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Biological Chemistry

Editor-in-Chief: Brüne, Bernhard

Editorial Board Member: Buchner, Johannes / Ludwig, Stephan / Sies, Helmut / Turk, Boris / Wittinghofer, Alfred

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Interfering with hepatitis C virus IRES activity using RNA molecules identified by a novel in vitro selection method

Cristina Romero-López1 / Alicia Barroso-delJesus2 / Elena Puerta-Fernández3 / Alfredo Berzal-Herranz4

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Corresponding author

Citation Information: Biological Chemistry. Volume 386, Issue 2, Pages 183–190, ISSN (Online) 1437-4315, ISSN (Print) 1431-6730, DOI: 10.1515/BC.2005.023, June 2005

Publication History

Received:
October 15, 2004
Accepted:
December 9, 2004
Published Online:
2005-06-01

Abstract

Hepatitis C virus (HCV) infection is one of the world's major health problems, and the identification of efficient HCV inhibitors is a major goal. Here we report the isolation of efficient anti-HCV internal ribosome entry site (IRES) RNA molecules identified by a new in vitro selection method. The newly developed procedure consists of two sequential steps that use distinct criteria for selection: selection for binding and selection for cleaving. The selection protocol was applied to a population of more than 1015 variants of an anti-hepatitis C virus ribozyme covalently linked to an aptamer motif. The ribozyme was directed against positions 357 to 369 of the HCV IRES, and the cleavage substrate was a 691-nucleotide-long RNA fragment that comprises the entire HCV IRES domain. After six selection cycles, seven groups of RNA variants were identified. A representative of each group was tested for its capacity to inhibit IRES activity using in vitro translation assays. All selected RNAs promoted significant inhibition, some by as much as 95%.

Keywords: anti-hepatitis C virus internal ribosome entry site (HCV IRES) RNAs; catalytic RNAs; hepatitis C virus internal ribosome entry site (HCV IRES); inhibitor RNAs; in vitro selection; RNA aptamers

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