nucleic acid conformation

Summary

Summary: The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.

Top Publications

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
  2. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
  3. pmc WebLogo: a sequence logo generator
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genome Res 14:1188-90. 2004
  4. ncbi The role of site accessibility in microRNA target recognition
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:1278-84. 2007
  5. ncbi Crystal structure of the nucleosome core particle at 2.8 A resolution
    K Luger
    Institut fur Molekularbiologie und Biophysik, Zurich, Switzerland
    Nature 389:251-60. 1997
  6. pmc Infernal 1.0: inference of RNA alignments
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1335-7. 2009
  7. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
  8. pmc The Vienna RNA websuite
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
    Nucleic Acids Res 36:W70-4. 2008
  9. pmc Rfam: Wikipedia, clans and the "decimal" release
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA
    Nucleic Acids Res 39:D141-5. 2011
  10. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004

Research Grants

  1. METALLOREGULATION BY MERR AND FUR PROTEIN FAMILIES
    THOMAS V O'HALLORAN; Fiscal Year: 2013
  2. STRUCTURE OF VIRAL RNA AND ITS ROLE IN ASSEMBLY
    Alexander McPherson; Fiscal Year: 2006
  3. X RAY STUDIES OF NUCLEIC ACID CONSTITUENTS
    Muttaiya Sundaralingam; Fiscal Year: 2001
  4. BIOCHEMICAL MECHANISM OF EXOCYCLIC ADDUCTS IN CANCER
    B Singer; Fiscal Year: 2004
  5. DNA/RNA Quadruplexes: Structure, Stability, Interactions
    RICHARD SHAFER; Fiscal Year: 2006
  6. CIRCULAR DICHROISM STOPPED FLOW SPECTROMETER
    LUIS MARKY; Fiscal Year: 1999
  7. Acquisition of a Circular Dichroism Spectrometer
    Barbara Brodsky; Fiscal Year: 2002
  8. NUCLEIC ACID CONFORMATION, PROPERTIES, AND INTERACTIONS
    WILMA OLSON; Fiscal Year: 2006
  9. Maintenance of the tRNA 3' end
    Ya Ming Hou; Fiscal Year: 2008
  10. Bioscope II - AFM system for Nanoimaging Core Facility
    Yuri Lyubchenko; Fiscal Year: 2007

Detail Information

Publications302 found, 100 shown here

  1. pmc Mfold web server for nucleic acid folding and hybridization prediction
    Michael Zuker
    Department of Mathematical Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
    Nucleic Acids Res 31:3406-15. 2003
    ..The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/mfold. This URL will be referred to as 'MFOLDROOT'...
  2. ncbi The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
    R C Lee
    Harvard University, Department of Cellular and Developmental Biology, Cambridge, Massachusetts 02138
    Cell 75:843-54. 1993
    ..elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin-4 regulates lin-14 translation via an antisense RNA-RNA interaction...
  3. pmc WebLogo: a sequence logo generator
    Gavin E Crooks
    Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
    Genome Res 14:1188-90. 2004
    ..A command line interface and the complete, open WebLogo source code are available for local installation and customization...
  4. ncbi The role of site accessibility in microRNA target recognition
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nat Genet 39:1278-84. 2007
    ..Our study thus demonstrates that target accessibility is a critical factor in microRNA function...
  5. ncbi Crystal structure of the nucleosome core particle at 2.8 A resolution
    K Luger
    Institut fur Molekularbiologie und Biophysik, Zurich, Switzerland
    Nature 389:251-60. 1997
    ..The lack of uniformity between multiple histone/DNA-binding sites causes the DNA to deviate from ideal superhelix geometry...
  6. pmc Infernal 1.0: inference of RNA alignments
    Eric P Nawrocki
    HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA
    Bioinformatics 25:1335-7. 2009
    ....
  7. pmc Fast and effective prediction of microRNA/target duplexes
    Marc Rehmsmeier
    Universitat Bielefeld, International NRW Graduate School in Bioinformatics and Genome Research, Postfach 10 01 31, 33501 Bielefeld, Germany
    RNA 10:1507-17. 2004
    ..RNAhybrid, with its accompanying programs RNAcalibrate and RNAeffective, is available for download and as a Web tool on the Bielefeld Bioinformatics Server (http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/)...
  8. pmc The Vienna RNA websuite
    Andreas R Gruber
    Institute for Theoretical Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Wien, Austria
    Nucleic Acids Res 36:W70-4. 2008
    ..The web server together with software packages for download is freely accessible at http://rna.tbi.univie.ac.at/...
  9. pmc Rfam: Wikipedia, clans and the "decimal" release
    Paul P Gardner
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA0, USA
    Nucleic Acids Res 39:D141-5. 2011
    ..We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at http://rfam.sanger.ac.uk...
  10. ncbi Computational identification of plant microRNAs and their targets, including a stress-induced miRNA
    Matthew W Jones-Rhoades
    Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Mol Cell 14:787-99. 2004
    ..The expression of miR395, the sulfurylase-targeting miRNA, increases upon sulfate starvation, showing that miRNAs can be induced by environmental stress...
  11. pmc Coding-sequence determinants of gene expression in Escherichia coli
    Grzegorz Kudla
    Department of Biology and Program in Applied Mathematics and Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
    Science 324:255-8. 2009
    ..In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness...
  12. pmc The role of DNA shape in protein-DNA recognition
    Remo Rohs
    Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
    Nature 461:1248-53. 2009
    ....
  13. pmc Architecture and secondary structure of an entire HIV-1 RNA genome
    Joseph M Watts
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 3290, USA
    Nature 460:711-6. 2009
    ..These results emphasize that the HIV-1 genome and, potentially, many coding RNAs are punctuated by previously unrecognized regulatory motifs and that extensive RNA structure constitutes an important component of the genetic code...
  14. pmc MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
    Ian W Davis
    Department of Biochemistry, Duke University, Durham, NC, USA
    Nucleic Acids Res 35:W375-83. 2007
    ..This service is available free to all users at http://molprobity.biochem.duke.edu...
