oligonucleotides

Summary

Summary: Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)

Top Publications

  1. ncbi Silencing of microRNAs in vivo with 'antagomirs'
    Jan Krutzfeldt
    Laboratory of Metabolic Diseases, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 438:685-9. 2005
  2. ncbi LNA-mediated microRNA silencing in non-human primates
    Joacim Elmen
    Santaris Pharma, Bøge Allé 3, DK 2970 Hørsholm, Denmark
    Nature 452:896-9. 2008
  3. pmc Silencing of microRNA families by seed-targeting tiny LNAs
    Susanna Obad
    Santaris Pharma, Hørsholm, Denmark
    Nat Genet 43:371-8. 2011
  4. pmc Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver
    Joacim Elmen
    Santaris Pharma, Bøge Allé 3, DK 2970 Hørsholm, Denmark
    Nucleic Acids Res 36:1153-62. 2008
  5. pmc OligoCalc: an online oligonucleotide properties calculator
    Warren A Kibbe
    Robert H Lurie Comprehensive Cancer Center, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    Nucleic Acids Res 35:W43-6. 2007
  6. ncbi Local dystrophin restoration with antisense oligonucleotide PRO051
    Judith C van Deutekom
    Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    N Engl J Med 357:2677-86. 2007
  7. pmc RMI, a new OB-fold complex essential for Bloom syndrome protein to maintain genome stability
    Dongyi Xu
    Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, USA
    Genes Dev 22:2843-55. 2008
  8. ncbi Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides
    Jiang Li
    Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
    ACS Nano 5:8783-9. 2011
  9. ncbi Protein detection using proximity-dependent DNA ligation assays
    Simon Fredriksson
    The Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, SE 75185 Uppsala, Sweden
    Nat Biotechnol 20:473-7. 2002
  10. ncbi Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial
    Frederick J Raal
    Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
    Lancet 375:998-1006. 2010

Detail Information

Publications372 found, 100 shown here

  1. ncbi Silencing of microRNAs in vivo with 'antagomirs'
    Jan Krutzfeldt
    Laboratory of Metabolic Diseases, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA
    Nature 438:685-9. 2005
    ..Here we show that a novel class of chemically engineered oligonucleotides, termed 'antagomirs', are efficient and specific silencers of endogenous miRNAs in mice...
  2. ncbi LNA-mediated microRNA silencing in non-human primates
    Joacim Elmen
    Santaris Pharma, Bøge Allé 3, DK 2970 Hørsholm, Denmark
    Nature 452:896-9. 2008
    ....
  3. pmc Silencing of microRNA families by seed-targeting tiny LNAs
    Susanna Obad
    Santaris Pharma, Hørsholm, Denmark
    Nat Genet 43:371-8. 2011
    ..a method that enables antagonism of miRNA function using seed-targeting 8-mer locked nucleic acid (LNA) oligonucleotides, termed tiny LNAs...
  4. pmc Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver
    Joacim Elmen
    Santaris Pharma, Bøge Allé 3, DK 2970 Hørsholm, Denmark
    Nucleic Acids Res 36:1153-62. 2008
    ....
  5. pmc OligoCalc: an online oligonucleotide properties calculator
    Warren A Kibbe
    Robert H Lurie Comprehensive Cancer Center, The Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
    Nucleic Acids Res 35:W43-6. 2007
    ..OligoCalc is available at http://basic.northwestern.edu/biotools/OligoCalc.html, with links to the full source code, usage patterns and statistics at that link as well...
  6. ncbi Local dystrophin restoration with antisense oligonucleotide PRO051
    Judith C van Deutekom
    Department of Human and Clinical Genetics, Leiden University Medical Center, The Netherlands
    N Engl J Med 357:2677-86. 2007
    ..We explored the safety, adverse-event profile, and local dystrophin-restoring effect of a single, intramuscular dose of an antisense oligonucleotide, PRO051, in patients with this disease...
  7. pmc RMI, a new OB-fold complex essential for Bloom syndrome protein to maintain genome stability
    Dongyi Xu
    Laboratory of Genetics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, Maryland 21224, USA
    Genes Dev 22:2843-55. 2008
    ..Our data suggest that multi-OB-fold complexes mediate two modes of BLM action: via RPA-mediated protein-DNA interaction, and via RMI-mediated protein-protein interactions...
  8. ncbi Self-assembled multivalent DNA nanostructures for noninvasive intracellular delivery of immunostimulatory CpG oligonucleotides
    Jiang Li
    Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
    ACS Nano 5:8783-9. 2011
    Designed oligonucleotides can self-assemble into DNA nanostructures with well-defined structures and uniform sizes, which provide unprecedented opportunities for biosensing, molecular imaging, and drug delivery...
  9. ncbi Protein detection using proximity-dependent DNA ligation assays
    Simon Fredriksson
    The Beijer Laboratory, Department of Genetics and Pathology, Rudbeck Laboratory, SE 75185 Uppsala, Sweden
    Nat Biotechnol 20:473-7. 2002
    ..in which the coordinated and proximal binding of a target protein by two DNA aptamers promotes ligation of oligonucleotides linked to each aptamer affinity probe...
  10. ncbi Mipomersen, an apolipoprotein B synthesis inhibitor, for lowering of LDL cholesterol concentrations in patients with homozygous familial hypercholesterolaemia: a randomised, double-blind, placebo-controlled trial
    Frederick J Raal
    Department of Medicine, University of the Witwatersrand, Johannesburg, South Africa
    Lancet 375:998-1006. 2010
    ..This study investigated whether an antisense inhibitor of apolipoprotein B synthesis, mipomersen, is effective and safe as an adjunctive agent to lower LDL cholesterol concentrations in patients with this disease...
  11. ncbi Passenger-strand cleavage facilitates assembly of siRNA into Ago2-containing RNAi enzyme complexes
    Christian Matranga
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
    Cell 123:607-20. 2005
    ..For siRNAs, virtually all RISC is assembled through this cleavage-assisted mechanism. In contrast, passenger-strand cleavage is not important for the incorporation of miRNAs that derive from mismatched duplexes...
  12. pmc Synthesis of DNA fragments in yeast by one-step assembly of overlapping oligonucleotides
    Daniel G Gibson
    The J Craig Venter Institute, Synthetic Biology Group, 9704 Medical Center Drive, Rockville, MD 20850, USA
    Nucleic Acids Res 37:6984-90. 2009
    ..that the yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event...
  13. ncbi LNA: a versatile tool for therapeutics and genomics
    Michael Petersen
    Nucleic Acid Center, Dept of Chemistry, University of Southern Denmark, DK 5230 Odense M, Denmark
    Trends Biotechnol 21:74-81. 2003
    ..Furthermore, convincing examples of the application of LNA to nucleic acid diagnostics have been reported, including high capturing efficiencies and unambiguous scoring of single-nucleotide polymorphisms...
  14. pmc Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering
    James A Sawitzke
    Molecular Control and Genetics Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    J Mol Biol 407:45-59. 2011
    Recombination with single-strand DNA oligonucleotides (oligos) in Escherichia coli is an efficient and rapid way to modify replicons in vivo...
  15. ncbi Improved synthesis and mutagenicity of oligonucleotides containing 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine
    Martin Münzel
    Center for Integrated Protein Science CiPSM at the Department of Chemistry, Ludwig Maximilians University, Butenandtstr 5 13, 81377 Munich, Germany
    Chemistry 17:13782-8. 2011
    ..Using a newly designed in vitro mutagenicity assay we show that fC and caC are only marginally mutagenic, which is a prerequisite for the bases to function as epigenetic control units...
  16. pmc Local restoration of dystrophin expression with the morpholino oligomer AVI-4658 in Duchenne muscular dystrophy: a single-blind, placebo-controlled, dose-escalation, proof-of-concept study
    Maria Kinali
    The Dubowitz Neuromuscular Centre, University College London Institute of Child Health London, London, UK
    Lancet Neurol 8:918-28. 2009
    ..b>Oligonucleotides targeted to splicing elements (splice switching oligonucleotides) in DMD pre-mRNA can lead to exon skipping, ..
