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. 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
  2. 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
  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. 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
  5. 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
  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. doi 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
  8. 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
  9. 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
  10. 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

Detail Information

Publications279 found, 100 shown here

  1. 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...
  2. 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'...
  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. 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...
  5. 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...
  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. doi 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...
  8. 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...
  9. 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/)...
  10. 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...
  11. 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
    ....
  12. 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/...
  13. 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...
  14. 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...
  15. 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...
  16. 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...
  17. doi 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...
  18. 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...
  19. 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
    ....
  20. 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...
  21. doi 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 ...
  22. 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...
  23. 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...
  24. 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...
  25. 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...
  26. 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...
  27. doi 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...
  28. 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...
  29. 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
    ....
  30. 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...
  31. 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...
  32. 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...
  33. 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...
  34. 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...
  35. 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...
  36. 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...
  37. 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...
  38. 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)...
  39. 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...
  40. 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
    ....
  41. 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...
  42. 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
    ....
  43. 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...
  44. 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...
  45. 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...
  46. 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
    ....
  47. 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...
  48. 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...
  49. 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...
  50. 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...
  51. 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...
  52. 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...
  53. doi Identification of soybean microRNAs and their targets
    Baohong Zhang
    Department of Biology, East Carolina University, Greenville, NC 27858, USA
    Planta 229:161-82. 2008
    ....
  54. doi 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
    ....
  55. 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...
  56. 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...
  57. 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...
  58. 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...
  59. 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...
  60. 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...
  61. 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...
  62. doi 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...
  63. 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...
  64. 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...
  65. 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...
  66. doi 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...
  67. 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...
  68. 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
    ....
  69. doi 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...
  70. 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...
  71. 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...
  72. 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
    ....
  73. 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...
  74. 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
    ....
  75. 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...
  76. 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...
  77. pmc Bridging IRES elements in mRNAs to the eukaryotic translation apparatus
    Kerry D Fitzgerald
    Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA 92697, USA
    Biochim Biophys Acta 1789:518-28. 2009
    ....
  78. 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...
  79. doi Computational approaches to 3D modeling of RNA
    Christian Laing
    Department of Chemistry and Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, NY 10012, USA
    J Phys Condens Matter 22:283101. 2010
    ..We conclude by outlining some suggestions for future RNA folding research...
  80. pmc Design of simple synthetic RNA thermometers for temperature-controlled gene expression in Escherichia coli
    Juliane Neupert
    Max Planck Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, D 14476 Potsdam Golm, Germany
    Nucleic Acids Res 36:e124. 2008
    ..Our data suggest that the thermometers function by a simple melting mechanism and thus provide minimum size on/off switches to experimentally induce or repress gene expression by temperature...
  81. pmc Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome
    Charles Addo-Quaye
    Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA
    RNA 15:2112-21. 2009
    ..MIR319 is thus a conserved exception to the general rule of loop-last processing of MIRNA hairpins. Loop-first MIR319 processing may contribute to the high efficacy of a widely used MIR319-based strategy for aMIRNA production in plants...
  82. pmc A new type of IRES within gag coding region recruits three initiation complexes on HIV-2 genomic RNA
    Laure Weill
    CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologique, Universite Paris Descartes, 4 avenue de l Observatoire, 75270 Paris Cedex 06, France