  15. pmc Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis
    Ramanjulu Sunkar
    Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521, USA
    Plant Cell 16:2001-19. 2004
    ....
  16. ncbi A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA
    G Hutvagner
    Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
    Science 293:834-8. 2001
    ..Thus, the RNA interference and stRNA pathways intersect. Both pathways require the RNA-processing enzyme Dicer to produce the active small-RNA component that represses gene expression...
  17. pmc VARNA: Interactive drawing and editing of the RNA secondary structure
    Kévin Darty
    LRI, UMR CNRS 8623, UMR CNRS 8621, Universite Paris Sud 11, F91405 Orsay Cedex, France
    Bioinformatics 25:1974-5. 2009
    ..VARNA is a tool for the automated drawing, visualization and annotation of the secondary structure of RNA, designed as a companion software for web servers and databases...
  18. ncbi Identification of novel genes coding for small expressed RNAs
    M Lagos-Quintana
    Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, , Germany
    Science 294:853-8. 2001
    ..This suggests that sequence-specific, posttranscriptional regulatory mechanisms mediated by small RNAs are more general than previously appreciated...
  19. pmc RNAstructure: software for RNA secondary structure prediction and analysis
    Jessica S Reuter
    Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester Medical Center, 601 Elmwood Avenue, Box 712, Rochester, NY 14642, USA
    BMC Bioinformatics 11:129. 2010
    ..RNA secondary structure prediction, using thermodynamics, can be used to develop hypotheses about the structure of an RNA sequence...
  20. pmc Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers
    Alberto Perez
    Molecular Modeling and Bioinformatics Unit, Institut de Recerca Biomèdica and Instituto Nacional de Bioinformatica, Parc Cientific de Barcelona, Barcelona 08028, Spain
    Biophys J 92:3817-29. 2007
    ..The total simulation time used to validate the force field includes near 1 mus of state-of-the-art molecular dynamics simulations in aqueous solution...
  21. pmc Vienna RNA secondary structure server
    Ivo L Hofacker
    Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universitat Wien, Wahringerstrasse 17, A 1090 Wien, Austria
    Nucleic Acids Res 31:3429-31. 2003
    ..All three services can be accessed via the Vienna RNA web server at http://rna.tbi.univie.ac.at/...
  22. ncbi Folding DNA to create nanoscale shapes and patterns
    Paul W K Rothemund
    Departments of Computer Science and Computation and Neural Systems, California Institute of Technology, Pasadena, California 91125, USA
    Nature 440:297-302. 2006
    ..Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex)...
  23. pmc Specific expression of long noncoding RNAs in the mouse brain
    Tim R Mercer
    Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD 4072, Australia
    Proc Natl Acad Sci U S A 105:716-21. 2008
    ..Our results show that the majority of ncRNAs are expressed in the brain and provide strong evidence that the majority of processed transcripts with no protein-coding capacity function intrinsically as RNAs...
  24. ncbi Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C)
    Marieke Simonis
    Department of Cell Biology and Genetics, Erasmus Medical Centre, PO Box 2040, 3000 CA Rotterdam, The Netherlands
    Nat Genet 38:1348-54. 2006
    ..Our data demonstrate that chromosomes fold into areas of active chromatin and areas of inactive chromatin and establish 4C technology as a powerful tool to study nuclear architecture...
  25. 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...
  26. ncbi An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans
    N C Lau
    Whitehead Institute for Biomedical Research, and Department of Biology, Massachusetts Institute of Technology, 9 Cambridge Center, Cambridge, MA 02142, USA
    Science 294:858-62. 2001
    ..The abundance of these tiny RNAs, their expression patterns, and their evolutionary conservation imply that, as a class, miRNAs have broad regulatory functions in animals...
  27. pmc Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization
    Reza Vafabakhsh
    Department of Physics, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Science 337:1097-101. 2012
    ..Many biologically important protein-DNA interactions that involve looping and bending of DNA below 100 bp likely use this intrinsic bendability of DNA...
  28. pmc Real-time quantification of microRNAs by stem-loop RT-PCR
    Caifu Chen
    Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94404, USA
    Nucleic Acids Res 33:e179. 2005
    ..Furthermore, the concept of stem-loop RT primer design could be applied in small RNA cloning and multiplex assays for better specificity and efficiency...
  29. pmc Genome-wide measurement of RNA secondary structure in yeast
    Michael Kertesz
    Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel
    Nature 467:103-7. 2010
    ..PARS is readily applicable to other organisms and to profiling RNA structure in diverse conditions, thus enabling studies of the dynamics of secondary structure at a genomic scale...
  30. pmc Origins of specificity in protein-DNA recognition
    Remo Rohs
    Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA
    Annu Rev Biochem 79:233-69. 2010
    ....
  31. ncbi UNAFold: software for nucleic acid folding and hybridization
    Nicholas R Markham
    Xerox Litigation Services, Albany, NY, USA
    Methods Mol Biol 453:3-31. 2008
    ..Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php ...
  32. ncbi Crystal structure of parallel quadruplexes from human telomeric DNA
    Gary N Parkinson
    The Cancer Research UK Biomolecular Structure Unit, Chester Beatty Laboratories, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK
    Nature 417:876-80. 2002
    ..This DNA structure suggests a straightforward path for telomere folding and unfolding, as well as ways in which it can recognize telomere-associated proteins...
  33. pmc Structural basis for RNA 3'-end recognition by Hfq
    Evelyn Sauer
    Department of Biochemistry, Max Planck Institute for Developmental Biology, 72076 Tubingen, Germany
    Proc Natl Acad Sci U S A 108:13065-70. 2011
    ..The capacity of Hfq to occupy and sequester the RNA 3' end has important implications for the mechanisms by which Hfq is thought to affect sRNA stability, turnover, and regulation...
