catalytic rna

Summary

Summary: RNA that has catalytic activity. The catalytic RNA sequence folds to form a complex surface that can function as an enzyme in reactions with itself and other molecules. It may function even in the absence of protein. There are numerous examples of RNA species that are acted upon by catalytic RNA, however the scope of this enzyme class is not limited to a particular type of substrate.

Top Publications

  1. ncbi Ribozyme catalysis of metabolism in the RNA world
    Xi Chen
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Chem Biodivers 4:633-55. 2007
  2. pmc A general two-metal-ion mechanism for catalytic RNA
    T A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 90:6498-502. 1993
  3. ncbi Mobile group II introns
    Alan M Lambowitz
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Texas 78712, USA
    Annu Rev Genet 38:1-35. 2004
  4. ncbi Crystal structure of a self-spliced group II intron
    Navtej Toor
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA
    Science 320:77-82. 2008
  5. ncbi Human 5' --> 3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites
    Steven West
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Nature 432:522-5. 2004
  6. ncbi RNA, the first macromolecular catalyst: the ribosome is a ribozyme
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Biochem Sci 28:411-8. 2003
  7. ncbi The paradoxical behavior of a highly structured misfolded intermediate in RNA folding
    Rick Russell
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    J Mol Biol 363:531-44. 2006
  8. ncbi The antiquity of RNA-based evolution
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nature 418:214-21. 2002
  9. ncbi Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site
    Feng Guo
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Mol Cell 16:351-62. 2004
  10. pmc Plant pathogenic RNAs and RNA catalysis
    R H Symons
    Department of Plant Science, Waite Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
    Nucleic Acids Res 25:2683-9. 1997

Research Grants

Detail Information

Publications265 found, 100 shown here

  1. ncbi Ribozyme catalysis of metabolism in the RNA world
    Xi Chen
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    Chem Biodivers 4:633-55. 2007
    ....
  2. pmc A general two-metal-ion mechanism for catalytic RNA
    T A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
    Proc Natl Acad Sci U S A 90:6498-502. 1993
    ..The role of the RNA is to position the two catalytic metal ions and properly orient the substrates via three specific binding sites...
  3. ncbi Mobile group II introns
    Alan M Lambowitz
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Texas 78712, USA
    Annu Rev Genet 38:1-35. 2004
    ..Finally, we describe the development of mobile group II introns into gene-targeting vectors, "targetrons," which have programmable target specificity...
  4. ncbi Crystal structure of a self-spliced group II intron
    Navtej Toor
    Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Avenue, Bass Building, New Haven, CT 06511, USA
    Science 320:77-82. 2008
    ..Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor...
  5. ncbi Human 5' --> 3' exonuclease Xrn2 promotes transcription termination at co-transcriptional cleavage sites
    Steven West
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Nature 432:522-5. 2004
    ..Degradation of the downstream cleavage product by Xrn2 results in transcriptional termination, as envisaged in the torpedo model...
  6. ncbi RNA, the first macromolecular catalyst: the ribosome is a ribozyme
    Thomas A Steitz
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Trends Biochem Sci 28:411-8. 2003
    ..The structures of the large subunit bound to a variety of antibiotics explain the effects of antibiotic resistance mutations and provide promise for the development of new antibiotics...
  7. ncbi The paradoxical behavior of a highly structured misfolded intermediate in RNA folding
    Rick Russell
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
    J Mol Biol 363:531-44. 2006
    ..We speculate that the complex topology of RNA secondary structures and the inherent rigidity of RNA helices render kinetic traps due to topological isomers considerably more common for RNA than for proteins...
  8. ncbi The antiquity of RNA-based evolution
    Gerald F Joyce
    Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Nature 418:214-21. 2002
    ..This earlier era is referred to as the 'RNA world', during which the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA...
  9. ncbi Structure of the Tetrahymena ribozyme: base triple sandwich and metal ion at the active site
    Feng Guo
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Mol Cell 16:351-62. 2004
    ..Therefore, we provide a picture of how the ribozyme active site positions both a catalytic metal ion and the nucleophilic guanosine for catalysis prior to binding its RNA substrate...
  10. pmc Plant pathogenic RNAs and RNA catalysis
    R H Symons
    Department of Plant Science, Waite Institute, University of Adelaide, Glen Osmond, SA 5064, Australia
    Nucleic Acids Res 25:2683-9. 1997
    ..It is feasible that more single-stranded circular pathogenic RNAs are waiting to be discovered and these could be prospective for new types of self-cleavage reactions...
  11. pmc Capturing hammerhead ribozyme structures in action by modulating general base catalysis
    Young In Chi
    Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, Kentucky, United States of America
    PLoS Biol 6:e234. 2008
    ..The predissociation enzyme-product complex structure reveals RNA and metal ion interactions potentially relevant to transition-state stabilization that are absent in precatalytic structures...
  12. pmc Catalytic diversity of extended hammerhead ribozymes
    Irina V Shepotinovskaya
    Department of Biochemistry, Molecular Biology, and Cellular Biology, Northwestern University, 2205 Tech Drive, Hogan 2 100, Evanston, Illinois 60208, USA
    Biochemistry 47:7034-42. 2008
    ..For example, differing hammerhead cleavage and ligation rates could affect the steady state concentrations of linear, circular, and polymeric genomes in infected cells...
  13. ncbi Exposing the kinetic traps in RNA folding
    D K Treiber
    Department of Molecular Biology, Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Curr Opin Struct Biol 9:339-45. 1999
    ..Newly developed mutant ribozymes that avoid kinetic traps should facilitate the study of the RNA folding problem...
  14. ncbi In vivo mobility of a group I twintron in nuclear ribosomal DNA of the myxomycete Didymium iridis
    S Johansen
    Department of Molecular Cell Biology, Institute of Medical Biology, University of Tromsø, Norway
    Mol Microbiol 24:737-45. 1997
    ..The endonuclease I-DirI seems to be a rare example of a protein that is expressed from a ribozyme-processed RNA polymerase I transcript in vivo...
  15. ncbi RNA folding: models and perspectives
    Tobin R Sosnick
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
    Curr Opin Struct Biol 13:309-16. 2003
    ..Future challenges include the validation of these models, and the correlation of experimental results and theoretical simulations...
  16. ncbi Long-term survival and concomitant gene expression of ribozyme-transduced CD4+ T-lymphocytes in HIV-infected patients
    Janet L MacPherson
    Johnson and Johnson Research Pty Limited, Locked Bag 4555, Strawberry Hills, Sydney, NSW Australia 2012
    J Gene Med 7:552-64. 2005
    ..We report here the results of a phase I gene transfer clinical trial using Rz2...