  17. pmc BLAP18/RMI2, a novel OB-fold-containing protein, is an essential component of the Bloom helicase-double Holliday junction dissolvasome
    Thiyam Ramsing Singh
    Division of Experimental Hematology and Cancer Biology, Cincinnati Children s Research Foundation, University of Cincinnati College of Medicine, Cincinnati, Ohio 45229, USA
    Genes Dev 22:2856-68. 2008
    ..Finally, BLAP18/RMI2 stimulates the dHJ resolution capability of the BTB complex. Together, these results establish BLAP18/RMI2 as an essential member of the BTB dHJ dissolvasome that is required for the maintenance of a stable genome...
  18. pmc Cellular uptake and intracellular trafficking of antisense and siRNA oligonucleotides
    Rudolph L Juliano
    Division of Molecular Pharmaceutics, UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina 27599, USA
    Bioconjug Chem 23:147-57. 2012
    Significant progress is being made concerning the development of oligonucleotides as therapeutic agents...
  19. ncbi Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections
    Gregor Obernosterer
    Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Dr Bohr Gasse 3, 1030 Vienna, Austria
    Nat Protoc 2:1508-14. 2007
    ..Setting up and conducting the in situ experiment is estimated to take approximately 1 week, assuming that all the component parts are readily available...
  20. 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...
  21. ncbi Site-specific characterization of HIV-1 nucleocapsid protein binding to oligonucleotides with two binding sites
    Sergiy V Avilov
    Laboratoire Biophotonique et Pharmacologie, UMR 7213 CNRS, Universite de Strasbourg, Faculte de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
    Biochemistry 48:2422-30. 2009
    ..of 2Ap by its close neighbors and slowing the picosecond to nanosecond conformational fluctuations of the oligonucleotides. The dodecanucleotides were found to bind two NC molecules at physiological salt concentrations, confirming ..
  22. ncbi In vivo site-directed mutagenesis using oligonucleotides
    F Storici
    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, P.O. Box 12233, Research Triangle Park, NC 27709, USA
    Nat Biotechnol 19:773-6. 2001
    ..b>Oligonucleotides, when combined with gap repair, have also been used to modify plasmids in yeast; however, this approach is ..
  23. pmc Polymerase mu is a DNA-directed DNA/RNA polymerase
    Stephanie A Nick McElhinny
    Department of Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
    Mol Cell Biol 23:2309-15. 2003
    ....
  24. ncbi A RNA antagonist of hypoxia-inducible factor-1alpha, EZN-2968, inhibits tumor cell growth
    Lee M Greenberger
    Enzon Pharmaceuticals Inc, 20 Kingsbridge Road, Piscataway, NJ 08854, USA
    Mol Cancer Ther 7:3598-608. 2008
    ..Ongoing phase I studies of EZN-2968 in patients with advanced malignancies will determine optimal dose and schedule for the phase II program...
  25. pmc Efficient gene silencing by delivery of locked nucleic acid antisense oligonucleotides, unassisted by transfection reagents
    C A Stein
    Albert Einstein Montefiore Cancer Center, Montefiore Medical Center, Bronx, NY 10467, USA
    Nucleic Acids Res 38:e3. 2010
    ..In addition, gymnotic delivery can efficiently deliver oligonucleotides to suspension cells that are known to be very difficult to transfect...
  26. pmc Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion
    Harris H Wang
    Wyss Institute for Biologically Inspired Engineering, Harvard University, Department of Genetics, Harvard Medical School, Harvard University, Boston, MA 02115, USA
    Nucleic Acids Res 39:7336-47. 2011
    Genome engineering using single-stranded oligonucleotides is an efficient method for generating small chromosomal and episomal modifications in a variety of host organisms...
  27. ncbi Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification
    Asli N Silahtaroglu
    Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK 2200 Copenhagen N, Denmark
    Nat Protoc 2:2520-8. 2007
    ....
  28. ncbi The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast
    Francesca Storici
    Laboratory of Molecular Genetics, Chromosome Stability Section, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, USA
    Methods Enzymol 409:329-45. 2006
    ..Here we describe our approach, referred to as delitto perfetto, that combines the versatility of synthetic oligonucleotides for targeting with the practicality of a general selection system...
  29. ncbi Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides
    Joseph R Warner
    Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado, USA
    Nat Biotechnol 28:856-62. 2010
    ..This approach can be applied to a broad range of traits to identify targets for future genome-engineering endeavors...
  30. ncbi The Dnmt1 DNA-(cytosine-C5)-methyltransferase methylates DNA processively with high preference for hemimethylated target sites
    Andrea Hermann
    Institut fur Biochemie, FB 08, Heinrich Buff Ring 58, Justus Liebig Universitat Giessen, 35392 Giessen, Germany
    J Biol Chem 279:48350-9. 2004
    ....
  31. ncbi Chemical modification and design of anti-miRNA oligonucleotides
    K A Lennox
    Molecular Genetics and Biophysics, Integrated DNA Technologies, Coralville, IA 52241, USA
    Gene Ther 18:1111-20. 2011
    ..Antisense techniques that employ synthetic oligonucleotides have been used to study miRNA function and some of these compounds may have potential as novel drug ..
  32. pmc G4-DNA formation in the HRAS promoter and rational design of decoy oligonucleotides for cancer therapy
    Alexandro Membrino
    Department of Medical and Biological Science, School of Medicine, Udine, Italy
    PLoS ONE 6:e24421. 2011
    ..Finally, we designed decoy oligonucleotides mimicking the HRAS quadruplexes, bearing (R)-1-O-[4-(1-Pyrenylethynyl) phenylmethyl] glycerol and LNA ..
  33. pmc Oligonucleotide recombination in Gram-negative bacteria
    Bryan Swingle
    United States Department of Agriculture Agricultural Research Service, Ithaca, NY 14853, USA
    Mol Microbiol 75:138-48. 2010
    ..We found that synthetic single-stranded DNA oligonucleotides (oligos) introduced into bacteria by transformation can site-specifically recombine with bacterial ..
  34. ncbi Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering
    Harris H Wang
    Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
    Methods Enzymol 498:409-26. 2011
    ..Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the ..
  35. pmc Short locked nucleic acid antisense oligonucleotides potently reduce apolipoprotein B mRNA and serum cholesterol in mice and non-human primates
    Ellen Marie Straarup
    Santaris Pharma A S, Kogle Alle 6, DK 2970 Hørsholm, Denmark
    Nucleic Acids Res 38:7100-11. 2010
    The potency and specificity of locked nucleic acid (LNA) antisense oligonucleotides was investigated as a function of length and affinity...
  36. pmc The triple helix: 50 years later, the outcome
    Maria Duca
    LCMBA CNRS UMR6001, University of Nice Sophia Antipolis, Parc Valrose, 06108 Nice Cedex 2, France
    Nucleic Acids Res 36:5123-38. 2008
    Triplex-forming oligonucleotides constitute an interesting DNA sequence-specific tool that can be used to target cleaving or cross-linking agents, transcription factors or nucleases to a chosen site on the DNA...
  37. pmc Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore
    David Stoddart
    Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
    Proc Natl Acad Sci U S A 106:7702-7. 2009
    ..The additional steps required to enable nanopore DNA sequencing are outlined...
  38. pmc Improved silencing properties using small internally segmented interfering RNAs
    Jesper B Bramsen
    Department of Molecular Biology, University of Aarhus, DK 8000, Aarhus C, Denmark
    Nucleic Acids Res 35:5886-97. 2007
    ..This suggests that the sisiRNA design has a clear potential of improving the pharmacokinetic properties of siRNA in vivo...
  39. ncbi Tetramolecular DNA quadruplexes in solution: insights into structural diversity and cation movement
    Primoz Sket
    Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI 1000 Ljubljana, Slovenia
    J Am Chem Soc 132:12724-32. 2010
    ..However, cation movement is slowed by the presence of a T-quartet at the 5' end...