  34. ncbi Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1
    Julius Rabl
    Institute of Molecular Biology and Biophysics, ETH Zurich, Schafmattstrasse 20, 8093 Zurich, Switzerland
    Science 331:730-6. 2011
    ..It provides insights into the eukaryotic-specific aspects of protein synthesis, including the function of eIF1 as well as signaling and regulation mediated by the ribosomal proteins RACK1 and rpS6e...
  35. pmc Conformational analysis of nucleic acids revisited: Curves+
    R Lavery
    Institut de Biologie et Chimie des Proteines, CNRS UMR 5086 Universite de Lyon, 7 passage du Vercors, 69367 Lyon, France
    Nucleic Acids Res 37:5917-29. 2009
    ..With the help of the accompanying program Canal, it is possible to produce a variety of graphical output including parameter variations along a given structure and time series or histograms of parameter variations during dynamics...
  36. pmc Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs
    J Graham Ruby
    Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genome Res 17:1850-64. 2007
    ....
  37. ncbi Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
    A G Nackley
    Center for Neurosensory Disorders, University of North Carolina, Chapel Hill, NC 27599, USA
    Science 314:1930-3. 2006
    ..These data highlight the functional significance of synonymous variations and suggest the importance of haplotypes over single-nucleotide polymorphisms for analysis of genetic variations...
  38. pmc GtRNAdb: a database of transfer RNA genes detected in genomic sequence
    Patricia P Chan
    Department of Biomolecular Engineering, University of California, Santa Cruz, 1156 High Street, SOE 2, Santa Cruz, CA 95064, USA
    Nucleic Acids Res 37:D93-7. 2009
    ..The database can be searched by primary sequence similarity, tRNA characteristics or phylogenetic group. The database is publicly available at http://gtrnadb.ucsc.edu...
  39. ncbi Conservation and divergence of plant microRNA genes
    Baohong Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Plant J 46:243-59. 2006
    ..Regulation of gene expression by miRNAs appears to have existed at the earliest stages of plant evolution and has been tightly constrained (functionally) for more than 425 million years...
  40. ncbi An extensive class of small RNAs in Caenorhabditis elegans
    R C Lee
    Dartmouth Medical School, Department of Genetics, Hanover, NH 03755, USA
    Science 294:862-4. 2001
    ..elegans larval development, and three of them have apparent homologs in mammals and/or insects. Small noncoding RNAs of the miRNA class appear to be numerous and diverse...
  41. pmc Translation efficiency is determined by both codon bias and folding energy
    Tamir Tuller
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Proc Natl Acad Sci U S A 107:3645-50. 2010
    ....
  42. pmc RNAalifold: improved consensus structure prediction for RNA alignments
    Stephan H Bernhart
    Department of Computer Science, University of Leipzig, Leipzig, Germany
    BMC Bioinformatics 9:474. 2008
    ..In recent years, several alternative approaches have been advocated, pointing to several shortcomings of the original RNAalifold approach...
  43. pmc A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana
    Ramya Rajagopalan
    Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
    Genes Dev 20:3407-25. 2006
    ....
  44. pmc Circular dichroism and conformational polymorphism of DNA
    Jaroslav Kypr
    Institute of Biophysics, vvi Academy of Sciences of the Czech Republic, Brno, Czech Republic
    Nucleic Acids Res 37:1713-25. 2009
    ..Due to its numerous advantages, CD spectroscopy significantly participated in all basic conformational findings on DNA...
  45. ncbi A system for stable expression of short interfering RNAs in mammalian cells
    Thijn R Brummelkamp
    Division of Molecular Carcinogenesis, Division of Tumor Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, Netherlands
    Science 296:550-3. 2002
    ..Therefore, the pSUPER vector constitutes a new and powerful system to analyze gene function in a variety of mammalian cell types...
  46. ncbi Crystal structure of the eukaryotic ribosome
    Adam Ben-Shem
    IGBMC Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP10142, Illkirch F 67400, France
    Science 330:1203-9. 2010
    ..We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation...
  47. pmc Accurate SHAPE-directed RNA structure determination
    Katherine E Deigan
    Department of Chemistry, University of North Carolina, Chapel Hill, NC 27599 3290, USA
    Proc Natl Acad Sci U S A 106:97-102. 2009
    ....
  48. ncbi Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions
    Zhihu Zhao
    Department of Development and Genetics, Evolution Biology Centre, Uppsala University, Norbyvagen 18A, SE 752 36 Uppsala, Sweden
    Nat Genet 38:1341-7. 2006
    ..These observations shed new light on development, cancer epigenetics and the evolution of imprinting...
  49. pmc Mouse ES cells express endogenous shRNAs, siRNAs, and other Microprocessor-independent, Dicer-dependent small RNAs
    Joshua E Babiarz
    Institute for Regeneration Medicine, Center for Reproductive Sciences, University of California at San Francisco, San Francisco, California 94143, USA
    Genes Dev 22:2773-85. 2008
    ..Our results extend the known diversity of mammalian small RNA-generating pathways and show that mammalian siRNAs exist in cell types other than oocytes...
  50. pmc Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)
    Julius B Lucks
    Department of Bioengineering, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 108:11063-8. 2011
    ....
  51. ncbi Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor
    Jubao Duan
    Schizophrenia Genetics Research Program, Department of Psychiatry, The University of Chicago, Jules F Knapp Medical Research Center, Chicago, IL 60637, USA
    Hum Mol Genet 12:205-16. 2003
    ....
  52. pmc The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution
    Katsutomo Okamura
    Sloan Kettering Institute, Department of Developmental Biology, 521 Rockefeller Research Laboratories, 1275 York Ave, Box 252, New York, New York 10065, USA
    Nat Struct Mol Biol 15:354-63. 2008
    ..These data broaden the reach of the miRNA regulatory network and suggest an important mechanism that diversifies miRNA function during evolution...
  53. pmc Understanding the transcriptome through RNA structure
    Yue Wan
    Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California 94305, USA
    Nat Rev Genet 12:641-55. 2011
    ....