  17. ncbi Mapping nucleic acid structure by hydroxyl radical cleavage
    Thomas D Tullius
    Department of Chemistry, Boston University, Boston MA 02215, USA
    Curr Opin Chem Biol 9:127-34. 2005
    ..Advances have been made in methods for analysis of hydroxyl radical data, so that the large datasets that result from kinetic folding experiments can be analyzed in a semi-automated and quantitative manner...
  18. ncbi Real ribozymes suggest a relaxed error threshold
    Adám Kun
    Collegium Budapest, Institute for Advanced Study, Szentháromság u 2 Budapest H 1014, Hungary
    Nat Genet 37:1008-11. 2005
    ..Incidentally, this genome size coincides with that estimated for a minimal cell achieved by top-down analysis, omitting the genes dealing with translation...
  19. pmc A rugged free energy landscape separates multiple functional RNA folds throughout denaturation
    Mark A Ditzler
    Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    Nucleic Acids Res 36:7088-99. 2008
    ..Our results demonstrate a surprising longevity of molecular heterogeneity and advance our current understanding beyond that of non-functional misfolds of RNA kinetically trapped on a rugged folding-free energy landscape...
  20. pmc The HIV-1 transcriptional activator Tat has potent nucleic acid chaperoning activities in vitro
    Monika Kuciak
    LaboRetro INSERM 758, Ecole Normale Superieure de Lyon, IFR 128 Biosciences Lyon Gerland, 69364 Lyon Cedex 07, France
    Nucleic Acids Res 36:3389-400. 2008
    ..The active Tat(44-61) peptide identified here corresponds to the smallest known sequence with DNA/RNA chaperoning properties...
  21. pmc Kinetic redistribution of native and misfolded RNAs by a DEAD-box chaperone
    Hari Bhaskaran
    Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, USA
    Nature 449:1014-8. 2007
    ..ATP-dependent unfolding of both the native conformation and a long-lived misfolded conformation of a group I catalytic RNA with efficiencies that depend on the stabilities of the RNA species but not on specific structural features...
  22. pmc Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance
    David Rueda
    Department of Chemistry, University of Michigan, Ann Arbor, 48109, USA
    Proc Natl Acad Sci U S A 101:10066-71. 2004
    ..Our findings also have broad implications for applications such as the action of drugs and ligands distal to the active site or the engineering of allostery into RNA...
  23. ncbi Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
    Robert Penchovsky
    Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520 8103, USA
    Nat Biotechnol 23:1424-33. 2005
    ..This engineering approach provides a rapid and inexpensive way to create allosteric RNAs for constructing complex molecular circuits, nucleic acid detection systems and gene control elements...
  24. ncbi Regulation of bacterial gene expression by riboswitches
    Wade C Winkler
    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
    Annu Rev Microbiol 59:487-517. 2005
    ..Numerous classes of riboswitches are present in bacteria and they comprise a common and robust metabolite-sensing system...
  25. pmc Higher-order cellular information processing with synthetic RNA devices
    Maung Nyan Win
    Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210 41, Pasadena, CA 91125, USA
    Science 322:456-60. 2008
    ..RNA devices process and transmit molecular inputs to targeted protein outputs, linking computation to gene expression and thus the potential to control cellular function...
  26. ncbi Intermediates and kinetic traps in the folding of a large ribozyme revealed by circular dichroism and UV absorbance spectroscopies and catalytic activity
    T Pan
    Department of Biochemistry and Molecular Biology, University of Chicago, Illinois 60637, USA
    Nat Struct Biol 4:931-8. 1997
    ..Taken together with previous submillisecond relaxation kinetics of tRNA tertiary structure, we suggest that error-free RNA folding can be on the order of milliseconds...
  27. ncbi Fast cleavage kinetics of a natural hammerhead ribozyme
    Marella D Canny
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309 0215, USA
    J Am Chem Soc 126:10848-9. 2004
    ..Under optimum pH and Mg(2+) conditions this ribozyme cleaves at over 870 min(-1) at 25 degrees C, further demonstrating the impressive catalytic power of this ribozyme...
  28. ncbi A preorganized active site in the crystal structure of the Tetrahymena ribozyme
    B L Golden
    Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309 0215, USA
    Science 282:259-64. 1998
    ..The binding pockets for both the 5' splice site helix and guanosine are formed and oriented in the absence of these substrates. Thus, this large ribozyme is largely preorganized for catalysis, much like a globular protein enzyme...
  29. pmc Visualizing the solvent-inaccessible core of a group II intron ribozyme
    J Swisher
    Integrated Program in Cellular, Molecular, and Biophysical Studies, Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
    EMBO J 20:2051-61. 2001
    ..In parallel, a model of the intron core was built based on known tertiary contacts. Although constructed independently of the footprinting data, the model implicates the same elements for involvement in the catalytic core of the intron...
  30. pmc Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme
    Prashanth Rangan
    T C Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218, USA
    Proc Natl Acad Sci U S A 100:1574-9. 2003
    ..The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding...
  31. ncbi The structural basis of ribosome activity in peptide bond synthesis
    P Nissen
    Department of Molecular Biophysics and Biochemistry and Department of Chemistry, Yale University, and Howard Hughes Medical Institute, New Haven, CT 06520 8114, USA
    Science 289:920-30. 2000
    ..The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e...
  32. pmc Single-molecule transition-state analysis of RNA folding
    Gregory Bokinsky
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
    Proc Natl Acad Sci U S A 100:9302-7. 2003
    ..Such a compact transition state without well formed tertiary contacts may be a general property of elementary RNA folding reactions...
  33. ncbi Mobile group II intron targeting: applications in prokaryotes and perspectives in eukaryotes
    Xiaoxia Cui
    Sigma Aldrich Biotechnology, Research and Development, St Louis, MO 63103, USA
    Front Biosci 12:4972-85. 2007
    ..Group II intron knockout technology is mature in bacteria and is currently being developed in eukaryotes. This technology has great potential to revolutionize fields such as functional genomics, gene therapy, and cell line engineering...
  34. pmc An obligate intermediate along the slow folding pathway of a group II intron ribozyme
    Linhui Julie Su
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Nucleic Acids Res 33:6674-87. 2005
    ..These findings provide a new paradigm for RNA folding and they underscore the diversity of RNA biophysical behaviors...
  35. pmc Exploring the folding landscape of a structured RNA
    Rick Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:155-60. 2002
    ..Together these results provide an unprecedented view of the topology of an RNA folding landscape and the RNA structural features that underlie this multidimensional landscape...