  40. ncbi Reduction of CpG-induced arthritis by suppressive oligodeoxynucleotides
    Rainald A Zeuner
    Center for Biologics Evaluation and Research, FDA, Bethesda, Maryland, and Christian Albrechts University Kiel, Kiel, Germany
    Arthritis Rheum 46:2219-24. 2002
    ..We examined whether synthetic oligodeoxynucleotides (ODN) that suppress CpG-induced immune responses prevent CpG-induced arthritis...
  41. ncbi Effect of mipomersen, an apolipoprotein B synthesis inhibitor, on low-density lipoprotein cholesterol in patients with familial hypercholesterolemia
    Fatima Akdim
    Department of Vascular Medicine, Academic Medical Center Amsterdam, Amsterdam, The Netherlands
    Am J Cardiol 105:1413-9. 2010
    ..In conclusion, mipomersen has an incremental LDL cholesterol lowering effect when added to conventional lipid-lowering therapy...
  42. 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
    We have achieved the ability to synthesize thousands of unique, long oligonucleotides (150mers) in fmol amounts using parallel synthesis of DNA on microarrays...
  43. ncbi Cell penetrating peptides: overview and applications to the delivery of oligonucleotides
    F Said Hassane
    UMR 5235 CNRS, Dynamique des Interactions Membranaires Normales et Pathologiques, Universite Montpellier 2, 34095, Montpellier Cedex 5, France
    Cell Mol Life Sci 67:715-26. 2010
    ..Encouraging data with CPP-conjugated oligonucleotides have been obtained both in vitro and in vivo in animal models of diseases such as Duchenne muscular dystrophy...
  44. ncbi Small change in a G-rich sequence, a dramatic change in topology: new dimeric G-quadruplex folding motif with unique loop orientations
    Martin Crnugelj
    NMR Center, National Institute of Chemistry, Hajdrihova 19, SI 1000 Ljubljana, Slovenia
    J Am Chem Soc 125:7866-71. 2003
    ..Further examination of the influence of different monovalent cations on the folding of d(G(3)T(4)G(4)) showed that it forms a bimolecular G-quadruplex in the presence of K+, Na+, and NH4+ ions with the same general fold...
  45. 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...
  46. ncbi Use of internally nuclease-protected single-strand DNA oligonucleotides and silencing of the mismatch repair protein, MSH2, enhances the replication of corrected cells following gene editing
    Ioannis Papaioannou
    Department of Medicine, Royal Free and University College Medical School, Royal Free Campus, London, UK
    J Gene Med 11:267-74. 2009
    ..is potentially a powerful technology for introducing genetic changes by using short single-stranded DNA oligonucleotides (ssODNs)...
  47. ncbi Pro-metastatic splicing of Ron proto-oncogene mRNA can be reversed: therapeutic potential of bifunctional oligonucleotides and indole derivatives
    Claudia Ghigna
    Istituto di Genetica Molecolare Consiglio Nazionale delle Ricerche IGM CNR, Pavia, Italy
    RNA Biol 7:495-503. 2010
    ..Notably, indole derivatives are also able to affect the invasive phenotype of the cells. Thus, these treatments may have therapeutic applications for anti-cancer purposes...
  48. ncbi Protein displacement by an assembly of helicase molecules aligned along single-stranded DNA
    Alicia K Byrd
    Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, Arkansas 72205, USA
    Nat Struct Mol Biol 11:531-8. 2004
    ..T4 Dda helicase can displace proteins bound to DNA, including streptavidin bound to biotinylated oligonucleotides. We investigated the mechanism of streptavidin displacement by varying the length of the oligonucleotide ..
  49. pmc Design of LNA probes that improve mismatch discrimination
    Yong You
    Integrated DNA Technologies, 1710 Commercial Park, Coralville, IA 52241, USA
    Nucleic Acids Res 34:e60. 2006
    ..New guidelines are suggested for design of LNA probes, which significantly improve mismatch discrimination in comparison with unmodified DNA probes...
  50. pmc Nucleic acids of mammalian origin can act as endogenous ligands for Toll-like receptors and may promote systemic lupus erythematosus
    Franck J Barrat
    Dynavax Technologies Corporation, Berkeley, CA 94710, USA
    J Exp Med 202:1131-9. 2005
    ..These inhibitors of TLR signaling thus represent novel therapeutic agents with potential for the treatment of lupus...
  51. ncbi Thermodynamic and biological evaluation of a thrombin binding aptamer modified with several unlocked nucleic acid (UNA) monomers and a 2'-C-piperazino-UNA monomer
    Troels B Jensen
    Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
    Bioorg Med Chem 19:4739-45. 2011
    ..Most of the studied variants bind thrombin, albeit with decreased affinity in reference to unmodified TBA. Thrombin time assay studies indicate three variants as being as potent as TBA in fibrin clotting inhibition...
  52. ncbi Deoxyribozyme-based three-input logic gates and construction of a molecular full adder
    Harvey Lederman
    Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Box 84, 630 West 168th Street, New York, New York 10032, USA
    Biochemistry 45:1194-9. 2006
    ..seven deoxyribozyme-based molecular logic gates that behaves as a full adder in a single solution, with three oligonucleotides as inputs and two independent fluorogenic cleavage reactions as carry and sum outputs...
  53. ncbi Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals
    Meghan A Campbell
    Nucleic Acid Center, Institute for Physics and Chemistry, University of Southern Denmark, Odense, Denmark
    Chem Soc Rev 40:5680-9. 2011
    ..of these oligonucleotide technologies has the potential to become a new type of therapy to treat a wide variety of diseases, and LNA and UNA will no doubt play a part in future developments of therapeutic and diagnostic oligonucleotides.
  54. ncbi Development of multiple W/O/W emulsions as dermal carrier system for oligonucleotides: effect of additives on emulsion stability
    T Schmidts
    Institute of Biopharmaceutical Technology, University of Applied Sciences Giessen Friedberg, 35390 Giessen, Germany
    Int J Pharm 398:107-13. 2010
    ..W/O/W) emulsions are of major interest as potential skin delivery systems for water-soluble drugs like oligonucleotides due to their distinct encapsulation properties...
  55. pmc T-oligos inhibit growth and induce apoptosis in human ovarian cancer cells
    Sibaji Sarkar
    Cancer Center, Boston University School of Medicine, Boston, Massachusetts, USA
    Oligonucleotides 21:47-53. 2011
    ..b>Oligonucleotides with sequence homology to telomeres (called T-oligos) have been shown to mimic DNA damage responses in cells ..
  56. pmc Anti-tumor activity of splice-switching oligonucleotides
    John A Bauman
    Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
    Nucleic Acids Res 38:8348-56. 2010
    Alternative splicing has emerged as an important target for molecular therapies. Splice-switching oligonucleotides (SSOs) modulate alternative splicing by hybridizing to pre-mRNA sequences involved in splicing and blocking access to the ..
  57. pmc Chemically programmed cell adhesion with membrane-anchored oligonucleotides
    Nicholas S Selden
    Department of Pharmaceutical Chemistry, University of California, San Francisco, 600 16th Street Box 2280, San Francisco, California 94158, USA
    J Am Chem Soc 134:765-8. 2012
    ..we describe a strategy for chemically controlling cell adhesion using membrane-anchored single-stranded DNA oligonucleotides. The reagents are pure chemical species prepared from phosphoramidites synthesized in a single chemical step ..
  58. ncbi Toll-like receptor 9 agonist IMO cooperates with cetuximab in K-ras mutant colorectal and pancreatic cancers
    Roberta Rosa
    Dipartmento di Endocrinologia ed Oncologia Molecolare e Clinica, Universita di Napoli Federico II, Naples, Italy
    Clin Cancer Res 17:6531-41. 2011
    ....
  59. ncbi Taking control of gene expression with light-activated oligonucleotides
    Ivan J Dmochowski
    Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
    Biotechniques 43:161, 163, 165 passim. 2007
    ..Indeed, caged oligonucleotides make it possible to control many different protein-oligonucleotide interactions...