  54. ncbi A bivalent chromatin structure marks key developmental genes in embryonic stem cells
    Bradley E Bernstein
    Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA
    Cell 125:315-26. 2006
    ..These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency...
  55. pmc Structural architecture of the human long non-coding RNA, steroid receptor RNA activator
    Irina V Novikova
    Theoretical Biology and Biophysics, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
    Nucleic Acids Res 40:5034-51. 2012
    ..We perform similar experiments on alternatively spliced SRA isoforms to assess their structural features...
  56. ncbi Structure of the human telomere in K+ solution: an intramolecular (3 + 1) G-quadruplex scaffold
    Kim Ngoc Luu
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA
    J Am Chem Soc 128:9963-70. 2006
    ..The topological characteristics of this (3 + 1) G-quadruplex scaffold should provide a unique platform for structure-based anticancer drug design targeted to human telomeric DNA...
  57. pmc Global or local? Predicting secondary structure and accessibility in mRNAs
    Sita J Lange
    Department of Computer Science and Centre for Biological Signalling Studies BIOSS, Albert Ludwigs Universitat Freiburg, Germany
    Nucleic Acids Res 40:5215-26. 2012
    ..Our method, LocalFold, diminished all border effects and produced the most robust performance...
  58. ncbi Quorum sensing in staphylococci
    Richard P Novick
    Kimmel Center for Biology and Medicine, New York University Medical Center, New York, New York 10016, USA
    Annu Rev Genet 42:541-64. 2008
    ..We conclude with the suggestion that agr autoactivation, unlike classical enzyme induction, can occur under suboptimal conditions and can distinguish self from non-self by inducing an exclusive and coordinated population wide response...
  59. ncbi RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE)
    Edward J Merino
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599 3290, USA
    J Am Chem Soc 127:4223-31. 2005
    ..Modest extensions of the SHAPE approach will allow RNA structure to be monitored comprehensively and at single nucleotide resolution for RNAs of arbitrary sequence and structural complexity and under diverse solution environments...
  60. pmc Composite effects of gene determinants on the translation speed and density of ribosomes
    Tamir Tuller
    Department of Biomedical Engineering, Tel Aviv University, Israel
    Genome Biol 12:R110. 2011
    ....
  61. pmc Group II introns: mobile ribozymes that invade DNA
    Alan M Lambowitz
    Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712, USA
    Cold Spring Harb Perspect Biol 3:a003616. 2011
    ..Further, their ribozyme-based DNA integration mechanism enabled the development of group II introns into gene targeting vectors ("targetrons"), which have the unique feature of readily programmable DNA target specificity...
  62. pmc A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    Qian Hao Zhu
    CSIRO Plant Industry, Canberra, ACT 2601, Australia
    Genome Res 18:1456-65. 2008
    ..Comparison of the population of miRNAs and miRNA-like siRNAs in grains to those in other parts of the rice plant reveals that many are expressed in an organ-specific manner...
  63. pmc High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
    Kevin A Wilkinson
    Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina, United States of America
    PLoS Biol 6:e96. 2008
    ..High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further application of this technology will make possible newly informative analysis of any RNA in a cellular transcriptome...
  64. pmc MiPred: classification of real and pseudo microRNA precursors using random forest prediction model with combined features
    Peng Jiang
    State Key Laboratory of Bioelectronics, Department of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
    Nucleic Acids Res 35:W339-44. 2007
    ..bioinf.seu.edu.cn/miRNA/. Given a sequence, MiPred decides whether it is a pre-miRNA-like hairpin sequence or not. If the sequence is a pre-miRNA-like hairpin, the RF classifier will predict whether it is a real pre-miRNA or a pseudo one...
  65. ncbi Evidence that miRNAs are different from other RNAs
    B H Zhang
    The Institute of Environmental and Human Health TIEHH, and Department of Environmental Toxicology, Texas Tech University, Lubbock, Texas 79409 1163, USA
    Cell Mol Life Sci 63:246-54. 2006
    ..001). The MFEI for miRNAs was 0.97, significantly higher than tRNAs (0.64), rRNAs (0.59), or mRNAs (0.65). Our findings should facilitate the prediction and identification of new miRNAs using computational and experimental strategies...
  66. pmc Positive regulation by small RNAs and the role of Hfq
    Toby Soper
    Johns Hopkins University, Program in Cell, Molecular, Developmental Biology and Biophysics, Baltimore, MD 21218, USA
    Proc Natl Acad Sci U S A 107:9602-7. 2010
    ..These studies demonstrate that binding of Hfq to the rpoS mRNA is critical for sRNA regulation under normal conditions, but if the stability of the sRNA*mRNA complex is sufficiently high, the requirement for Hfq can be bypassed...
  67. pmc Genomic regions flanking E-box binding sites influence DNA binding specificity of bHLH transcription factors through DNA shape
    Raluca Gordân
    Division of Genetics, Department of Medicine, Brigham and Women s Hospital and Harvard Medical School, Boston, MA 02115, USA
    Cell Rep 3:1093-104. 2013
    ..Thus, the local shape of target sites might play a widespread role in achieving regulatory specificity within TF families...
  68. ncbi RNA-binding proteins: modular design for efficient function
    Bradley M Lunde
    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
    Nat Rev Mol Cell Biol 8:479-90. 2007
    ..These studies have shown how, for many RNA-binding proteins, multiple modules define the fundamental structural unit that is responsible for biological function...
  69. pmc NMR detection of structures in the HIV-1 5'-leader RNA that regulate genome packaging
    Kun Lu
    Howard Hughes Medical Institute HHMI and Department of Chemistry and Biochemistry, University of Maryland Baltimore County UMBC, Baltimore, MD 21250, USA
    Science 334:242-5. 2011
    ..Our findings support a packaging mechanism in which translation, dimerization, NC binding, and packaging are regulated by a common RNA structural switch...
  70. pmc RNAMotif, an RNA secondary structure definition and search algorithm
    T J Macke
    Ibis Therapeutics, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
    Nucleic Acids Res 29:4724-35. 2001
    ....