    Nucleic Acids Res 38:1367-81. 2010
    ..The structural and functional properties of gag coding sequence define a new type of IRES. Although its precise role is unknown, the conservation of the IRES among fast evolving lentiviruses suggests an important physiological role...
  83. pmc 2-D structure of the A region of Xist RNA and its implication for PRC2 association
    Sylvain Maenner
    Faculte des Sciences et Techniques, AREMS, Nancy Universite, UMR 7214 CNRS UHP 1, Vandoeuvre les Nancy, France
    PLoS Biol 8:e1000276. 2010
    ..Our data with their emphasis on the importance of inter-repeat pairing change fundamentally our conception of the 2-D structure of the A region of Xist RNA and support its possible implication in recruitment of the PRC2 complex...
  84. pmc NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
    Douglas H Turner
    Department of Chemistry and Center for RNA Biology, Box 0216, University of Rochester, Rochester, NY 14627 0216, USA
    Nucleic Acids Res 38:D280-2. 2010
    ..The initial release covers parameters for predicting RNA folding free energy and enthalpy changes...
  85. 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...
  86. pmc CENTROIDFOLD: a web server for RNA secondary structure prediction
    Kengo Sato
    Japan Biological Informatics Consortium, 2 45 Aomi, Koto ku, Tokyo 135 8073, Japan
    Nucleic Acids Res 37:W277-80. 2009
    ..The major advantage of this server is that it employs our original CentroidFold software as its prediction engine which scores the best accuracy in our benchmark results. Our web server is freely available with no login requirement...
  87. pmc The long and the short of riboswitches
    Alexander Serganov
    Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10021, USA
    Curr Opin Struct Biol 19:251-9. 2009
    ....
  88. pmc Folding of a transcriptionally acting preQ1 riboswitch
    Ulrike Rieder
    Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria
    Proc Natl Acad Sci U S A 107:10804-9. 2010
    ..A model is presented how a riboswitch that provides no obvious overlap between aptamer and terminator stem-loop solves this communication problem by involving bistable sequence determinants...
  89. pmc Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis
    Nathan J Baird
    Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 1024, USA
    RNA 16:598-609. 2010
    ..It is possible that the range of behaviors observed by SAXS, rather than being a biophysical idiosyncrasy, reflects adaptation of riboswitches to the regulatory requirements of their individual genomic context...
  90. pmc The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization
    R H Crozier
    Department of Genetics and Human Variation, La Trobe University, Bundoora, Victoria, Australia
    Genetics 133:97-117. 1993
    ....
  91. pmc Atomic accuracy in predicting and designing noncanonical RNA structure
    Rhiju Das
    Departments of Biochemistry and Physics, Stanford University, Stanford, California, USA
    Nat Methods 7:291-4. 2010
    ..Sequence redesign calculations recovered native bases at 65% of residues engaged in noncanonical interactions, and we experimentally validated mutations predicted to stabilize a signal recognition particle domain...
  92. ncbi First snapshots of the HIV-1 RNA structure in infected cells and in virions
    Jean Christophe Paillart
    Unité Propre de Recherche 9002 du CNRS conventionnée à l Université Louis Pasteur, Institut de Biologie Moleculaire et Cellulaire, 15 rue Rene Descartes, 67084 Strasbourg Cedex, France
    J Biol Chem 279:48397-403. 2004
    ..Taken together, our results provided the first analysis of the dynamic of RNA structure of the human immunodeficiency virus type 1 RNA genome during virus assembly ex vivo...
  93. ncbi The Strepsiptera problem: phylogeny of the holometabolous insect orders inferred from 18S and 28S ribosomal DNA sequences and morphology
    M F Whiting
    Department of Zoology and M L Bean Life Science Museum, Brigham Young University, Provo, Utah 84602, USA
    Syst Biol 46:1-68. 1997
    ....
  94. pmc Selective stabilization of mammalian microRNAs by 3' adenylation mediated by the cytoplasmic poly(A) polymerase GLD-2
    Takayuki Katoh
    Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo ku, Tokyo 113 8656, Japan
    Genes Dev 23:433-8. 2009
    ....
  95. pmc RNA structure of trinucleotide repeats associated with human neurological diseases
    Krzysztof Sobczak
    Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Science, Noskowskiego 12 14, 61 704 Poznan, Poland
    Nucleic Acids Res 31:5469-82. 2003
    ..We have provided experimental evidence that CCUG repeats implicated in myotonic dystrophy type 2 also form hairpin structures with properties similar to that composed of the CUG repeats...
  96. pmc mRNA secondary structures fold sequentially but exchange rapidly in vivo
    Elisabeth M Mahen
    Department of Molecular Biology, The Scripps Research Institute, La Jolla, California, USA
    PLoS Biol 8:e1000307. 2010
    ....
  97. pmc Using DNA mechanics to predict in vitro nucleosome positions and formation energies
    Alexandre V Morozov
    Department of Physics and Astronomy and BioMaPS Institute for Quantitative Biology, Rutgers University, 136 Frelinghuysen Road, Piscataway, NJ 08854, USA
    Nucleic Acids Res 37:4707-22. 2009
    ..We find that DNABEND can successfully predict in vitro nucleosome positions and free energies, providing a physical explanation for the intrinsic sequence dependence of histone-DNA interactions...
  98. pmc Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs
    Sander Granneman
    Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Kings Buildings, Mayfield Road, Edinburgh EH9 3JR, Scotland
    Proc Natl Acad Sci U S A 106:9613-8. 2009
    ..This finding demonstrates that the snoRNP proteins directly contact the pre-rRNA substrate, suggesting roles in snoRNA recruitment. The techniques reported here should be widely applicable to analyses of RNA-protein interactions...
  99. ncbi Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV
    Ian Brierley
    Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
    Virus Res 119:29-42. 2006
    ..The role of frameshifting in the replication cycle of the two pathogens and potential antiviral therapies targeting frameshifting will also be discussed...
  100. pmc Comparative genomics reveals 104 candidate structured RNAs from bacteria, archaea, and their metagenomes
    Zasha Weinberg
    Howard Hughes Medical Institute, Yale University, New Haven, CT 06520 8103, USA
    Genome Biol 11:R31. 2010
    ..Structured RNAs can be detected by comparative genomics, in which homologous sequences are identified and inspected for mutations that conserve RNA secondary structure...
  101. ncbi CAG repeats containing CAA interruptions form branched hairpin structures in spinocerebellar ataxia type 2 transcripts
    Krzysztof Sobczak
    Laboratory of Cancer Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12 14, 61 704 Poznan, Poland
    J Biol Chem 280:3898-910. 2005
    ..The structural organization of the repeat interruption systems present in other human transcripts, such as SCA1, TBP, FOXP2, and MAML2, are also discussed...

