations in Cancer
    Lee Jun Wong; Fiscal Year: 2008
    ..Results from this research project will help us understand the functional role of mitochondrial DNA alterations in cancer and identify potential novel targets for more effective therapeutic development. ..
  59. Computational Statistic Approaches to Gene-Environment Interaction
    SEBASTIAN ZOELLNER; Fiscal Year: 2009
    ..We intend to use this dataset as well as simulated datasets and other GWA datasets to evaluate and calibrate our methods for estimating genotype-phenotype interaction and for planning replication studies. (End of Abstract) ..