  71. pmc Posttranscriptional regulation of miRNAs harboring conserved terminal loops
    Gracjan Michlewski
    Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, Western General Hospital, Edinburgh EH4 2XU, UK
    Mol Cell 32:383-93. 2008
    ..Altogether, these data suggest the existence of auxiliary factors for the processing of specific miRNAs, revealing an additional level of complexity for the regulation of miRNA biogenesis...
  72. ncbi Mechanisms of site-specific recombination
    Nigel D F Grindley
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520 8114, USA
    Annu Rev Biochem 75:567-605. 2006
    ..Details of the site-specific recombination processes have been revealed by recent structural and biochemical studies of members of both families...
  73. pmc Self-assembly of DNA into nanoscale three-dimensional shapes
    Shawn M Douglas
    Department of Cancer Biology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 459:414-8. 2009
    ..We anticipate that our strategy for self-assembling custom three-dimensional shapes will provide a general route to the manufacture of sophisticated devices bearing features on the nanometre scale...
  74. pmc Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein
    Maria A Schumacher
    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97201 3098, USA
    EMBO J 21:3546-56. 2002
    ..Such binding suggests a mechanism for Hfq function...
  75. pmc Structural determinants and mechanism of HIV-1 genome packaging
    Kun Lu
    Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore, MD 21250, USA
    J Mol Biol 410:609-33. 2011
    ..Here, we review efforts that have been made to identify the molecular determinants and mechanism of human immunodeficiency virus type 1 genome packaging...
  76. pmc Expression profiling of microRNAs by deep sequencing
    Chad J Creighton
    Dan L Duncan Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX 77030, USA
    Brief Bioinform 10:490-7. 2009
    ..Here we discuss tools and methodologies for the analysis of microRNA expression data from deep sequencing...
  77. ncbi Identification of soybean microRNAs and their targets
    Baohong Zhang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    Planta 229:161-82. 2008
    ....
  78. ncbi microPred: effective classification of pre-miRNAs for human miRNA gene prediction
    Rukshan Batuwita
    Oxford University Computing Laboratory, University of Oxford, Wolfson Building, Oxford, UK
    Bioinformatics 25:989-95. 2009
    ....
  79. pmc Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Victor Kunin
    DOE Joint Genome Institute, Walnut Creek, CA 94598, USA
    Genome Biol 8:R61. 2007
    ..It has been recently shown that CRISPR provides acquired resistance against viruses in prokaryotes...
  80. pmc Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility
    Ci Ji Lim
    NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, Singapore, 119077, Singapore
    Nucleic Acids Res 40:3316-28. 2012
    ..We also show that >1 mM magnesium promotes higher order DNA condensation, suggesting StpA may also play a role in chromosomal DNA packaging...
  81. pmc Disease-associated mutations that alter the RNA structural ensemble
    Matthew Halvorsen
    Biomedical Sciences Department, University at Albany, Albany, New York, USA
    PLoS Genet 6:e1001074. 2010
    ..Our SNPfold algorithm can help identify RiboSNitches by leveraging GWAS data and an analysis of the mRNA structural ensemble...
  82. pmc Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
    Leonardo G Trabuco
    Beckman Institute, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
    Structure 16:673-83. 2008
    ..The MDFF method is then used to obtain high-resolution structures of the E. coli ribosome in different functional states imaged by cryo-EM...
  83. ncbi Identification and characterization of new plant microRNAs using EST analysis
    Bao Hong Zhang
    The Institute of Environmental and Human Health, and Department of Environmental Toxicology, Texas Tech University, Lubbock, TX 79409 1163, USA
    Cell Res 15:336-60. 2005
    ..Environmental stresses and developmental switching may be the signals for synthesis and regulation of miRNAs in plants. A model for miRNA induction and expression, and gene regulation by miRNA is hypothesized...
  84. ncbi Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution
    S DOUBLIE
    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
    Nature 391:251-8. 1998
    ..The structure illustrates how nucleotides are selected in a template-directed manner, and provides a structural basis for a metal-assisted mechanism of phosphoryl transfer by a large group of related polymerases...
  85. pmc Prospects for riboswitch discovery and analysis
    Ronald R Breaker
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520 8103, USA
    Mol Cell 43:867-79. 2011
    ..Some of the greatest prospects for riboswitch research and some of the more interesting mysteries are discussed in this review...
  86. pmc Dual coding of siRNAs and miRNAs by plant transposable elements
    Jittima Piriyapongsa
    School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332 0230, USA
    RNA 14:814-21. 2008
    ..The siRNA-to-miRNA evolutionary transition is representative of a number of other regulatory mechanisms that evolved to silence TEs and were later co-opted to serve as regulators of host gene expression...
  87. pmc Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA
    Cameron Smith
    Bioinformatics Group, University of Freiburg, Freiburg 79110, Germany
    Nucleic Acids Res 38:W373-7. 2010
    ..The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de...
  88. pmc FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing
    Jason G Underwood
    Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, California, USA
    Nat Methods 7:995-1001. 2010
    ..We probed in two cell types to verify reproducibility. We also identified and experimentally validated structured regions in ncRNAs with, to our knowledge, no previously reported probing data...
  89. pmc The transcriptionally active regions in the genome of Bacillus subtilis
    Simon Rasmussen
    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
    Mol Microbiol 73:1043-57. 2009
    ..One of the genes having this tail is efeN, which encodes a target of the twin-arginine translocase (Tat) protein translocation system...
  90. ncbi X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution
    Christopher D Putnam
    Ludwig Institute for Cancer Research, La Jolla, CA, USA
    Q Rev Biophys 40:191-285. 2007
    ....
  91. ncbi The structural and functional diversity of metabolite-binding riboswitches
    Adam Roth
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8103, USA
    Annu Rev Biochem 78:305-34. 2009
    ..This diverse set of metabolite-sensing RNAs is found to exploit a variety of distinct mechanisms to regulate genes that are fundamental to metabolism...