  60. ncbi Detecting RNA and DNA with templated chemical reactions
    Adam P Silverman
    Department of Chemistry, Stanford University, Stanford, California 94305, USA
    Chem Rev 106:3775-89. 2006
  61. ncbi Circular dichroism and guanine quadruplexes
    Michaela Vorlíčková
    Institute of Biophysics, Academy of Sciences of the Czech Republic, v v i, Kralovopolska 135, CZ 612 65 Brno, Czech Republic
    Methods 57:64-75. 2012
    ..This article aims to show that CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies...
  62. ncbi MicroRNA detection by northern blotting using locked nucleic acid probes
    Eva Várallyay
    Agricultural Biotechnology Center, Plant Virology Group, Szent Gyorgyi Albert ut 4, Gödöllõ H 2100, Hungary
    Nat Protoc 3:190-6. 2008
    ..Using this approach, the hybridization, washing and signal-detection steps can be performed ideally in 4 h...
  63. ncbi Selective release of multiple DNA oligonucleotides from gold nanorods
    Andy Wijaya
    Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
    ACS Nano 3:80-6. 2009
    ..Here we demonstrate that we can load and selectively release two different DNA oligonucleotides from two different gold nanorods. DNA was loaded on the nanorods via thiol conjugation...
  64. pmc BLM helicase measures DNA unwound before switching strands and hRPA promotes unwinding reinitiation
    Jaya G Yodh
    Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    EMBO J 28:405-16. 2009
    ..The reported activities may facilitate BLM processing of stalled replication forks and illegitimately formed recombination intermediates...
  65. ncbi Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing
    Mitsuoki Kawano
    RIKEN Omics Science Center, Yokohama, Japan
    Biotechniques 49:751-5. 2010
    ..This method improves the sequencing yield and efficiency, while simplifying library construction, and makes it easier to perform large-scale small RNA analysis under multiple conditions with next-generation sequencers...
  66. ncbi Crystal structures of Λ-[Ru(phen)₂dppz]²⁺ with oligonucleotides containing TA/TA and AT/AT steps show two intercalation modes
    Hakan Niyazi
    Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
    Nat Chem 4:621-8. 2012
    ..The TA/TA specificity of the perpendicular intercalation arises from the packing of phenanthroline ligands against the adenosine residue...
  67. ncbi Apolipoprotein B synthesis inhibition: results from clinical trials
    Maartje E Visser
    Department of Vascular Medicine, Academic Medical Center Amsterdam, The Netherlands
    Curr Opin Lipidol 21:319-23. 2010
    ..In this review we will summarize the results of recent preclinical and clinical studies addressing safety and low-density lipoprotein-cholesterol (LDL-c) lowering efficacy of this new compound...
  68. pmc Drosophila lacking microRNA miR-278 are defective in energy homeostasis
    Aurelio A Teleman
    European Molecular Biology Laboratory, 69117 Heidelberg, Germany
    Genes Dev 20:417-22. 2006
    ..We provide evidence that miR-278 mutants are insulin resistant and that miR-278 acts through regulation of the expanded transcript...
  69. pmc Phosphorothioate oligonucleotides reduce PrP levels and prion infectivity in cultured cells
    Marcela V Karpuj
    Institute for Neurodegenerative Diseases and Department of Neurology, University of California, San Francisco, CA 94143 0518, USA
    Mol Med 13:190-8. 2007
    ..Here we report that short phosphorothioate DNA (PS-DNA) oligonucleotides diminished the levels of both PrPC and PrPSc in prion-infected neuroblastoma (ScN2a) cells...
  70. ncbi Efficacy of apolipoprotein B synthesis inhibition in subjects with mild-to-moderate hyperlipidaemia
    Fatima Akdim
    Department of Vascular Medicine, Academic Medical Center Amsterdam, Meibergdreef 9, PO Box 22660, 1100 DD, Amsterdam, The Netherlands
    Eur Heart J 32:2650-9. 2011
    ..A randomized, double-blind, placebo-controlled, dose-escalation study was designed to evaluate the efficacy and safety of mipomersen monotherapy with or without dose loading in subjects with mild-to-moderate hyperlipidaemia...
  71. ncbi Triplex formation with alpha-L-LNA (alpha-L-ribo-configured locked nucleic acid)
    Niti Kumar
    Nucleic Acid Center, Department of Chemistry, University of Southern Denmark, 5230 Odense M, Denmark
    J Am Chem Soc 128:14-5. 2006
    Using UV melting and CD spectroscopy, we show that alpha-l-LNA-modified oligonucleotides possess the ability to form triplexes at pH 6.8 with significantly increased thermostability relative to DNA triplexes.
  72. pmc Regulation of transcription through light-activation and light-deactivation of triplex-forming oligonucleotides in mammalian cells
    Jeane M Govan
    Department of Chemistry, North Carolina State University, Raleigh, 27695, United States
    ACS Chem Biol 7:1247-56. 2012
    Triplex-forming oligonucleotides (TFOs) are efficient tools to regulate gene expression through the inhibition of transcription...
  73. pmc Mipomersen, an apolipoprotein B synthesis inhibitor, lowers low-density lipoprotein cholesterol in high-risk statin-intolerant patients: a randomized, double-blind, placebo-controlled trial
    Maartje E Visser
    Department of Vascular Medicine, Academic Medical Center, Amsterdam, The Netherlands
    Eur Heart J 33:1142-9. 2012
    ....
  74. pmc Ctp1 and the MRN-complex are required for endonucleolytic Rec12 removal with release of a single class of oligonucleotides in fission yeast
    Maja Rothenberg
    Institute of Cell Biology, University of Bern, Switzerland
    PLoS Genet 5:e1000722. 2009
    ..In fission yeast, we found only one class of oligonucleotides bound to Rec12 ranging in length from 17 to 27 nucleotides...
  75. pmc High-quality gene assembly directly from unpurified mixtures of microarray-synthesized oligonucleotides
    Alex Y Borovkov
    Center for Innovations in Medicine of the Biodesign Institute at the Arizona State University, Tempe, AZ 85287, USA
    Nucleic Acids Res 38:e180. 2010
    ..a protocol for high-quality gene assembly directly from low-cost marginal-quality microarray-synthesized oligonucleotides. Significantly, we eliminated the time- and money-consuming oligonucleotide purification steps through the ..
  76. ncbi Locked nucleic acid as a novel class of therapeutic agents
    Rakesh N Veedu
    Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, Odense, Denmark
    RNA Biol 6:321-3. 2009
    ..acid analogue with unprecedented binding affinity and excellent specificity toward complementary RNA and DNA oligonucleotides. The remarkable properties of LNA have led to applications within various gene silencing strategies both in ..
  77. pmc Allele-selective inhibition of mutant huntingtin by peptide nucleic acid-peptide conjugates, locked nucleic acid, and small interfering RNA
    Jiaxin Hu
    Department of Pharmacology and Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390 9041, USA
    Ann N Y Acad Sci 1175:24-31. 2009
    ..Our data suggest that antisense oligomers are promising subjects for further development as an anti-HD therapeutic strategy...
  78. ncbi Genome-wide in situ exon capture for selective resequencing
    Emily Hodges
    Howard Hughes Medical Institute, Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
    Nat Genet 39:1522-7. 2007
    ..This methodology provides an adaptable route toward rapid and efficient resequencing of any sizeable, non-repeat portion of the human genome...
  79. pmc BTA, a novel reagent for DNA attachment on glass and efficient generation of solid-phase amplified DNA colonies
    Milan Fedurco
    Manteia Predictive Medicine S A Zone Industrielle Coinsins, CH 1267, Switzerland
    Nucleic Acids Res 34:e22. 2006
    ..We have characterized the derivatized surfaces for the chemical attachment of oligonucleotides and evaluate the properties relevant for the amplification process: surface density, thermal stability ..
  80. pmc Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array
    Bin Wang
    Department of Mathematics and Statistics, University of South Alabama College of Arts and Sciences, Mobile, Alabama, United States of America
    PLoS ONE 6:e17167. 2011
    ..In this study, we systematically analyze three representative microRNA profiling platforms: Locked Nucleic Acid (LNA) microarray, beads array, and TaqMan quantitative real-time PCR Low Density Array (TLDA)...