Research Grants117 found, 100 shown here

  1. 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 ..
  2. 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 ..
  3. BIOCHEMICAL MECHANISM OF EXOCYCLIC ADDUCTS IN CANCER
    Bo Hang; 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...
  4. DNA/RNA Quadruplexes: Structure, Stability, Interactions
    RICHARD SHAFER; Fiscal Year: 2006
    This project focuses on the unusual nucleic acid conformation of quadruplexes, built upon the guanine quartet...
  5. NUCLEIC ACID CONFORMATION, PROPERTIES, AND INTERACTIONS
    WILMA OLSON; Fiscal Year: 1980
    ..energy calculations and statistical mechanical analyses it is possible both to elucidate details of nucleic acid conformation and also to provide a rational understanding of observed experimental phenomena...
  6. 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 ..
  7. 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. ..
  8. NUCLEIC ACID CONFORMATION, PROPERTIES, AND INTERACTIONS
    WILMA OLSON; Fiscal Year: 2001
    ....
  9. 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. ..
  10. 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. ..
  11. CONFORMATIONAL PROPERTIES OF DNA CATENANES
    Alexander Vologodskii; Fiscal Year: 2006
    ..New computational methods will be developed in the project which will allow us to estimate probabilities of very rare events, related to juxtaposition of specific DNA sites. ..
  12. CONFORMATIONAL PROPERTIES OF DNA CATENANES
    Alexander Vologodskii; Fiscal Year: 2002
    ....
  13. 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. ..
  14. Retroviral Genomic RNA Dimer Structure and Function
    KEVIN WEEKS; Fiscal Year: 2009
    ....
  15. PHYSICAL CHEMISTRY OF RECOMBINATIONAL INTERMEDIATES
    NADRIAN SEEMAN; Fiscal Year: 2000
    ..The ultimate goal is to provide molecular control over natural recombination phenomena and over recombinational interventions done today in the laboratory and tomorrow in the clinic. ..
  16. Basis of gene regulation by a guanine-binding mRNA
    Robert Batey; Fiscal Year: 2007
    ..In parallel, the energetics of ligand recognition will be probed using isothermal calorimetry (ITC) and a series of RNAs that contain functional group deletions. ..
  17. THEORETICAL ASPECTS OF DNA SUPERCOILING
    WILMA OLSON; Fiscal Year: 2007
    ....
  18. LOCAL AND GLOBAL STRUCTURES OF SUPERCOILED DNA
    Yuri Lyubchenko; Fiscal Year: 2003
    ..The studies outlined above will utilize atomic force microscopy (AFM), 2-dimensional agarose gel electrophoresis, and chemical probe analysis for structural studies of DNA and nucleoprotein complexes. ..
  19. PHYSICAL CHEMISTRY OF RECOMBINATIONAL INTERMEDIATES
    NADRIAN SEEMAN; Fiscal Year: 1992
    ..This series of experiments will yield information which will provide detailed understanding about recombination in the development and evolution of organisms...
  20. LOCAL AND GLOBAL CONFORMATIONS OF SUPERCOILED DNA
    Yuri Lyubchenko; Fiscal Year: 2007
    ..abstract_text> ..
  21. A hybrid 12T Q-FTMS for the investigation of nucleic acids non-cov./cov.adducts
    Daniele Fabris; Fiscal Year: 2006
    ....
  22. Biosynthetic Protein Models of Heme-copper Oxidases and Nitric Oxide Reductases
    Yi Lu; Fiscal Year: 2007
    ..The work will make important contributions to healthcare, as it will provide a molecular basis for understanding two enzymes important to human health. ..
  23. Regulation of Transcription at the Human IL-2 Promoter
    James Goodrich; Fiscal Year: 2006
    ..abstract_text> ..