  36. pmc In vitro selection of a novel catalytic RNA: characterization of a sulfur alkylation reaction and interaction with a small peptide
    M Wecker
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder 80304, USA
    RNA 2:982-94. 1996
    ..This hairpin structure is also implicated in the recognition of the peptide substrate...
  37. ncbi A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction
    Scott C Walker
    Department of Biomolecular Sciences, UMIST, P O Box 88, Manchester, M60 1QD, UK
    J Mol Biol 341:375-88. 2004
    ..The enzyme possesses a putatively catalytic RNA subunit, structurally related to that of RNase P...
  38. ncbi Comparative enzymology and structural biology of RNA self-cleavage
    Martha J Fedor
    Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
    Annu Rev Biophys 38:271-99. 2009
    Self-cleaving hammerhead, hairpin, hepatitis delta virus, and glmS ribozymes comprise a family of small catalytic RNA motifs that catalyze the same reversible phosphodiester cleavage reaction, but each motif adopts a unique structure and ..
  39. ncbi In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity
    Peter Szabo
    Department of Plant Taxonomy and Ecology, Research Group of Ecology and Theoretical Biology, Eotvos University, 1 C Pázmány P sétány, H 1117 Budapest, Hungary
    Nature 420:340-3. 2002
    ..Although where the first RNA molecules came from is still unknown, it is nevertheless assumed that catalytic RNA enzymes (ribozymes) with replicase function emerged at some early stage of evolution...
  40. ncbi Ribozymes, the first 20 years
    T R Cech
    Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815 6789, USA
    Biochem Soc Trans 30:1162-6. 2002
    In 1982 we reported the first catalytic RNA or ribozyme: the self-splicing intron of the Tetrahymena pre-rRNA...
  41. pmc Aptamer database
    Jennifer F Lee
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, 1 University Station A4800, Austin, TX 78712, USA
    Nucleic Acids Res 32:D95-100. 2004
    ..The database is updated monthly and is publicly available at http://aptamer. icmb.utexas.edu/...
  42. pmc 4-thio-U cross-linking identifies the active site of the VS ribozyme
    Shawna L Hiley
    Department of Molecular and Medical Genetics, University of Toronto, 1 King s College Circle, Toronto, Ontario, Canada M5S 1A8
    EMBO J 21:4691-8. 2002
    ..This localization of the active site is consistent with previous mutational, biochemical and biophysical data, and provides direct evidence that the cleavage site in helix I interacts with the 730 loop in helix VI...
  43. ncbi The effect of long-range loop-loop interactions on folding of the Tetrahymena self-splicing RNA
    J Pan
    College Park, University of Maryland, College Park, MD 20742 2021, USA
    J Mol Biol 294:955-65. 1999
    ....
  44. pmc Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements
    J Carlos Penedo
    Cancer Research UK Nucleic Acid Structure Research Group, Department of Biochemistry, The University of Dundee, Dow Street, Dundee DD1 5EH, Scotland, United Kingdom
    RNA 10:880-8. 2004
    ..The loops clearly act as important auxiliary elements in the function of the ribozyme, permitting folding to occur efficiently under physiological conditions...
  45. ncbi Control of gene expression by a natural metabolite-responsive ribozyme
    Wade C Winkler
    Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, Connecticut 06520 8103, USA
    Nature 428:281-6. 2004
    ..These findings demonstrate that ribozyme switches may have functioned as metabolite sensors in primitive organisms, and further suggest that modern cells retain some of these ancient genetic control systems...
  46. ncbi In vitro evolution suggests multiple origins for the hammerhead ribozyme
    K Salehi-Ashtiani
    Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston 02114, USA
    Nature 414:82-4. 2001
    ..Our results suggest that the evolutionary process may have been channelled, in nature as in the laboratory, towards repeated selection of the simplest solution to a biochemical problem...
  47. ncbi Probing the folding landscape of the Tetrahymena ribozyme: commitment to form the native conformation is late in the folding pathway
    R Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305-5307, USA
    J Mol Biol 308:839-51. 2001
    ..These results allow the misfolded conformation to be incorporated into a folding framework that reconciles previous data and gives quantitative information about the energetic topology of the folding landscape for this RNA...
  48. ncbi Antisense technologies. Improvement through novel chemical modifications
    Jens Kurreck
    Institut für Chemie Biochemie, Freie Universitat Berlin, Germany
    Eur J Biochem 270:1628-44. 2003
    ....
  49. ncbi The residue immediately upstream of the RNase P cleavage site is a positive determinant
    Mathias Brännvall
    Department of Cell and Molecular Biology, Box 596, Biomedical Centre, 751 24, Uppsala, Sweden
    Biochimie 84:693-703. 2002
    ..e. in the leader and spacer regions of tRNA transcripts...
  50. ncbi The complete VS ribozyme in solution studied by small-angle X-ray scattering
    Jan Lipfert
    Department of Physics, Geballe Laboratory of Advanced Materials, Stanford University, Stanford, CA 94305, USA
    Structure 16:1357-67. 2008
    ..This is consistent with the current view of the probable mechanism of trans-esterification in which adenine and guanine nucleobases contributed by the interacting loops combine in general acid-base catalysis...
  51. ncbi Exploration of the transition state for tertiary structure formation between an RNA helix and a large structured RNA
    Laura E Bartley
    Department of Biochemistry, B400 Beckman Center, Stanford University, Stanford, CA 94305 5307, USA
    J Mol Biol 328:1011-26. 2003
    ..The results described here, combined with previous work, provide an in-depth view of an RNA tertiary structure formation event and suggest that large, highly structured RNAs may have local regions that are misordered...
  52. pmc On the occurrence of the T-loop RNA folding motif in large RNA molecules
    Andrey S Krasilnikov
    RNA 9:640-3. 2003
    ....
  53. ncbi Kinetics and thermodynamics make different contributions to RNA folding in vitro and in yeast
    Elisabeth M Mahen
    Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, MB35, La Jolla, California 92037, USA
    Mol Cell 19:27-37. 2005
    ..Evidently, some feature unique to the intracellular environment modulates the influence of transcription polarity and enhances the contribution of thermodynamic stability to RNA folding in vivo...
  54. ncbi An mRNA is capped by a 2', 5' lariat catalyzed by a group I-like ribozyme
    Henrik Nielsen
    Department of Medical Biochemistry and Genetics, Panum Institute, University of Copenhagen, DK 2200N Copenhagen, Denmark
    Science 309:1584-7. 2005
    ..The resulting short lariat, by forming a protective 5' cap, might have been useful in a primitive RNA world...