  81. pmc Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids
    Erik B Pedersen
    Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, 5230 Odense, Denmark
    Nucleic Acids Res 39:2470-81. 2011
    ..the first time a detailed analysis of the effect the incorporation of INA/TINA monomers in quadruplex forming oligonucleotides (QFOs) and the effect of LNA monomers in the context of biologically active QFOs...
  82. ncbi Aptamers: an emerging class of molecules that rival antibodies in diagnostics
    S D Jayasena
    NeXstar Pharmaceuticals, Inc, 2860 Wilderness Place, Boulder, CO 80301, USA
    Clin Chem 45:1628-50. 1999
    ..It is also likely that existing diagnostic formats may change according to the need to better harness the unique properties of aptamers...
  83. ncbi Multiplexed protein detection by proximity ligation for cancer biomarker validation
    Simon Fredriksson
    Stanford Genome Technology Center, Stanford, California 94305, USA
    Nat Methods 4:327-9. 2007
    ..The procedure can use a single polyclonal antibody batch for each target protein, simplifying affinity-reagent creation for new biomarker candidates...
  84. ncbi Identification of novel argonaute-associated proteins
    Gunter Meister
    Laboratory of RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, Box 186, New York, New York 10021, USA
    Curr Biol 15:2149-55. 2005
    ..The new proteins localize, similar to Ago proteins, to mRNA-degrading cytoplasmic P bodies, and they are functionally required to mediate miRNA-guided mRNA cleavage...
  85. pmc Evaluation of spoligotyping in a study of the transmission of Mycobacterium tuberculosis
    Y O Goguet de la Salmonière
    Unite de Genetique Mycobacterienne, Institut Pasteur, Paris, France
    J Clin Microbiol 35:2210-4. 1997
    ..IS6I10-RFLP analysis split some of the spoligotyping clusters, particularly when the IS6110 copy number was high. Therefore, we propose a strategy for typing M. tuberculosis strains in which both markers are used...
  86. ncbi Deoxyribozyme-based logic gates
    Milan N Stojanovic
    Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, New York 10032, USA
    J Am Chem Soc 124:3555-61. 2002
    ..Importantly, as the gates have oligonucleotides as both inputs and output, they open the possibility of communication between various computation elements in ..
  87. ncbi Click chemistry with DNA
    Afaf H El-Sagheer
    School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
    Chem Soc Rev 39:1388-405. 2010
    ..It has been used to label oligonucleotides with fluorescent dyes, sugars, peptides and other reporter groups, to cyclise DNA, to synthesise DNA ..
  88. pmc Stabilization of expanded (CTG)•(CAG) repeats by antisense oligonucleotides
    Masayuki Nakamori
    Department of Neurology, University of Rochester Medical Center, Rochester, New York, USA
    Mol Ther 19:2222-7. 2011
    ..This RNA dominant mechanism is amenable to therapeutic intervention with antisense oligonucleotides (ASOs)...
  89. pmc Oligodeoxynucleotides lacking CpG dinucleotides mediate Toll-like receptor 9 dependent T helper type 2 biased immune stimulation
    Jorg Vollmer
    Coley Pharmaceutical, Langenfeld, Germany
    Immunology 113:212-23. 2004
    ..Our study indicates that TLR9 can mediate either efficient Th1- or Th2-dominated effects depending on whether it is stimulated by CpG or certain non-CpG ODN...
  90. pmc Delineation of the high-affinity single-stranded telomeric DNA-binding domain of Saccharomyces cerevisiae Cdc13
    Emily M Anderson
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, UCB 215, Boulder, CO 80309 0215, USA
    Nucleic Acids Res 30:4305-13. 2002
    ..The full-length protein exhibited the same rate of dissociation as both domains, however, indicating that the full-length protein contains a region that inhibits association with single-stranded telomeric DNA...
  91. pmc Kinetic analysis of the nucleic acid chaperone activity of the hepatitis C virus core protein
    Kamal Kant Sharma
    Laboratorie de Biophotonique et Pharmacologie, UMR 7213 CNRS, Faculte de Pharmacie, Universite de Strasbourg, 74, route du Rhin, 67401, Illkirch, Cedex, France
    Nucleic Acids Res 38:3632-42. 2010
    ..The three peptides operate similarly, confirming that the core chaperone properties are mostly supported by its basic clusters...
  92. ncbi Deoxyribozyme-based ligase logic gates and their initial circuits
    Milan N Stojanovic
    Division of Clinical Pharmacology and Experimental Therapeutics, Department of Medicine, Columbia University, Box 84, 630 West 168th Street, New York, NY 10032, USA
    J Am Chem Soc 127:6914-5. 2005
    ..The activity of these gates was visualized through the formation of cascades with downstream phosphodieseterase YES gates, which performed fluorogenic cleavage...
  93. ncbi Folding of the thrombin aptamer into a G-quadruplex with Sr(2+): stability, heat, and hydration
    B I Kankia
    Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
    J Am Chem Soc 123:10799-804. 2001
    ....
  94. ncbi Efficient and persistent splice switching by systemically delivered LNA oligonucleotides in mice
    Jennifer Roberts
    Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina, CB 7295, Chapel Hill, NC 27599 7295, USA
    Mol Ther 14:471-5. 2006
    ..results indicate that the LNA backbone confers sequence- and organ-specific functional biodistribution of the oligonucleotides and that these potent compounds have the potential to be safe and long-acting modulators of diseases ..
  95. ncbi MutSalpha binds to and promotes synapsis of transcriptionally activated immunoglobulin switch regions
    Erik D Larson
    Department of Immunology, Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, 1959 N E Pacific Street, Box 357650, Seattle, WA 98195, USA
    Curr Biol 15:470-4. 2005
    ..G mismatches, initial products of DNA deamination by AID. These results suggest that MutSalpha interacts with the S regions in switching B cells to promote DNA synapsis and recombination...
  96. pmc MicroRNA fate upon targeting with anti-miRNA oligonucleotides as revealed by an improved Northern-blot-based method for miRNA detection
    Adrian G Torres
    Medical Research Council, Laboratory of Molecular Biology, Cambridge, United Kingdom
    RNA 17:933-43. 2011
    MicroRNAs (miRNAs) are small non-coding RNAs involved in fine-tuning of gene regulation. Antisense oligonucleotides (ONs) are promising tools as anti-miRNA (anti-miR) agents toward therapeutic applications and to uncover miRNA function...
  97. ncbi Extending recognition by peptide nucleic acids (PNAs): binding to duplex DNA and inhibition of transcription by tail-clamp PNA-peptide conjugates
    Kunihiro Kaihatsu
    Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75390 9041, USA
    Biochemistry 42:13996-4003. 2003
    ..and Nielsen, P. E. (2003) Biochemistry 42, 13987-13995], expand the range of sequences within duplex DNA that are accessible to PNAs and suggest that TC-PNA-peptide conjugates are good candidates for further testing as antigene agents...
  98. pmc The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes
    Elzbieta Kierzek
    Department of Chemistry, University of Rochester RC Box 270216, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 33:5082-93. 2005
    ..Internal mismatches with LNA nucleotides significantly destabilize duplexes with RNA...
  99. ncbi Spontaneous formation of nucleic acid-based nanoparticles is responsible for high interferon-alpha induction by CpG-A in plasmacytoid dendritic cells
    Miren Kerkmann
    Department of Internal Medicine, Division of Clinical Pharmacology, Ludwig Maximilians University of Munich, 80336 Muenchen, Germany
    J Biol Chem 280:8086-93. 2005
    ..Based on these results we propose a model in which the spatial configuration of CpG motifs as particle is responsible for the virus-like potency of CpG-A to induce IFN-alpha in PDC...
  100. pmc IDT SciTools: a suite for analysis and design of nucleic acid oligomers
    Richard Owczarzy
    Department of Molecular Genetics and Biophysics, Integrated DNA Technologies, Inc, 1710 Commercial Park, Coralville, IA 52241, USA
    Nucleic Acids Res 36:W163-9. 2008
    DNA and RNA oligomers are used in a myriad of diverse biological and biochemical experiments. These oligonucleotides are designed to have unique biophysical, chemical and hybridization properties...