  92. ncbi Prediction of RNA secondary structure using generalized centroid estimators
    Michiaki Hamada
    Mizuho Information and Research Institute, Inc, 2 3 Kanda Nishikicho, Chiyoda ku, Tokyo 101 8443, Japan
    Bioinformatics 25:465-73. 2009
    ..However, there is room for improvement in the objective functions presented in previous studies, which are maximized in the posterior decoding with respect to the accuracy measures for secondary structures...
  93. ncbi RNA chaperones, RNA annealers and RNA helicases
    Lukas Rajkowitsch
    Max F Perutz Laboratories, University of Vienna, Vienna, Austria
    RNA Biol 4:118-30. 2007
    ..Finally, we present a new website for proteins with RNA chaperone activity which compiles all the information on these proteins with the perspective to promote the understanding of their activity...
  94. pmc Structural basis of gate-DNA breakage and resealing by type II topoisomerases
    Ivan Laponogov
    Randall Division of Cell and Molecular Biophysics, King s College London, London, United Kingdom
    PLoS ONE 5:e11338. 2010
    ....
  95. pmc Dissecting the influence of Mg2+ on 3D architecture and ligand-binding of the guanine-sensing riboswitch aptamer domain
    Janina Buck
    Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max von Laue Strasse 7 and 9, 60438 Frankfurt am Main, Germany
    Nucleic Acids Res 38:4143-53. 2010
    ..We propose that reduction of conformational dynamics in remote regions of the riboswitch aptamer domain is the minimal pre-requisite to pre-organize the core region for specific ligand binding...
  96. ncbi Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome
    Julia A Chekanova
    School of Biological Sciences, University of Missouri Kansas City, Kansas City, MO 64110, USA
    Cell 131:1340-53. 2007
    ..These first genome-wide maps of exosome substrates will aid in illuminating new fundamental components and regulatory mechanisms of eukaryotic transcriptomes...
  97. ncbi microRNA target predictions in animals
    Nikolaus Rajewsky
    Center for Comparative Functional Genomics Department of Biology, 100 Washington Square East, New York, New York 10003, USA
    Nat Genet 38:S8-13. 2006
    ....
  98. pmc Improved RNA secondary structure prediction by maximizing expected pair accuracy
    Zhi John Lu
    Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
    RNA 15:1805-13. 2009
    ..Using MaxExpect, the average PPV of optimal structure is improved from 66% to 68% at the same sensitivity level (73%) compared with free energy minimization...
  99. ncbi The structure of alpha-thrombin inhibited by a 15-mer single-stranded DNA aptamer
    K Padmanabhan
    Department of Chemistry, Michigan State University, East Lansing 48824 1322
    J Biol Chem 268:17651-4. 1993
    ..Although G-quadruplexes are favored in the presence of monovalent cations, there is no evidence of the latter in the thrombin complex...
  100. pmc Analysis of four-way junctions in RNA structures
    Christian Laing
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, New York, 10012, USA
    J Mol Biol 390:547-59. 2009
    ..Such analyses of RNA building blocks can ultimately help in the difficult task of RNA 3D structure prediction...
  101. pmc Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking
    Sander Granneman
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland, UK
    EMBO J 29:2026-36. 2010
    ..Nob1 binds before pre-rRNA cleavage, and we conclude that structural reorganization is needed to bring together the catalytic PIN domain and its target...

Research Grants65

  1. METALLOREGULATION BY MERR AND FUR PROTEIN FAMILIES
    THOMAS V O'HALLORAN; Fiscal Year: 2013
    ..will enable us to understand how metal-binding events are communicated through explicit protein and nucleic acid conformation changes into a direct effect on polymerase activity...
  2. STRUCTURE OF VIRAL RNA AND ITS ROLE IN ASSEMBLY
    Alexander McPherson; Fiscal Year: 2006
    ..To extend our investigations of nucleic acid conformation and packaging to larger, more complex viruses we will extend our AFM investigations of the internal ..
  3. X RAY STUDIES OF NUCLEIC ACID CONSTITUENTS
    Muttaiya Sundaralingam; Fiscal Year: 2001
    ..The work will provide the limits of nucleic acid conformation, details of the tertiary structures of the duplexes, novel base-pairing schemes, base triples and ..
  4. BIOCHEMICAL MECHANISM OF EXOCYCLIC ADDUCTS IN CANCER
    B Singer; Fiscal Year: 2004
    ..These adducts, when incorporated into DNA, will be studied in terms of resulting changes in nucleic acid conformation using thermodynamics, molecular modeling and NMR...
  5. DNA/RNA Quadruplexes: Structure, Stability, Interactions
    RICHARD SHAFER; Fiscal Year: 2006
    unreadable] DESCRIPTION (provided by applicant): This project focuses on the unusual nucleic acid conformation of quadruplexes, built upon the guanine quartet...
  6. CIRCULAR DICHROISM STOPPED FLOW SPECTROMETER
    LUIS MARKY; Fiscal Year: 1999
    ..Kabanov), (5) Biodegradable nanospheres for drug delivery (V. Labhasetwar) (6) Thermodynamics of Nucleic acid conformation and interactions (L. A. Marky), and (7) Determinants for toxicity of calcineurin inhibitors (P. Stemmer)...
  7. Acquisition of a Circular Dichroism Spectrometer
    Barbara Brodsky; Fiscal Year: 2002
    ..The present CD instrument (an Aviv 62 DS provided a cutting edge research tool for studying protein and nucleic acid conformation, stability, and ligand binding to the laboratories of 5 NIH-funded major users, and more than 20 funded ..
  8. NUCLEIC ACID CONFORMATION, PROPERTIES, AND INTERACTIONS
    WILMA OLSON; Fiscal Year: 2006
    ..New approaches to build atomic models of DNA that take explicit account of the closely associated cloud of bound waters are also under development. ..
  9. Maintenance of the tRNA 3' end
    Ya Ming Hou; Fiscal Year: 2008
    ..Because of the importance of CCA in maintenance of cellular life, the proposed studies will have a strong impact on human health and diseases. ..