  55. pmc Purification and characterization of the nuclear RNase P holoenzyme complex reveals extensive subunit overlap with RNase MRP
    J R Chamberlain
    Program in Cellular and Molecular Biology, University of Michigan Medical School, Ann Arbor, Michigan 48109 0606 USA
    Genes Dev 12:1678-90. 1998
    ..RNase P in eubacteria has a large, catalytic RNA subunit and a small protein subunit that are required for precursor tRNA cleavage in vivo...
  56. pmc Rapid compaction during RNA folding
    Rick Russell
    Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 99:4266-71. 2002
    ..The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding...
  57. ncbi Ionization of a critical adenosine residue in the neurospora Varkud Satellite ribozyme active site
    Fatima D Jones
    Department of Molecular Biophysics and Biochemistry, Yale University, P O Box 208114, 260 Whitney Avenue, New Haven, Connecticut 06520 8114, USA
    Biochemistry 42:4265-76. 2003
    ..These include residues in helix II, helix VI (730 loop), the II-III-VI and III-IV-V helix junctions, and loop V...
  58. ncbi Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase I study: myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients
    Rafael G Amado
    Department of Medicine and UCLA AIDS Institute, University of California, Los Angeles, CA 90095, USA
    Hum Gene Ther 15:251-62. 2004
    ....
  59. pmc Hammerhead redux: does the new structure fit the old biochemical data?
    Jennifer A Nelson
    Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois 60208, USA
    RNA 14:605-15. 2008
    ..Since all the biochemical data were collected on minimal hammerheads that have a very different structure, the minimal hammerhead must be dynamic and occasionally adopt the quite different extended structure in order to cleave...
  60. pmc Short-term sequence evolution and vertical inheritance of the Naegleria twin-ribozyme group I intron
    Odd Gunnar Wikmark
    Department of Molecular Biotechnology, RNA Research Group, Institute of Medical Biology, University of Tromsø, N 9037 Tromsø, Norway
    BMC Evol Biol 6:39. 2006
    ..NaGIR1, however, is essential for NaHEG expression by generating the 5' end of the homing endonuclease messenger RNA. Interestingly, this unusual class of ribozyme adds a lariat-cap at the mRNA...
  61. ncbi An alcohol dehydrogenase ribozyme
    Shinya Tsukiji
    Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260 3000, USA
    Nat Struct Biol 10:713-7. 2003
    ..Our demonstration of the redox ability of RNA adds support to an RNA-based metabolic system in ancient life...
  62. ncbi Nucleic acid molecular switches
    G A Soukup
    Department of Molecular, Cellular and Developmental Biology, Yale University, PO Box 208103, New Haven, CT 06520 8103, USA
    Trends Biotechnol 17:469-76. 1999
    ..These allosteric ribozymes function as effector-dependent molecular switches that could find application as novel genetic-control elements, biosensor components or precision switches for use in nanotechnology...
  63. ncbi Principles of RNA compaction: insights from the equilibrium folding pathway of the P4-P6 RNA domain in monovalent cations
    Keiji Takamoto
    Department of Physiology and Biophysics, Albert Einstein College of Medicine of Yeshiva University, New York, NY 10461, USA
    J Mol Biol 343:1195-206. 2004
    ..The folding model derived from these and previous results provides a robust framework for understanding the equilibrium and kinetic folding of RNA...
  64. pmc RNA-protein interactions in the human RNase MRP ribonucleoprotein complex
    H Pluk
    Department of Biochemistry, University of Nijmegen, The Netherlands
    RNA 5:512-24. 1999
    ..Furthermore, UV crosslinking followed by anti-Th/To and anti-Rpp38 immunoprecipitation revealed that the 40-kDa protein we detected in UV crosslinking is probably identical to Rpp38...
  65. pmc Rapid formation of a solvent-inaccessible core in the Neurospora Varkud satellite ribozyme
    S L Hiley
    Department of Molecular and Medical Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
    EMBO J 20:5461-9. 2001
    ....
  66. ncbi Probing the active site of a diels-alderase ribozyme by photoaffinity cross-linking
    Richard Wombacher
    University of Heidelberg, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
    J Am Chem Soc 130:8594-5. 2008
    ..This work establishes photoaffinity cross-linking as an empirical approach that is applied here for the first time to an artificial ribozyme...
  67. pmc Low-magnesium, trans-cleavage activity by type III, tertiary stabilized hammerhead ribozymes with stem 1 discontinuities
    Donald H Burke
    Department of Chemistry, Indiana University, Bloomington, IN 47405 7102, USA
    BMC Biochem 6:14. 2005
    ....
  68. ncbi Building a kinetic framework for group II intron ribozyme activity: quantitation of interdomain binding and reaction rate
    A M Pyle
    Department of Biochemistry and Molecular Biophysics, Columbia University College of Physicians and Surgeons, New York, New York 10032
    Biochemistry 33:2716-25. 1994
    ..2, consistent with a form of general base catalysis within this linear range. The shape of the plot suggests that the active site responsible for 5' splice site hydrolysis has a pKa of > or = 7.0...
  69. ncbi Calcium(II)-dependent catalytic activity of the Azoarcus ribozyme: testing the limits of resolution for in vitro selection
    Aaron S Burton
    Department of Chemistry, Portland State University, P O Box 751, Portland, OR 97207, USA
    Biochimie 88:819-25. 2006
    ..This work also serves to caution that although a selection may be successful, isolates may not be catalytically proficient enough to provide useful levels of activity...
  70. pmc Antigenomic delta ribozyme variants with mutations in the catalytic core obtained by the in vitro selection method
    Michał Łegiewicz
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 14, 61 704, Poznan, Poland
    Nucleic Acids Res 34:1270-80. 2006
    ..Thus, the functional properties of the variants were dependent on both the structure of their catalytic sites and divalent metal ions performing catalysis...
  71. ncbi Ribozyme-catalyzed excision of targeted sequences from within RNAs
    Michael A Bell
    Department of Chemistry, University of Kentucky, Lexington, Kentucky 40506, USA
    Biochemistry 41:15327-33. 2002
    ..The potential usefulness of this reaction is demonstrated by engineering a ribozyme that excises the triplet-repeat expansion region from a truncated myotonic dystrophy protein kinase transcript mimic in vitro...