  101. ncbi Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of the Escherichia coli/lambdaRed and Sulfolobus acidocaldarius recombination systems
    Dennis W Grogan
    Department of Biological Sciences, University of Cincinnati, 614 Rieveschl Hall, ML 0006, Cincinnati, OH 45221 0006, USA
    Mol Microbiol 69:1255-65. 2008
    ..The two OMT systems showed similar responses to certain end modifications of the oligonucleotides, but E...

Research Grants77

  1. Personalized Clinical Diagnostics and Beyond: Integrated Ring Resonator Arrays
    Ryan Bailey; Fiscal Year: 2009
    ..This technology promises to broadly impact the landscape of the biomedical sciences, both meeting the clinical diagnostic challenges of today and pioneering the paradigm-shifting discoveries of tomorrow. ..
  2. High Throughput Genotyping and DNA Sequencing for Studying the Genetic Contributi
    Sonia Dua; Fiscal Year: 2013
    ..ii. Ensure storage of oligonucleotides and reagent kits and mixes which shall include but is not limited to the following inventory and quality ..
  3. Targeting Galectin-3 with novel drugs for treatment of eczema
    Fu Tong Liu; Fiscal Year: 2010
    ..These molecules are a newly-established, but growing class of drugs called aptamers (RNA oligonucleotides), and may offer improved safety and specificity over traditional therapies...
  4. Reactive (AA)Amyloidosis
    Merrill D Benson; Fiscal Year: 2013
    ..of AA amyloidosis to test the hypothesis that reduction of hepatic synthesis of SAA by specific antisense oligonucleotides (ASO) can reduce SAA and stop progression of amyloid fibril formation by limiting availability of AA fibril ..
  5. Targeted siRNA nanotechnology for intravesical treatment of urologicaldiseases
    Robert M Weiss; Fiscal Year: 2010
    ..Because of their robust, gene selective silencing of target protein expression, siRNA oligonucleotides are an attractive therapeutic option with high selectivity and specificity and minimal toxicity to ..
  6. Chemical modulators of Tet-family proteins
    Anjana Rao; Fiscal Year: 2010
    ..of TET1, TET2 or TET3 expressed in insect cells to convert 5mC to hmC in methylated double-stranded DNA oligonucleotides. The appearance of hmC will be monitored by using an antibody to hmC...
  7. Novel Collagen II Alternative Transcripts and Mouse Skeletal Development
    Audrey McAlinden; Fiscal Year: 2010
    ..chondrogenic differentiation when treated with insulin (ATDC5) we will transfect these cells with antisense oligonucleotides that will block splicing at the IIC splice site...
  8. Validation of microRNAs as therapeutic targets in hematological malignancies
    Natarajan Muthusamy; Fiscal Year: 2013
    ..to target RNAs regulate their translation rate, has offered a sound alternative to the antisense DNA oligonucleotides. This concept has been supported by the recent discovery that alterations in the levels of specific miRs are ..
  9. MicroRNA Regulation of Macrophage Polarization in Muscle Regeneration
    Paula K Shireman; Fiscal Year: 2013
    ..Given the availability of locked-nucleic-acid-modified oligonucleotide (LNA-antimiR), RNA oligonucleotides complementary to specific miRNAs that can be used in animals to decrease miRNA expression, a new therapeutic ..
  10. Inflammation and Repair in Cardiac Ischemia-Reperfusion
    Lewis C Becker; Fiscal Year: 2011
    ..expression profiling with cDNA arrays, gene transfer by recombinant adenoviral vectors, transfection of decoy oligonucleotides or interfering RNAs, use of bone marrow derived stromal cells, and use of mice with targeted genetic ..
  11. Developing Immunotherapeutics for Methamphetamine Abuse
    THOMAS RICHARD KOSTEN; Fiscal Year: 2010
    ..These adjuvants include CpG oligonucleotides, MPL, and a squalene-based adjuvant;CFA and alum will be included as controls...
  12. Regulation of TGF-beta Signaling and Embryonic Development by GTPases
    Gerald H Thomsen; Fiscal Year: 2010
    ..Blocking endogenous GTPBP 1 or 2 in developing embryos with antisense oligonucleotides disrupts mesoderm differentiation, body patterning and organogenesis...
  13. MicroRNA-Based Therapeutics for Rare Cystic Kidney Diseases
    Peter Igarashi; Fiscal Year: 2010
    ..Antagomirs are chemically modified oligonucleotides that can be administered parenterally and that specifically and durably inactivate target miRNAs...
  14. Small Oligonucleotides As Therapeutic Agents Of Spinal Muscular Atrophy
    Ravindra N Singh; Fiscal Year: 2012
    ..The success of this proposal will provide a mechanism-based and target- specific drug for the treatment of SMA. ) ..
  15. The bioorganic chemistry of RNA editing by ADARs
    Peter A Beal; Fiscal Year: 2013
    ..Methods for site-selective inhibition of RNA editing will be developed. Backbone modified antisense oligonucleotides and helix- threading peptoids that target RNA editing substrates will be investigated for this purpose...
  16. Mechanisms of Lipid-Induced Hepatic Insulin Resistance
    Gerald I Shulman; Fiscal Year: 2013
    ..as well as awake rats with liver specific knockdown expression of INDY utilizing mRNA selective antisense oligonucleotides. INDY encodes a non-electrogenic dicarboxylate and citrate transporter and has been shown to promote ..
  17. Catalytic inactivation of miRNA function by customized RNase P-based ribozymes
    DANIEL R contact SCHOENBERG; Fiscal Year: 2010
    ..A number of antisense approaches, which involve the repeated high-dose administration of modified oligonucleotides, have been described for antagonizing miR-122 function...
  18. Targets of a cytidine deaminase required for left-right axis in Xenopus
    Alin Vonica; Fiscal Year: 2010
    ..of the biochemical (large amounts of embryonic material), genomic (gene arrays), and molecular (morpholino oligonucleotides, MO) tools available in Xenopus and C2C12 cells, the goal will be completed in two aims: 1...
  19. Development of Ets2-Inhibitors
    DEV ARYA; Fiscal Year: 2009
    ..Recognition of duplex DNA by oligonucleotides, forming DNA triple helices, provides a promising approach to a chemical solution for DNA recognition...
  20. Small Molecule Probes for TAR DNA Binding Protein 43_TDP-43
    Allen B Reitz; Fiscal Year: 2012
    ..TDP-43 suitable for high throughput compound library screening that looks at the inhibition of the binding of oligonucleotides and have identified four chemotypes that possess the novel ability to inhibit the binding of TDP-43 to ..
  21. Beta-Globin Gene Correction Using Peptide Nucleic Acids for the Treatment of Sick
    GERALD FRANCIS VOVIS; Fiscal Year: 2010
    DESCRIPTION (provided by applicant): This is a proposal to test the feasibility of using triplex-forming oligonucleotides to correct the sickle cell disease (SCD) mutation in human CD34+ cells...
  22. A Comparative Approach to Globin Regulation/Thalassemia
    LEONARD IRA ZON; Fiscal Year: 2012
    ..The technology of morpholinos in which antisense oligonucleotides against specific genes are injected into the one cell embryo can knock-down gene function and will reveal ..
  23. Triplex-mediated DNA repair as a novel therapy for Hurler Syndrome patients
    Elizabeth Peterson-Roth; Fiscal Year: 2012
    ..genome modification in CD34+ cells is the use of triplex molecules, either in the form of triplex-forming oligonucleotides or peptide nucleic acids...
  24. Antisense oligonucleotides for the treatment of spinocerebellar ataxia type 2
    Daniel R Scoles; Fiscal Year: 2013
    ..Our objective is identification of antisense oligonucleotides (ASOs) that lower ATXN2 expression...
  25. Neuron-specific block of T-type calcium channels
    Edward Perez-Reyes; Fiscal Year: 2012
    ..2 directed antisense oligonucleotides reverse the mechanical hyperalgesia and allodynia observed in these animals. Importantly, Cav3...
