Table of Contents

November 2007; 13 (11)

PERSPECTIVE

  • PERSPECTIVE:

    p53–RNA interactions: New clues in an old mystery

    • Kasandra J.-L. Riley
    • and L. James Maher III
    RNA November 2007 13:1825-1833; Published in Advance September 5, 2007, doi:10.1261/rna.673407

REVIEW

  • REVIEW:

    RNA-specific ribonucleotidyl transferases

    • Georges Martin
    • and Walter Keller
    RNA November 2007 13:1834-1849; Published in Advance September 13, 2007, doi:10.1261/rna.652807

BIOINFORMATICS

  • BIOINFORMATICS:

    Semiautomated improvement of RNA alignments

    • Ebbe S. Andersen,
    • Allan Lind-Thomsen,
    • Bjarne Knudsen,
    • Susie E. Kristensen,
    • Jakob H. Havgaard,
    • Elfar Torarinsson,
    • Niels Larsen,
    • Christian Zwieb,
    • Peter Sestoft,
    • Jørgen Kjems,
    • and Jan Gorodkin
    RNA November 2007 13:1850-1859; Published in Advance September 5, 2007, doi:10.1261/rna.215407

REPORTS

  • REPORT:

    Dynactin suppresses the retrograde movement of apically localized mRNA in Drosophila blastoderm embryos

    • Georgia Vendra,
    • Russell S. Hamilton,
    • and Ilan Davis
    RNA November 2007 13:1860-1867; Published in Advance September 27, 2007, doi:10.1261/rna.509007
  • REPORT:

    RluD, a highly conserved pseudouridine synthase, modifies 50S subunits more specifically and efficiently than free 23S rRNA

    • Pavanapuresan P. Vaidyanathan,
    • Murray P. Deutscher,
    • and Arun Malhotra
    RNA November 2007 13:1868-1876; Published in Advance September 13, 2007, doi:10.1261/rna.711207
  • REPORT:

    First experimental evidence for the preferential stabilization of the natural D- over the nonnatural L-configuration in nucleic acids

    • Sarah Bolik,
    • Michael Rübhausen,
    • Stephan Binder,
    • Benjamin Schulz,
    • Markus Perbandt,
    • Nicolay Genov,
    • Volker Erdmann,
    • Sven Klussmann,
    • and Christian Betzel
    RNA November 2007 13:1877-1880; Published in Advance September 5, 2007, doi:10.1261/rna.564507
  • REPORT:

    Phenylalanyl-tRNA synthetase editing defects result in efficient mistranslation of phenylalanine codons as tyrosine

    • Jiqiang Ling,
    • Srujana S. Yadavalli,
    • and Michael Ibba
    RNA November 2007 13:1881-1886; Published in Advance September 5, 2007, doi:10.1261/rna.684107
  • REPORT:

    Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum

    • John A.H. Hoerter
    • and Nils G. Walter
    RNA November 2007 13:1887-1893; Published in Advance September 5, 2007, doi:10.1261/rna.602307

ARTICLES

  • ARTICLE:

    Determinants of targeting by endogenous and exogenous microRNAs and siRNAs

    • Cydney B. Nielsen,
    • Noam Shomron,
    • Rickard Sandberg,
    • Eran Hornstein,
    • Jacob Kitzman,
    • and Christopher B Burge
    RNA November 2007 13:1894-1910; Published in Advance September 13, 2007, doi:10.1261/rna.768207
  • ARTICLE:

    Gene silencing mechanisms mediated by Aubergine–piRNA complexes in Drosophila male gonad

    • Kazumichi M. Nishida,
    • Kuniaki Saito,
    • Tomoko Mori,
    • Yoshinori Kawamura,
    • Tomoko Nagami-Okada,
    • Sachi Inagaki,
    • Haruhiko Siomi,
    • and Mikiko C. Siomi
    RNA November 2007 13:1911-1922; Published in Advance September 13, 2007, doi:10.1261/rna.744307
  • ARTICLE:

    Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

    • Kausik Chakrabarti,
    • Michael Pearson,
    • Leslie Grate,
    • Timothy Sterne-Weiler,
    • Jonathan Deans,
    • John Paul Donohue,
    • and Manuel Ares, Jr
    RNA November 2007 13:1923-1939; Published in Advance September 27, 2007, doi:10.1261/rna.751807
  • ARTICLE:

    Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon

    • Carla Guarraia,
    • Laura Norris,
    • Ana Raman,
    • and Philip J. Farabaugh
    RNA November 2007 13:1940-1947; Published in Advance September 19, 2007, doi:10.1261/rna.735107
  • ARTICLE:

    The three-dimensional structure of the Moorella thermoacetica selenocysteine insertion sequence RNA hairpin and its interaction with the elongation factor SelB

    • Alexander V. Beribisky,
    • Tony J. Tavares,
    • Andrew N. Amborski,
    • Mina Motamed,
    • Anne E. Johnson,
    • Tobi L. Mark,
    • and Philip E. Johnson
    RNA November 2007 13:1948-1956; Published in Advance September 27, 2007, doi:10.1261/rna.686607
  • ARTICLE:

    Exoribonuclease R in Mycoplasma genitalium can carry out both RNA processing and degradative functions and is sensitive to RNA ribose methylation

    • Maureen S. Lalonde,
    • Yuhong Zuo,
    • Jianwei Zhang,
    • Xin Gong,
    • Shaohui Wu,
    • Arun Malhotra,
    • and Zhongwei Li
    RNA November 2007 13:1957-1968; Published in Advance September 13, 2007, doi:10.1261/rna.706207
  • ARTICLE:

    Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE

    • Georgeta N. Basturea
    • and Murray P. Deutscher
    RNA November 2007 13:1969-1976; Published in Advance September 13, 2007, doi:10.1261/rna.700507
  • ARTICLE:

    Yeast Rrp14p is a nucleolar protein involved in both ribosome biogenesis and cell polarity

    • Hiroko Yamada,
    • Chihiro Horigome,
    • Takafumi Okada,
    • Chiharu Shirai,
    • and Keiko Mizuta
    RNA November 2007 13:1977-1987; Published in Advance September 5, 2007, doi:10.1261/rna.553807
  • ARTICLE:

    Regulation of transcription of the RNA splicing factor hSlu7 by Elk-1 and Sp1 affects alternative splicing

    • Moti Alberstein,
    • Maayan Amit,
    • Keren Vaknin,
    • Amanda O'Donnell,
    • Chen Farhy,
    • Yaniv Lerenthal,
    • Noam Shomron,
    • Ohad Shaham,
    • Andrew D. Sharrocks,
    • Ruth Ashery-Padan,
    • and Gil Ast
    RNA November 2007 13:1988-1999; Published in Advance September 5, 2007, doi:10.1261/rna.492907
  • ARTICLE:

    Conformational energy and structure in canonical and noncanonical forms of tRNA determined by temperature analysis of the rate of s4U8–C13 photocrosslinking

    • Wayne Huggins,
    • Tatjana Shapkina,
    • and Paul Wollenzien
    RNA November 2007 13:2000-2011; Published in Advance September 13, 2007, doi:10.1261/rna.656907
  • ARTICLE:

    Nucleotide synthetase ribozymes may have emerged first in the RNA world

    • Wentao Ma,
    • Chunwu Yu,
    • Wentao Zhang,
    • and Jiming Hu
    RNA November 2007 13:2012-2019; Published in Advance September 18, 2007, doi:10.1261/rna.658507
  • ARTICLE:

    TRAP-5′ stem–loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region

    • Adam P. McGraw,
    • Philip C. Bevilacqua,
    • and Paul Babitzke
    RNA November 2007 13:2020-2033; Published in Advance September 19, 2007, doi:10.1261/rna.719507

METHODS

  • METHOD:

    Selective quenching of fluorescence from unbound oligonucleotides by gold nanoparticles as a probe of RNA structure

    • Huixiang Li,
    • Ruiting Liang,
    • Douglas H. Turner,
    • Lewis J. Rothberg,
    • and Shenghua Duan
    RNA November 2007 13:2034-2041; Published in Advance September 25, 2007, doi:10.1261/rna.138807
  • METHOD:

    Substitution of the use of radioactivity by fluorescence for biochemical studies of RNA

    • Bei-Wen Ying,
    • Dominique Fourmy,
    • and Satoko Yoshizawa
    RNA November 2007 13:2042-2050; Published in Advance September 11, 2007, doi:10.1261/rna.637907

ERRATUM

  • ERRATUM:

    Genetic analysis of the E site during RF2 programmed frameshifting

    • Christina L. Sanders
    • and James F. Curran
    RNA November 2007 13:2051
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This Issue

November 2007; 13 (11)
Cover
  1. PERSPECTIVE
  2. REVIEW
  3. BIOINFORMATICS
  4. REPORTS
  5. ARTICLES
  6. METHODS
  7. ERRATUM

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