  72. ncbi Productive folding to the native state by a group II intron ribozyme
    Jennifer F Swisher
    Integrated Program in Cellular, Molecular, and Biophysical Studies, Columbia University, New York, NY 10032, USA
    J Mol Biol 315:297-310. 2002
    Group II introns are large catalytic RNA molecules that fold into compact structures essential for the catalysis of splicing and intron mobility reactions...
  73. pmc Sfold web server for statistical folding and rational design of nucleic acids
    Ye Ding
    Bioinformatics Center, Wadsworth Center, New York State Department of Health, 150 New Scotland Avenue, Albany, NY 12208, USA
    Nucleic Acids Res 32:W135-41. 2004
    ..Detailed output in both graphical and text formats is available for all modules. The Sfold server is available at http://sfold.wadsworth.org and http://www.bioinfo.rpi.edu/applications/sfold...
  74. ncbi Viroids: the minimal non-coding RNAs with autonomous replication
    Ricardo Flores
    Instituto de Biología Molecular y Celular de Plantas UPV CSIC, Universidad Politecnica de Valencia, 46022 Valencia, Spain
    FEBS Lett 567:42-8. 2004
    ..Disease induction might result from the accumulation of viroid-specific small interfering RNAs that, via RNA silencing, could interfere with normal developmental pathways...
  75. ncbi Catalytic properties of hairpin ribozymes derived from Chicory yellow mottle virus and arabis mosaic virus satellite RNAs
    M DeYoung
    Department of Biological Sciences, Northern Illinois University, DeKalb 60115, USA
    Biochemistry 34:15785-91. 1995
    ..The sTRSV ribozyme is most efficient at cleaving GUC complexes, while the sCYMV1 and sArMV ribozymes are most efficient for cleaving GUA-containing sequences...
  76. pmc Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube
    Carolina Díaz Arenas
    Department of Chemistry, Portland State University, Portland, OR 97207, USA
    BMC Evol Biol 10:80. 2010
    ..Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous...
  77. ncbi Persistence length changes dramatically as RNA folds
    G Caliskan
    TC Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, USA
    Phys Rev Lett 95:268303. 2005
    ..Variations in l(p) with increasing Na(+) concentration are more gradual. In accord with the predictions of polyelectrolyte theory we find l(p) alpha 1/kappa(2) where kappa is the inverse Debye-screening length...
  78. ncbi Metal ions in ribozyme folding and catalysis
    R Hanna
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
    Curr Opin Chem Biol 4:166-70. 2000
    ..Similarly, reaction conditions can allow different folding pathways to predominate, with divalent cations sometimes playing opposing roles...
  79. pmc Rube Goldberg goes (ribo)nuclear? Molecular switches and sensors made from RNA
    Scott K Silverman
    Department of Chemistry, University of Illinois at Urbana Champaign, Urbana, Illinois 61801, USA
    RNA 9:377-83. 2003
    ..Also discussed are ribozymes whose activities are controlled by various nonallosteric strategies...
  80. ncbi An alternative route for the folding of large RNAs: apparent two-state folding by a group II intron ribozyme
    Linhui Julie Su
    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
    J Mol Biol 334:639-52. 2003
    ....
  81. ncbi Multiple folding pathways for the P4-P6 RNA domain
    S K Silverman
    Department of Chemistry and Biochemistry and Howard Hughes Medical Institute, University of Colorado at Boulder, Boulder, Colorado 80309, USA
    Biochemistry 39:12465-75. 2000
    ..The fast kinetic phase reflects folding that is facilitated by these interactions, whereas the slow kinetics are observed when these interactions are disrupted at lower ionic strength and higher temperature...
  82. ncbi Control of stereoselectivity in an enzymatic reaction by backdoor access
    Richard Wombacher
    Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120 Heidelberg, Germany
    Angew Chem Int Ed Engl 45:2469-72. 2006
  83. pmc Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli
    E Westhof
    Institut de Biologie Moleculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France
    Proc Natl Acad Sci U S A 91:5133-7. 1994
    A three-dimensional model of M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, was constructed with the aid of a computer...
  84. pmc Functional equivalence of hairpins in the RNA subunits of RNase MRP and RNase P in Saccharomyces cerevisiae
    L Lindahl
    Department of Biological Sciences, University of Maryland Baltimore County, Baltimore 21250, USA
    RNA 6:653-8. 2000
    ..We propose that the MRP3 and P3 hairpins in S. cerevisiae perform similar functions and have coevolved to maintain common features that are different from those of MRP3 and P3 hairpins in other species...
  85. pmc Emergence of a dual-catalytic RNA with metal-specific cleavage and ligase activities: the spandrels of RNA evolution
    L F Landweber
    Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 96:173-8. 1999
    ..Further experiments revealed that we have selected a dual-catalytic RNA from random sequences: the RNA promotes both cleavage at one site and ligation at another site, suggesting two ..
  86. pmc The rate-limiting step in the folding of a large ribozyme without kinetic traps
    X W Fang
    Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 99:8518-23. 2002
    ..Before the rate-limiting step, more than 98% of the total structure has formed. The rate-limiting step is a small-scale structural rearrangement involving prebound metal ions...
  87. ncbi Insights into functional modulation of catalytic RNA activity
    Anastassios Vourekas
    Department of Biological Chemistry, School of Medicine, University of Patras, Rio Patras, Greece
    IUBMB Life 60:669-83. 2008
    ..In this review, we will describe some representative examples of such modulators to illustrate the potential of catalytic RNAs as tools and targets in research and clinical approaches...
  88. ncbi Monovalent cations mediate formation of native tertiary structure of the Tetrahymena thermophila ribozyme
    Keiji Takamoto
    Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA
    Nat Struct Biol 9:928-33. 2002
    ....
  89. ncbi Evolutionary origins and directed evolution of RNA
    Andrew D Ellington
    Department of Chemistry and Biochemistry, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, United States
    Int J Biochem Cell Biol 41:254-65. 2009
    ..Self-replication would have inexorably led to life...
  90. ncbi High-throughput-compatible assay for glmS riboswitch metabolite dependence
    Gunter Mayer
    Universitat Bonn, Kekule Institut fur Organische Chemie und Biochemie, Gerhard Domagk Strasse 1, 53121 Bonn, Germany
    Chembiochem 7:602-4. 2006
  91. ncbi Multiple monovalent ion-dependent pathways for the folding of the L-21 Tetrahymena thermophila ribozyme
    Takeshi Uchida
    Department of Physiology and Biophysics, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
    J Mol Biol 328:463-78. 2003
    ..These results provide a map of the early steps in the ribozyme's folding landscape and the degree to which the preferred pathways are dependent upon the initial reaction conditions...