  26. Intra- and Extra-Chromosomal Probes for Mutagenesis by Carcinogens
    John M Essigmann; Fiscal Year: 2013
    ..human carcinogens and (2) the emphasis on rigorous synthetic methodology for preparation of adduct containing oligonucleotides and genomes...
  27. Nicotinamide N-methyltransferase (NNMT) in obesity and insulin resistance
    Qin Yang; Fiscal Year: 2013
    ..Knockdown of NNMT with antisense oligonucleotides (ASO) in adipose tissue and liver of mice fed a high fat diet induces expression of spermine/spermidine ..
  28. Mechanisms of Perchlorate-Induced Disruption of Sexual Differentiation
    FRANK ARTHUR VON HIPPEL; Fiscal Year: 2013
    ..2a), loss-of-function experiments to knock down expression of NIS and NIS-paralogs with morpholino anti-sense oligonucleotides and induced mutations using zinc finger nucleases (Aim 2b), and gain-of-function experiments by over- ..
  29. EICOSANOIDS, VASCULAR TONE AND BLOOD PRESSURE
    WILLIAM BRYSON CAMPBELL; Fiscal Year: 2010
    ..THETA synthesis using wild type (WT), transgenic (TG) and/or knockout (KO) mice, antisense phosphorothiolated oligonucleotides (pOGNs) or short interfering RNAs (siRNAs) and pharmacological inhibitors...
  30. The S1P1 receptor regulates sarcomere assembly and cardiac development
    Roland S Wu; Fiscal Year: 2013
    ..In Aim 1, the timing of S1P1 function in zebrafish cardiac development will be examined. Light-activated oligonucleotides will be injected into zebrafish embryos and ultraviolet light will be used to initiate inhibition of S1P ..
  31. Role of Splicing Factors in Breast Cancer
    OLGA ANCZUKOW-CAMARDA; Fiscal Year: 2013
    ..the K99 phase and leading into the R00 phase, I will determine the therapeutic potential of using antisense oligonucleotides to modulate specific oncogenic alternative splicing events identified in Aims 1-3...
  32. Synthesis, StructUre and Replication of Carcirogen-Modified Oligonucleotides
    Carmelo J Rizzo; Fiscal Year: 2013
    ..A foundation of this program is the ability of the PIs lab to synthesize oligonucleotides containing structurally defined C8- and N2-dG adducts of HCAs (Aim 1)...
  33. Novel Nanopolymers to Inhibit Angiogenesis and Increase the Anti-tumor Immunity
    Manuel L Penichet; Fiscal Year: 2013
    ..TfR) monoclonal antibody for delivery through the endothelial system of the tumor vasculature, antisense oligonucleotides (AON) to inhibit angiogenesis, and/or potent immunostimulatory antibody-cytokine fusion proteins specific for ..
  34. Hormonal and Paracrine Regulation of Spermatogenesis
    Barry R Zirkin; Fiscal Year: 2010
    ..method to assess the level of oxidative DNA damage in germ cells will be developed using beacon aptamers, oligonucleotides that have the ability to bind ligands in a highly specific manner...
  35. Therapeutic Development for Amyotrophic Lateral Sclerosis in a Canine Model
    JOAN RIPLEY COATES; Fiscal Year: 2013
    ..A promising therapeutic strategy using antisense oligonucleotides (ASOs) that target SOD1 mRNA to suppress SOD1 protein was recently demonstrated in a rodent ALS model...
  36. Role of Calcium-Activated Chloride Channels in Airway Disease Phenotypes
    ANAND CHAMPAK PATEL; Fiscal Year: 2011
    ..disease phenotypes driven by viral infection or allergen challenge, using AAV vectors to deliver antisense oligonucleotides that selectively inhibit mClca gene expression. This will be compared to effects of targeted mutagenesis (i.e...
  37. Novel RNAi therapy for ALS and other Neurodegenerative Disorders
    Lyn Libertine; Fiscal Year: 2011
    ..In these mice, suppression of expression of the transgene using either antisense oligonucleotides or siRNA slows progression and improves survival...
  38. microRNA Uncoupling of Protein and Transcript Expression in Liver Regeneration
    CLIFFORD JOHN STEER; Fiscal Year: 2010
    ..Knockdown of Dicer or Ago2 will be carried out in vivo using siRNAs, antisense oligonucleotides or plasmid-based expression-systems. mina levels will be quantitated via microarray analysis in rats after PH...
  39. Role of the Bradykinin Pathway in Craniofacial Development
    LAURA ANNE JACOX; Fiscal Year: 2013
    ..These hypotheses will be tested after local loss of CPN function using antisense oligonucleotides and a face transplant assay developed in the Sive lab...
  40. DNA-Binding Protein Discovery by the Combinatorial Method REPSA
    Michael van Dyke; Fiscal Year: 2013
    ..3) Validate protein-DNA binding and determine binding specificity using recombinant proteins, point-mutated oligonucleotides, and fluorescence polarization binding assays...
  41. Stimulated by Retinoic Acid (STra6) in Energy Homeostasis
    LAURA H ZEMANY; Fiscal Year: 2013
    ..sensitivity, body composition, and energy expenditure will be studied in mice treated with STRA6 antisense oligonucleotides and in the adipose tissue STRA6 knockout mouse...
  42. Antisense oligonucleotide treatment for myotonic dystrophy
    Charles A Thornton; Fiscal Year: 2013
    ..To this end, we are proposing to develop RNase H-active antisense oligonucleotides (ASOs) targeting the mutant human DMPK {mut-hDMPK) mRNA...
  43. Cellular Responses to Radiation and Other Types of Damage
    Gray F Crouse; Fiscal Year: 2012
    ..Another assay uses transformation of yeast with single-stranded oligonucleotides, thereby placing a defined base-base mismatch in the genome at a given location, with the possibility of an ..
  44. Changing tau Protein Levels and tau Protein Isoforms in Mouse Models of Dementia
    Timothy M Miller; Fiscal Year: 2012
    ..Building on prior experience using antisense oligonucleotides to down regulate genes in the brain and spinal cord, Dr...
  45. Exosome based therapeutics in Huntington's disease
    Neil Aronin; Fiscal Year: 2013
    ..of mutant huntingtin mRNA;this therapeutic can be accomplished in HD mouse models by siRNA, antisense oligonucleotides (ASO) and adeno-associated virus (AAV) with shRNAmir directed against huntingtin mRNA...
  46. Micro-RNA Molecules as Regulators of Diabetic Wound Healing
    Marjana Tomic-Canic; Fiscal Year: 2013
    ..wound healing process, and to determine if targeting them with antagomirs (sequence-specific anti-miRNA oligonucleotides) reverses the healing impairment...
  47. Testing Substrate-Flux Therapies for Glycosylation Disorders using Zebrafish
    Richard Steet; Fiscal Year: 2010
    ..the power and speed of zebrafish genetics to generate new vertebrate CDG-I zebrafish models with morpholino oligonucleotides (essentially a "knockdown" approach). These are being validated both pathologically and biochemically...
  48. Mechanisms Underlying Tauopathy Following Traumatic Brain Injury
    David Brody; Fiscal Year: 2013
    ..We propose for our third aim to create antisense oligonucleotides specifically targeting each type of JNK...
  49. Micro RNA-146a (miRNA-146a) signaling in Alzheimers disease (AD)
    Walter J Lukiw; Fiscal Year: 2013
    ..peptide generation in AD tissues, and testing if added exogenous miRNA-146a or anti-miRNA-146a oligonucleotides will promote or neutralize these changes;and (3) testing whether miRNA-146a, anti-miRNA-146a and modulation ..
  50. Social and Motivational Properties of Vasoactive Intestinal Polypeptide Circuits
    James L Goodson; Fiscal Year: 2013
    ..will employ central antagonism of VIP receptors and site-specific knockdown of VIP production using antisense oligonucleotides to examine effects on sociality, anxiety, nesting, and parental care in male and female zebra finches...