  10. Bioscope II - AFM system for Nanoimaging Core Facility
    Yuri Lyubchenko; Fiscal Year: 2007
    ..There are two NIH funded investigators outside the campus who also want to use the unique features of the integrated Bioscope/IX71 system. [unreadable] [unreadable] [unreadable]..
  11. In-depth Biology Foundations:Quantitative Scientists (RMI)
    WILMA OLSON; Fiscal Year: 2008
    ..unreadable] [unreadable]..
  12. FUNCTIONAL ANALYSIS OF AN RNA STRUCTURAL MOTIF
    Ya Ming Hou; Fiscal Year: 2005
    ..coli CysRS for its ability to distinguish cysteine from serine. These studies shall shed new light on the molecular interactions responsible for the accurate translation of the genetic code. ..
  13. Nanomedicine Center for Protein Deposition Diseases(RMI)
    Yuri Lyubchenko; Fiscal Year: 2004
    ..We assembled a multidisciplinary team of 12 investigators with broad expertise in nanobiology, imaging, spectroscopy, single molecule biophysics, proteomics, drug delivery and medicine. ..
  14. Aminoacyl-tRNA synthetases in Archaea
    Ya Ming Hou; Fiscal Year: 2006
    ..jannaschii to gain a broader insight into its aminoacyl-tRNA synthetases as a basis for understanding the origin and evolution of contemporary mRNA-encoded protein synthesis in extant organisms. [unreadable] [unreadable]..
  15. Structural Studies of Metabolic Membrane Proteins
    Joanne Yeh; Fiscal Year: 2006
    ..Our specific aims are to obtain atomic resolution structures of both membrane proteins, both of which are likely to be novel targets for antibiotic design and therapy. ..
  16. CONFORMATIONAL PROPERTIES OF DNA CATENANES
    Alexander V Vologodskii; Fiscal Year: 2010
    ..Combining computer simulations and experiments, we will try to understand the mechanism of high topological selectivity of DNA resolvases. ..
  17. Mechanisms of mutagenesis in hot spots causing cancer
    Barbara Wright; Fiscal Year: 2007
    ..These investigations should provide new insights into the mechanisms of mutagenesis and carcinogenesis. ..
  18. LOCAL AND GLOBAL CONFORMATIONS OF SUPERCOILED DNA
    Yuri Lyubchenko; Fiscal Year: 2007
    ..abstract_text> ..
  19. Identification and Characterization of Antiterminator RNAs
    RODNEY KING; Fiscal Year: 2007
    ..unreadable] [unreadable] [unreadable]..
  20. Upstream ORFs: A general strategy for virus attenuation
    Theo Dreher; Fiscal Year: 2006
    ..abstract_text> ..
  21. DYNAMICS AND FUNCTION OF G4 DNA
    Nancy Maizels; Fiscal Year: 2007
    ..abstract_text> ..
  22. STRUCTURAL ORGANIZATION AND PROTEOMICS OF TB
    Thomas Terwilliger; Fiscal Year: 2005
    ..The structural and functional information obtained in this project is to be placed in the public domain by timely deposition in publicly available databases. ..
  23. SATB1 IN T CELL APOPTOSIS
    Terumi Kohwi Shigematsu; Fiscal Year: 2007
    ..We will also test whether the SATB 1 cleavage, which normally occurs in apoptosis, is also important in other biological processes, such as T cell differentiation (Specific Aim 3). ..
  24. Proteins Mediating Interaction of HIV-1 and JCV in CNS
    Edward M Johnson; Fiscal Year: 2011
    ..Results will help elucidate pathways of activation of JCV in the brain and will help target particular molecular interactions for therapy. ..
  25. Cellular Membrane RNA Activities
    MICHAEL J YARUS; Fiscal Year: 2010
    ..The intended net effect ofthese three protocols is to detect a subset of membrane-resident RNAs in human cells that have bilayer affinity built into their covalent structures, ..
  26. Mechanistic studies of DNA repair and damage response
    Dorothy A Erie; Fiscal Year: 2010
    ..abstract_text> ..
  27. 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. ..
  28. GERM LINE ESTABLISHMENT IN DROSOPHILA MELANOGASTER
    Paul Lasko; Fiscal Year: 2009
    ..Finally, in the 5th aim the relationship between Tud, a protein essential downstream of Vas for germ line establishment, Cup, a translational regulator, TACC, a microtubule binding protein, and Dynein heavy chain will be examined. ..
  29. Characterization of MeCP2 target genes in Rett Syndrome
    Terumi Kohwi Shigematsu; Fiscal Year: 2008
    ..Our study will provide information about the molecular mechanisms underlying Mecp2 activity and how MECP2 mutations might cause Rett syndrome. ..
  30. MOLECULAR MECHANISMS OF ISOTYPE SWITCH RECOMBINATION
    Nancy Maizels; Fiscal Year: 2009
    ..abstract_text> ..
  31. ACS Symposium, Frontiers in Chemical Toxicology
    Michael Stone; Fiscal Year: 2008
    ..Highly respected scientists from a variety of disciplines have agreed to present their most recent findings. [unreadable] [unreadable] [unreadable] [unreadable]..
  32. Packaging of the Segmented Genome of Bacteriophage Phi6
    Leonard Mindich; Fiscal Year: 2008
    ..There is no current understanding of the genomic packaging of the reoviridae, segmented dsRNA viruses that cause disease in plants and animals, including humans. ..
  33. A High-Throughput Crystallization Screening System for the UCSC Macromolecular X-
    Harry Noller; Fiscal Year: 2008
    ..unreadable] [unreadable] [unreadable]..
  34. 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. ..
  35. CAUSATIVE GENETIC VARIATION IN HUMAN TELOMERE GENES
    Victoria Lundblad; Fiscal Year: 2006
    ..This will, we hope, set the stage for elucidating the target(s) of telomere-based human aging, with the potential for clinical intervention to alleviate the onset of at least some age-dependent diseases. ..
