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Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

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Bioinformatics Research and Development (BIRD 2008)

Part of the book series: Communications in Computer and Information Science ((CCIS,volume 13))

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Abstract

The thermodynamics of RNA-RNA interaction consists of two components: the energy necessary to make a potential binding region accessible, i.e. unpaired, and the energy gained from the base pairing of the two interaction partners. We show here that both components can be efficiently computed using an improved variant of RNAup. The method is then applied to a set of bacterial small RNAs involved in translational control. In all cases of biologically active sRNA target interactions, the target sites predicted by RNAup are in perfect agreement with literature. In addition to prediction of target site location, RNAup can also be used to determine the mode of sRNA action. Using information about target site location and the accessibility change resulting from sRNA binding we can discriminate between positive and negative regulators of translation.

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Authors and Affiliations

  1. Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090, Vienna, Austria

    Ulrike Mückstein, Hakim Tafer, Peter F. Stadler & Ivo L. Hofacker

  2. Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107, Leipzig, Germany

    Stephan H. Bernhart, Maribel Hernandez-Rosales & Peter F. Stadler

  3. RNA Biology, Max Planck Institut für Infektionsbiologie, Charitéplatz 1, Campus Charité Mitte, D-10117, Berlin, Germany

    Jörg Vogel

  4. RNomics Group, Fraunhofer Institut for Cell Therapy and Immunology (IZI), Deutscher Platz 5e, D-04103, Leipzig, Germany

    Peter F. Stadler

  5. Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA

    Peter F. Stadler

Authors
  1. Ulrike Mückstein
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  2. Hakim Tafer
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  3. Stephan H. Bernhart
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  4. Maribel Hernandez-Rosales
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  5. Jörg Vogel
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  6. Peter F. Stadler
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  7. Ivo L. Hofacker
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Editor information

Mourad Elloumi Josef Küng Michal Linial Robert F. Murphy Kristan Schneider Cristian Toma

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Mückstein, U. et al. (2008). Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics. In: Elloumi, M., Küng, J., Linial, M., Murphy, R.F., Schneider, K., Toma, C. (eds) Bioinformatics Research and Development. BIRD 2008. Communications in Computer and Information Science, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-70600-7_9

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  • DOI: https://doi.org/10.1007/978-3-540-70600-7_9

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-70598-7

  • Online ISBN: 978-3-540-70600-7

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