  51. Mechanisms of Altered Gastrointestinal Dysfunction
    QiQi Zhou; Fiscal Year: 2013
    ..results should lead to the development of innovative therapeutic strategies via development of synthesized oligonucleotides that inhibit or mimic specific miRNAs that modulate epigenetic regulation of down-stream target genes (e.g...
  52. Assembly and Secretion of ApoB Containing Lipoproteins
    Henry N Ginsberg; Fiscal Year: 2013
    ..g., inhibition of apoB synthesis using antisense oligonucleotides (ASO)...
  53. Defining Target Contribution to Orofacial Pain by Antisense Oligonucleotides
    Zhigang Luo; Fiscal Year: 2009
    ..In this Competitive Revision, we plan to test if nanoparticle encapsulated antisense oligonucleotides against the Cava2d1 and TSP4 mRNA better efficacy than free antisense oligonucleotides in reversing Cava2d1 ..
  54. Identification of Enhancers of Therapeutic Exon Skipping for DMD
    MELISSA JAN SPENCER; Fiscal Year: 2010
    ..Areas of interest include ..., methods for editing gene products in vivo, such as exon-skipping antisense oligonucleotides and small RNAs...
  55. DEVELOPMENT OF IDENTIFIED MOTONEURONS
    Judith S Eisen; Fiscal Year: 2012
    ..development, we propose to knock down expression of specific transcription factors using morpholino oligonucleotides and to examine motoneuron and interneuron markers, including axons, neurotransmitters, receptors, and ion ..
  56. Mechanisms of Embryo Response to Oxidative Stress
    Mark E Hahn; Fiscal Year: 2013
    ..during development in embryos in vivo, using targeted knock-down of NRF protein synthesis with morpholino oligonucleotides. Aim 3 will establish the mechanism of regulation of anti-oxidant response genes during embryonic development ..
  57. Innate Immune Activation in Malaria
    Douglas T Golenbock; Fiscal Year: 2013
    ..DNA, and oligonucleotides derived from the malarial genome, will be compared to purified malarial GPI anchors...
  58. New Models to Assay Gene Silencing Therapies
    Ronald J Mandel; Fiscal Year: 2012
    ..RNAi and RNAi complexed with various reagents to facilitate uptake, and delivery of modified antisense DNA oligonucleotides. The mechanisms of action for these approaches include modulation of mRNA translation, modulation of pre-mRNA ..
  59. An integrated NMR/magnetic nanosensor system for detection of bacteria and toxins
    J Manuel Perez; Fiscal Year: 2011
    ..The principal investigator of this grant application has previously shown that this technology can detect oligonucleotides in the femtomolemole range with extremely high molecular specificity [Nature Biotech...
  60. Therapy for Spinal Muscular Atrophy
    Arthur H M Burghes; Fiscal Year: 2013
    ..remain concerning optimal deployment of therapeutics in SMA, including compounds that activate SMN2, oligonucleotides that stimulate incorporation of SMN exon7 by SMN2, or gene therapy...
  61. DNA damage repair by MUTYH and MUTYH variants associated with colorectal cancer
    SHEILA SUE DAVID; Fiscal Year: 2013
    ..Using pre-steady kinetics and noncleavable 2'-deoxyadenosine analogue-containing oligonucleotides, we provided information on the functional defects of two missense variants of MUTYH found in colorectal ..
  62. Gene Discovery for Hearing Loss in Middle East by Massively Parallel Sequencing
    Moien Kanaan; Fiscal Year: 2013
    ..6 MB design of cRNA oligonucleotides. We will use a multiplex barcoding strategy and sequence on an Illumina GAIIx Genome Analyzer...
  63. NEW GENE THERAPY FOR CONNECTIVE TISSUE DISEASES
    Eric Kmiec; Fiscal Year: 1999
    ..These oligonucleotides increase the specificity of homologous alignment by the recombinase and facilitate the recognition and ..
  64. Tumor drug delivery systems based on polymalic acid
    Julia Y Ljubimova; Fiscal Year: 2010
    ..human brain tumors after a limited number of treatments with Polycefin bearing Morpholino antisense oligonucleotides to chains of vascular tumor protein, laminin-8 showed significantly increased survival (p<0...
  65. Pyrophosphorolysis-activatable helicase dependent amplification assay for lung ca
    BERTRAND LEMIEUX; Fiscal Year: 2007
    ..This extraordinary specificity is possible because oligonucleotides with a 3' dideoxy terminated nucleotide that is not matched to its template DNA target are not ..
  66. Computational Suite for RNA-Targeted Drug Design
    Erin Duffy; Fiscal Year: 2005
    ..lack of high-resolution structural and associated biochemical data for systems beyond very small model oligonucleotides. In fact, the high-resolution crystal structures of the SOS ribosomal subunit of Haloarcula marismortui (H50S)..
  67. CHIRAL PHOSPHORUS LIGANDS AND ANTISENSE OLIGONUCLEOTIDES
    William Hersh; Fiscal Year: 1999
    ..be incorporated directly into the biologically active compounds themselves, specifically, chiral "antisense" oligonucleotides. Reaction of readily available N-sulfonyl amino acids with PhPCl2 gives enantiomerically pure chiral-at-..
  68. Chemical Pathology of 5-aza-2'-deoxycytidine
    Lawrence Sowers; Fiscal Year: 2007
    ..In the second aim, we will build DAC into synthetic oligonucleotides using established phosphoramidite methods...
  69. DNA-linked dendrimer nanoparticle systems for cancer diagnosis and treatment
    James Baker; Fiscal Year: 2009
    ..a unique solution to this limitation by developing single function dendrimer modules linked by complementary oligonucleotides. This allows targeting, imaging, and therapeutic dendrimers to be combined into multifunctional therapeutics ..
  70. DEVELOPMENT OF DNA MICROARRAY FABRICATION METHOD
    Maureen Cronin; Fiscal Year: 1999
    ..We are developing a DNA microarray synthesizer capable of synthesizing DNA oligonucleotides in situ on two dimensional substrates...
  71. Hybridization of Oligonucleotide Probes with Duplex DNA
    Maxim Frank Kamenetskii; Fiscal Year: 2005
    ..project continues and significantly extends the development of an innovative strategy for hybridization of oligonucleotides and other probes to double-stranded (ds)DNA...
  72. DESIGN AND SYNTHESIS OF OLIGONUCLEOTIDE ANALOGUE ANTIVIR
    Donald Bergstrom; Fiscal Year: 1993
    A long-range goal of this research program will be the development of modified oligonucleotides, which will inhibit the ability of human cytomegalovirus (HCMV) to infect and replicate in human cells...
  73. SPECIFIC INHIBITION OF K-RAS EXPRESSION IN LUNG CANCER
    CHARLES MAYFIELD; Fiscal Year: 1999
    ..We have developed stable nuclease resistant oligonucleotides which form triplex DNA in a sequence specific manner and inhibits nuclear protein binding in the K-ras ..
  74. Upregulation of soluble TNFR2 as treatment for Rheumatoid Arthritis
    Peter Sazani; Fiscal Year: 2007
    ..In this technology, chemically modified antisense oligonucleotides alter the expression of splice-variants either by inducing exon skipping, exon inclusion, intron inclusion or ..
  75. Antisense Treatment for Thalassemia. Preclinical study.
    Ryszard Kole; Fiscal Year: 2007
    The ultimate goal of this project is treatment of beta-thalassemia, a genetic blood disease, with antisense oligonucleotides. The project is based on the technology developed by the PI in which antisense oligonucleotides are used to ..
  76. MECHANISM OF ACTION OF RADIATION REPAIR ENZYMES
    YOKE KOW; Fiscal Year: 1999
    ..coli N-glycosylases and AP endonucleases. Oligonucleotides containing sugar modifications, in particular the C-1' and C-2' positions, as well as other base lesions will ..
  77. NMR AND UV STUDIES OF ANTISENSE OLIGONUCLEOTIDES
    Xiaolian Gao; Fiscal Year: 2002
    Antisense oligonucleotides (AONs) are by far the most sequence-specific reagents, which are able to recognize more than ten designated residues in RNA sequences...