FEBS Letters
Volume 582, Issue 20 , Pages 3061-3066, 3 September 2008

Design of LNA-modified siRNAs against the highly structured 5′ UTR of coxsackievirus B3

Edited by Shou-Wei Ding

  • Mariola Dutkiewicz

      Affiliations

    • Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
    • Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
    • ,
  • Hans-Peter Grunert

      Affiliations

    • Institute of Virology, Campus Benjamin Franklin, Charité – University Medicine, Berlin, Germany
    • ,
  • Heinz Zeichhardt

      Affiliations

    • Institute of Virology, Campus Benjamin Franklin, Charité – University Medicine, Berlin, Germany
    • ,
  • Suzy W. Lena

      Affiliations

    • RiboTask ApS, Odense C, Denmark
    • ,
  • Jesper Wengel

      Affiliations

    • Nucleic Acid Center, University of Southern Denmark, Odense M, Denmark
    • ,
  • Jens Kurreck

      Affiliations

    • Institute of Chemistry and Biochemistry, Free University Berlin, Berlin, Germany
    • Institute of Industrial Genetics, University of Stuttgart, Stuttgart, Germany
    • Corresponding Author InformationCorresponding author. Present address: Institute of Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany. Fax: +49 711 685 66973.

Received 14 March 2008; received in revised form 11 July 2008; accepted 28 July 2008. published online 05 August 2008.

Abstract 

This study describes a strategy to develop LNA-modified small interfering RNA (siRNAs) against the highly structured 5′ UTR of coxsackievirus B3 (CVB-3), which is an attractive target site due to its high degree of conservation. Accessible sites were identified based on structural models and RNase H assays with DNA oligonucleotides. Subsequently, LNA gapmers, siRNAs, siLNAs and small internally segmented interfering RNA (sisiLNAs) were designed against sites, which were found to be accessible in the in vitro assays, and tested in reporter assays and experiments with the infectious virus. The best siLNA improved viability of infected cells by 92% and exerted good antiviral activity in plaque reduction assays.

Abbreviations: CVB-3, coxsackievirus B3, IRES, internal ribosome entry site, RNAi, RNA interference, siRNA, small interfering RNA, sisiRNA, small internally segmented interfering RNA

Keywords: Coxsackievirus, Locked nucleic acid, RNA interference, RNA structure, Small interfering RNA

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PII: S0014-5793(08)00653-4

doi:10.1016/j.febslet.2008.07.051

FEBS Letters
Volume 582, Issue 20 , Pages 3061-3066, 3 September 2008

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