  92. pmc Phase 2 gene therapy trial of an anti-HIV ribozyme in autologous CD34+ cells
    Ronald T Mitsuyasu
    Center for Clinical AIDS Research and Education, University of California Los Angeles, 9911 West Pico Boulevard, Suite 980, Los Angeles, California 90035, USA
    Nat Med 15:285-92. 2009
    ..This study indicates that cell-delivered gene transfer is safe and biologically active in individuals with HIV and can be developed as a conventional therapeutic product...
  93. ncbi Cleavage reaction of HDV ribozymes in the presence of Mg2+ is accompanied by a conformational change
    Yoichiro Tanaka
    Department of Environment and Natural Sciences, Graduate School of Environment and Information Sciences, Yokohama National University, 79 7 Tokiwadai, Hodogaya ku, Yokohama 240 8501, Japan
    Genes Cells 7:567-79. 2002
    ..We have previously elucidated the solution conformation of a minimized trans-acting HDV ribozyme and obtained evidence by NMR study that an Mg2+ ion binds to a site close to the cleavage site...
  94. ncbi Hydrolytic cleavage by a group I intron ribozyme is dependent on RNA structures not important for splicing
    Peik Haugen
    Department of Molecular Biotechnology, Institute of Medical Biology, University of Tromsø, Norway
    Eur J Biochem 271:1015-24. 2004
    ..2) and a consensus kink-turn motif in the proximal stem. We suggest that the L9.2 adenosines and the kink-motif represent key regulatory elements in the splicing and hydrolytic reaction pathways...
  95. ncbi HDV ribozymes
    M D Been
    Department of Biochemistry, Duke University Medical Center, Durham, NC, USA
    Curr Top Microbiol Immunol 307:47-65. 2006
    ..HDV ribozymes have provided a tractable system for studying the mechanism of catalytic RNA, and results of biochemical and structural studies on the HDV ribozymes, from a number of labs, have enhanced ..
  96. ncbi Catalytic activity of hammerhead ribozymes in a clay mineral environment: implications for the RNA world
    Elisa Biondi
    Department of Animal Biology and Genetics, University of Florence, Florence, Italy
    Gene 389:10-8. 2007
    ....
  97. ncbi Domains 2 and 3 interact to form critical elements of the group II intron active site
    Olga Fedorova
    Department of Molecular Biophysics Biochemistry, Yale University Howard Hughes Medical Institute, 266 Whitney Avenue, Bass Buildings Rm 334, New Haven, CT 06520, USA
    J Mol Biol 330:197-209. 2003
    ..These results establish that D3 and the base of D2 are key elements of the group II intron core and they suggest a hierarchy for active-site assembly...
  98. pmc Catalytic cleavage of cis- and trans-acting antigenomic delta ribozymes in the presence of various divalent metal ions
    J Wrzesinski
    Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
    Nucleic Acids Res 29:4482-92. 2001
    ..Some implications concerning further studies and possible applications of delta ribozymes are also considered...
  99. pmc Coevolution of group II intron RNA structures with their intron-encoded reverse transcriptases
    N Toor
    Department of Biological Sciences, University of Calgary, Alberta, Canada
    RNA 7:1142-52. 2001
    ..The model is supported by the distribution of ORF-containing and ORF-less introns, and by numerous examples of ORF-less introns that contain ORF remnants...
  100. ncbi pK(a) perturbation in genomic Hepatitis Delta Virus ribozyme catalysis evidenced by nucleotide analogue interference mapping
    Adegboyega K Oyelere
    Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520 8114, USA
    Biochemistry 41:3667-75. 2002
    ....
  101. pmc Identification of gene function and functional pathways by systemic plasmid-based ribozyme targeting in adult mice
    Mohammed Kashani-Sabet
    Auerback Melanoma Research Laboratory, Cutaneous Oncology Program, University of California at San Francisco Cancer Center and Department of Dermatology, University of California, San Francisco, CA 94115, USA
    Proc Natl Acad Sci U S A 99:3878-83. 2002
    ..These studies demonstrate the utility of gene targeting by means of systemic, plasmid-based ribozymes to dissect out the functional genomics of complex biologic phenotypes, including tumor metastasis...

Research Grants64

  1. Catalytic inactivation of miRNA function by customized RNase P-based ribozymes
    DANIEL R contact SCHOENBERG; Fiscal Year: 2010
    ..This proposal describes a new approach to inactivating miR-122 using a catalytic RNA enzyme. The long term goal is to apply this strategy to the treatment of HCV infection.
  2. POLYMERASE PROTEINS IN CORONAVIRUS REPLICATION
    Mark R Denison; Fiscal Year: 2013
    ..and significance by establishing universally applicable systems for identification and testing of novel non-catalytic RNA virus protease targets for inhibition or attenuation of virus replication...
  3. Proteins in RNA-Based Enzymes
    Andrey S Krasilnikov; Fiscal Year: 2012
    ..P/MRP family acquired more and more proteins as evolution progressed, or why RNase MRP needs proteins when the catalytic RNA moiety seems to be essentially preserved...
  4. Structural studies of RNase P
    ALFONSO MONDRAGON; Fiscal Year: 2013
    ..RNase P was one of the first catalytic RNA molecules discovered and its study has been pivotal to our understanding of the role of RNA molecules in ..
  5. ENZYMOLOGY OF A CATALYTIC RNA MOLECULE
    Daniel Herschlag; Fiscal Year: 2013
    ..Finally, we will take on the grand challenge of understanding how a functional RNA is assembled, in particular probing the roles and mode of action of remote elements that facilitate function within the catalytic core. ..
  6. 2013 Nucleosides, Nucleotides, and Oligonucleotides Gordon Research Conference
    William B Parker; Fiscal Year: 2013
    ..In addition, nucleic acids analogs as siRNA, miRNA, antisense, catalytic RNA belong to one of the most exciting new areas in drug development...
  7. Antibiotic Properties of Artificial Agonists for a Bacterial Riboswitch
    JULIANE K STRAUSS SOUKUP; Fiscal Year: 2010
    ..functionalities are essential for binding of the metabolite to the riboswitch RNA and for catalysis by the catalytic RNA (ribozyme)...
  8. Structure and Function in Catalytic RNP Assembly
    Mark Foster; Fiscal Year: 2009
    ..structural insights into the interaction between individual protein components, free and in complex, with the catalytic RNA subunit. The aims are to: 1...