  36. Luminescence Studies of Lanthanide Contrast Agents
    JANET MORROW; Fiscal Year: 2006
    ..The new laser system will also be available to researchers throughout the country and will be at the heart of a center for Ln(lll) luminescence research. [unreadable] [unreadable] [unreadable]..
  37. Assemby and Recombination of dsRNA Bacteriophage phi8
    Leonard Mindich; Fiscal Year: 2004
    ..Since reverse genetic techniques and in vitro genomic packaging are not available for these viruses, the cystoviridae (dsRNA bacteriophages) offer a valuable model for system for the study of the eukaryotic systems. ..
  38. Nuclease-Resistant Aptamers to Botox and Anthrax Toxins
    John Bruno; Fiscal Year: 2004
    ..Such reagents could also be used in environmental biosensors or diagnostic test kits for detection of BOTOX and anthrax toxins in body fluids or environmental samples. ..
  39. Nuclease-Resistant Aptamers for Anthrax Opsonization
    John Bruno; Fiscal Year: 2004
    ..Such shielded aptamers could even be used in inhalers to enhance alveolar macrophage phagocytosis. ..
  40. Lymphocytes and the Immune System: Mechanisms
    Amy Kenter; Fiscal Year: 2003
    ..The meeting will produce a contemporary perspective and overview of the immune system as well as a critical review of the recent research and will permit evaluation of future research directions. ..
  41. Novel Targets for Treatment of Smallpox
    Stewart Shuman; Fiscal Year: 2003
    ....
  42. CHARACTERIZING ISOTYPE SWITCHING USING SWITCH SUBSTRATES
    Amy Kenter; Fiscal Year: 2003
    ..The role of transcription in cleavage of S regions during recombination will be explored. Finally, a major effort toward cloning factors involved in the switch recombination reaction is proposed. ..
  43. MOLECULAR DYNAMICS SIMULATIONS OF DNA OLIGONUCLEOTIDES
    David Beveridge; Fiscal Year: 2003
    ..abstract_text> ..
  44. 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. ..
  45. 2002 Gordon Research Conference on Biopolymers
    DOROTHY ERIE; Fiscal Year: 2002
    ..The program encompasses some of the most exciting research in the field of nucleic acid and protein biophysics and promises to generate lively discussions both in and outside of the sessions. ..
  46. STRUCTURE OF DNA LESIONS IN SUPERHELICAL DOMAINS
    STEPHEN LEVENE; Fiscal Year: 2001
    ..The conformation of super coiled, lesion-containing DNA molecules deduced from these solution studies will be compared with that observed by independent conventional and cryoelectron microscopy experiments. ..
  47. BIOPHYSICAL AND SCANNING FORCE MICROSCOPY STUDIES
    DOROTHY ERIE; Fiscal Year: 2001
    ..3) How do polymorphisms affect the above properties? ..
  48. Base unpairing regions and chromatin folding
    Terumi Kohwi Shigematsu; Fiscal Year: 2004
    ..The research proposed here will test whether certain BURs can act as long-range regulatory elements by forming a specific loop domain structure during T cell differentiation. ..
  49. Regulation of West Nile virus gene expression
    Theo Dreher; Fiscal Year: 2004
    ..Our studies will also be applicable to other flaviviruses for which there is at present no vaccine, including dengue virus. ..
  50. Nucleic Acid Gordon Research Conference
    ANNA PYLE; Fiscal Year: 2004
    ..Poster sessions and optional recreational activities will stimulate informal interactions among participants. ..
  51. CONTROL OF INITIATION OF DNA REPLICATION IN LUNG CANCER
    Edward Johnson; Fiscal Year: 2006
    ..Results will allow identification of links between control of initiation of replication and imposition of checkpoint controls that are critical in preventing progression to cancer...
  52. X-Ray Crystallography Imaging Plate Detector
    Harry Noller; Fiscal Year: 2002
    ....
  53. 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...
  54. RNA STRUCTURE AND FUNCTION STUDIES VIA GENE CONSTRUCTION
    Michael Yarus; Fiscal Year: 2005
    ..In addition, this this project proposes to find and characterize new classes of RNA enzymes that use enzymatic cofactors as and intrinsic part of their reaction mechanisms. ..
  55. Crystallographic Studies of Ribosome Functional Sites
    Susan Schroeder; Fiscal Year: 2005
    ....
  56. New Inhibitors of HIV Replication
    Gabriele Varani; Fiscal Year: 2005
    ..While the project is challenging and partly untested, the introduction of new structures leading to therapeutic options for treating drug-resistant viruses would have substantial impact. ..
  57. SATB1 IN T CELL APOPTOSIS
    Terumi Kohwi Shigematsu; Fiscal Year: 2004
    ..abstract_text> ..
  58. Workshop on Methods for Macromolecular Modeling
    Tamar Schlick; Fiscal Year: 2004
    ....
  59. The Mammalian Signal Recognition Particle
    KEVIN WEEKS; Fiscal Year: 2006
    ..Moreover, the work is designed to identify principles generalizable to other biologically and medically prominent ribonucleoprotein complexes. ..
  60. CHARACTERIZATION & ORGANIZATION OF TRANSPOSABLE ELEMENTS
    Zhijian Tu; Fiscal Year: 2006
    ..Finally, this work will enhance our understanding of the basic genetics of An. gambiae by systematically investigating TEs, which are substantial and potentially potent components of the genome...
  61. A hybrid 12T Q-FTMS for the investigation of nucleic acids non-cov./cov.adducts
    Daniele Fabris; Fiscal Year: 2006
    ..unreadable] [unreadable] [unreadable] [unreadable]..
  62. Protein-Facilitates RNA Catalysts
    KEVIN WEEKS; Fiscal Year: 2007
    ..5) To begin to explore the molecular mechanism by which Mrs1 facilitates catalysis of the bl3 group I intron. (6) To develop a high resolution model for the maturase-bl3 RNA complex. ..