  9. Characterization of a New Model Spliceosomal Ribozyme: Activity and Structure Pro
    JOSHUA ALAN BOYER; Fiscal Year: 2012
    ..This proposal aspires to design a new catalytic RNA that better recapitulates splicing's two-step reaction by using these nucleotide mimics that are ..
  10. Monovalent metal ion binding sites in nucleic acids
    SCOTT STROBEL; Fiscal Year: 2004
    ..These objectives are: (i) Identification of a K+ metal ion site within all three major classes of large catalytic RNA; (ii) Determination of the structural and biological relevance of a monovalent ion binding site within the ..
  11. Multi-scale Quantum Models for Ribozyme Catalysis
    Darrin M York; Fiscal Year: 2013
    ..view of mechanism that may, ultimately, contribute to a deeper understanding of more complex cellular catalytic RNA systems such as the ribosome and spliceosome...
  12. Structural Biology of the Catalytic Domain of Bacteriophage T4 Primase
    David Rovnyak; Fiscal Year: 2009
    ..This domain comprises both the catalytic RNA polymerase activity and the helicase interacting domain of the primase...
  13. TRANSGENIC IN HYPERTENSION--RAS RIBOZYNE INHIBITION
    John Mullins; Fiscal Year: 1992
    ..we want to develop the methodology of enzymatic cleavage of the target mRNA by the use of synthetic catalytic RNA sequences (ribozymes) which are included within an antisense RNA construct...
  14. THREE SPLICE-SITE OF A SELF-SPLICING GROUP I INTRON
    Richard Waring; Fiscal Year: 1993
    ..RNA catalysis may play in cell function, it is essential in the long-term to determine the structure of this catalytic RNA and the function of each of its domains...
  15. AUTOSOMAL DOMINANT EYE DISEASE: CATALYTIC RNA TREATMENT
    Alfred Lewin; Fiscal Year: 2005
    ..The genetic tool we will employ for this purpose is a catalytic RNA molecule or ribozyme. Small ribozymes can be engineered to sever almost any RNA in a sequence-specific manner...
  16. NOVEL ANTISENSE THERAPEUTIC FOR RHEUMATOID ARTHRITIS
    Brian Johnston; Fiscal Year: 1999
    We have developed a novel antisense technology based on catalytic RNA which can potentially be applied to human therapeutics...
  17. Analysis of ribozyme targets within the HIV-1 genome
    William Jackson; Fiscal Year: 2002
    Since the tirst description of catalytic RNA s, or ribozymes, in 1982 , investigators recognized that the unique ability to catalytically cleave complementary target RNAs made these molecules potential therapeutic agents...
  18. Targeting RNA to develop novel antibacterial agents
    CHRISTOPHER TROTTA; Fiscal Year: 2003
    ..There are currently no therapies that target this essential catalytic RNA enzyme...
  19. FUNCTION AND METABOLISM OF RNA
    Norman Pace; Fiscal Year: 2003
    ..analysis of the molecular biology of ribonuclease (RNase) P, a ribonucleoprotein enzyme that contains a catalytic RNA involved in tRNA processing...
  20. STRUCTURE AND CATALYSIS OF AN RNA ENZYME
    William Scott; Fiscal Year: 2002
    ..In doing so, an understanding of the relationship between catalytic RNA structure and function (i.e., catalysis) will be obtained...
  21. RNA Editing Complex
    Kenneth Stuart; Fiscal Year: 2006
    ..abstract_text> ..
  22. RNASE P RIBOZYMES FOR ANTIVIRAL APPLICATIONS
    Fenyong Liu; Fiscal Year: 2000
    ..The applicant has constructed a ribozyme engineered from the catalytic RNA subunit of RNase P from E. coli...
  23. STRUCTURAL BIOLOGY OF RNA FOLDING
    MARK CHANCE; Fiscal Year: 2003
    ..and kinetic picture of the formation of the individual tertiary contacts that stabilize this large catalytic RNA. Many of these tertiary contacts represent motifs that are present in a wide variety of RNA structures and ..
  24. CATALYTIC RNA AND DNA AS ANTIHIV 1 THERAPEUTIC AGENTS
    GERALD JOYCE; Fiscal Year: 2000
    ..Finally, in vitro evolution methods will be used to develop DNA enzymes with glycosidase activity. Such molecules might be used to cleave cell-surface glycoproteins , such as the HIV-1 gp 120 envelope glycoproteins. ..
  25. EPR STUDIES OF METAL/NUCLEI ACID INTERACTIONS
    R Britt; Fiscal Year: 2003
    Divalent metal ions are a key component in the structure and function of nucleic acids in general and catalytic RNA molecules (ribozymes) in particular...
  26. Natural mRNA Genetic Switches that Bind Metabolites
    Ronald Breaker; Fiscal Year: 2006
    ..These findings will aid in the discovery of new riboswitches and will provide a solid foundation for the generation of designer genetic control elements based on RNA. ..
  27. ENGINEERING ALLOSTERIC RIBOZYMES AND DEOXYRIBOZYMES
    Ronald Breaker; Fiscal Year: 2002
    ..In addition, we will test the function of these 'molecular switches' in vivo, to establish a new method of controlled gene expression. ..
  28. Measuring Metabolites using Riboswitch reports
    Ronald Breaker; Fiscal Year: 2006
    ..Moreover, bioinformatics searches can be expanded to uncover examples of known or new riboswitches in humans and other eukaryotes. ..
  29. Catalytic Mechanisms of RNA Ezymes
    Martha J Fedor; Fiscal Year: 2010
    ..The results of these studies also will provide a framework to guide the development of technical and therapeutic applications involving RNAs as targets and reagents. ..
  30. Nucleic Acids Gordon Research Conference 2005
    MARTHA FEDOR; Fiscal Year: 2005
    ..Considerable time is allotted for discussion following formal lectures. Poster sessions and optional recreational activities will stimulate informal interactions. ..
  31. Trekking with the Ribognome: Single Molecule Microscopy of Intracellular miRNPs
    Nils G Walter; Fiscal Year: 2010
    ..concept? What are the lower limits for DNA repeat sequence and protein polymerization detection and can these limits be further pushed? Can multiple different biopolymers be detected in parallel and how does this affect detection limits? ..
  32. STRUCTURE AND CATALYSIS OF AN RNA ENZYME
    William Scott; Fiscal Year: 2008
    ..In doing so, an understanding of the relationship between catalytic RNA structure and function (i.e., catalysis) will be obtained...
  33. Nucleic Acids Gordon Research Conference
    SCOTT STROBEL; Fiscal Year: 2006
    ..Considerable time is allotted for discussion following formal lectures. Poster sessions and optional recreational activities will stimulate informal interactions. [unreadable] [unreadable] [unreadable] [unreadable]..
  34. MECHANISM OF RNA HELICASE ACTIVITY BY DEXH/D PROTEINS
    ANNA PYLE; Fiscal Year: 2008
    ..The results will fundamentally extend our knowledge of helicase mechanism and facilitate the development of new HCV inhibitors. ..
  35. Allosteric DNAzyme sensors for practical detection of mycotoxins
    SCOTT SILVERMAN; Fiscal Year: 2007
    ..Improved sensors for detecting mycotoxins and thereby revealing the presence of fungi will allow proper remedial actions to be taken. [unreadable] [unreadable] [unreadable]..
  36. ENHANCING THE INTRACELLULAR FUNCTIONING OF HIV RIBOZYMES
    John Rossi; Fiscal Year: 2001
    ..The results from this program will greatly facilitate the effective use of ribozyme treatment for HIV-1 infection in a gene therapy setting. ..
  37. RNA-PROTEIN INTERACTIONS
    Donald Burke; Fiscal Year: 2002
    ..In addition, experiments will be carried out to see what kinds of RT resistant mutants arise in response to various candidate aptamers. ..
  38. RNA aptamers to inhibit natural and evolved RT variants
    Donald Burke; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable]..
  39. Nucleic Acid Gordon Research Conference
    ANNA PYLE; Fiscal Year: 2004
    ..Poster sessions and optional recreational activities will stimulate informal interactions among participants. ..
  40. Site-specific incorporation of FRET pairs into intracellular proteins
    Andrew Ellington; Fiscal Year: 2009
    ..This will allow us to follow and track proteins in a cell, and to determine where, when, and how proteins reside next to one another, in either normal or malformed complexes. ..
  41. Cellular uptake of glycoside-based transporters
    Yitzhak Tor; Fiscal Year: 2010
    ..The proposed work thus aims to acquire information about new transporters and provide a platform for treating disease. ..
  42. Genetic circuits based on allosteric ribozymes
    Andrew D Ellington; Fiscal Year: 2010
    ....
  43. METAL CONTAINING DNA--SYNTHESIS AND PROPERTIES
    Yitzhak Tor; Fiscal Year: 2002
    ..Evaluating the mechanisms leading to the generation and migration of oxidative damage in duplex DNA will facilitate the development of novel approaches to anti-cancer therapy. ..
  44. Structural Biology of RNA
    ADRIAN FERRE D AMARE; Fiscal Year: 2009
    ..These 'molecular movies'will provide the basic understanding that will help manipulate the functions of RNAs in human health and disease, and in the life cycle of pathogenic organisms. ..
  45. DETECTOR & GENERATOR FOR CRYSTALLOGRAPHY CORE FACILITY
    Joseph Wedekind; Fiscal Year: 2001
    ..Such work has practical applications to human diseases in terms of diagnosis, prevention, and therapeutic development...
  46. Peptidomimetic Opioids, Synthesis, Structure & Biology
    Yitzhak Tor; Fiscal Year: 2006
    ..With the combination of pharmacology, organic chemistry, and molecular biology the design of new highly potent and selective peptidomimetic opioids will be accomplished. [unreadable] [unreadable]..
  47. MSC BLUE-3 AND MSC PURPLE-3 CONFOCAL X-RAY OPTICS
    ADRIAN FERRE D AMARE; Fiscal Year: 2001
    ..We are requesting funds to purchase MSC/Max-Flux confocal optics that will result in up to 27-fold increase in useable X-ray flux, relative to the current configuration. ..
  48. KINETIC ANALYSIS OF MICROTUBULE-DEPENDENT ATPASES
    Kenneth Johnson; Fiscal Year: 2003
    ..The combination of approaches outlined here will provide rigorous and direct information to define the structural and mechanistic basis for force production by kinesin. ..
  49. APTAMER BASED DETECTOR TO QUANTIFY MACROMOLECULES
    Andrew Ellington; Fiscal Year: 2006
    ....
  50. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2002
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  51. MicroRNA Profiles of Pathogen Infection
    Andrew Ellington; Fiscal Year: 2005
    ..3. Apply these methods to the detection of changes in microRNA expression during influenza infection. 4. Apply these methods to the detection of changes in microRNA expression with other infectious agents. ..
  52. Transducing Tumor Cell Antigens to Amplicons
    Andrew Ellington; Fiscal Year: 2006
    ..abstract_text> ..
  53. NOVEL APPROACHES TO THE DISCOVERY OF ANTI-HIV AGENTS
    Yitzhak Tor; Fiscal Year: 2007
    ..Potent and specific effectors of essential regulatory events will significantly advance the development of highly active antiretroviral agents. ..
  54. Ribozymes for Peptide- and Protein- Sensing Chip Arrays
    Andrew Ellington; Fiscal Year: 2004
    ..1.-D.3), and (2)Adapting peptide and protein-activated aptazymes to function in chip arrays (D.4). ..
  55. Auto Selection of aptamers binding to pX01 proteome
    Andrew Ellington; Fiscal Year: 2004
    ..abstract_text> ..
  56. Elementary Steps in DNA Polymerization
    Kenneth Johnson; Fiscal Year: 2008
    ..abstract_text> ..
  57. PHYSICAL CHEMISTRY OF NUCLEIC ACIDS
    Carlos Bustamante; Fiscal Year: 2008
    ..Finally, in the experiments described here, mechanical force will be used as a new controllable variable to characterize the process of mechanochemical transduction in this motor enzyme. ..
  58. Design and Selection of Aptamer Beacons
    Andrew Ellington; Fiscal Year: 2008
    ..abstract_text> ..
  59. T7 RNA polymerase engineering and RNA amplification
    Andrew Ellington; Fiscal Year: 2008
    ..This will enable microarray gene analysis with as little as 1 ng of total RNA with a single round of amplification or microarray profiling from a single cell (-10 pg of total RNA) after two rounds of amplification. ..
  60. REV DECOYS FOR GENE THERAPY AND DRUG DEVELOPMENT
    Andrew Ellington; Fiscal Year: 2004
    ....
  61. Structure, dynamics, and function of the packaging RNA
    Peter Z Qin; Fiscal Year: 2010
    ..Understanding phi29 packaging motor function will aid in developing pharmacological approaches to combat these viruses. ..
  62. TRNA: STUDIES OF PRECURSORS, MUTANTS AND FUNCTIONS
    Sidney Altman; Fiscal Year: 2003
    ....