This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Smith, R. M.
Right arrow Articles by Wu, G. Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Smith, R. M.
Right arrow Articles by Wu, G. Y.

Next Article 

Journal of Virology, October 2002, p. 9563-9574, Vol. 76, No. 19
0022-538X/02/$04.00+0     DOI: 10.1128/JVI.76.19.9563-9574.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

Secondary Structure and Hybridization Accessibility of Hepatitis C Virus 3'-Terminal Sequences

Robert M. Smith, Cherie M. Walton, Catherine H. Wu, and George Y. Wu*

Division of Gastroenterology-Hepatology, Department of Medicine, University of Connecticut Health Center, Farmington, Connecticut

Received 26 March 2002/ Accepted 26 June 2002

The 3'-terminal sequences of hepatitis C virus (HCV) positive- and negative-strand RNAs contribute cis-acting functions essential for viral replication. The secondary structure and protein-binding properties of these highly conserved regions are of interest not only for the further elucidation of HCV molecular biology, but also for the design of antisense therapeutic constructs. The RNA structure of the positive-strand 3' untranslated region has been shown previously to influence binding by various host and viral proteins and is thus thought to promote HCV RNA synthesis and genome stability. Recent studies have attributed analogous functions to the negative-strand 3' terminus. We evaluated the HCV negative-strand secondary structure by enzymatic probing with single-strand-specific RNases and thermodynamic modeling of RNA folding. The accessibility of both 3'-terminal sequences to hybridization by antisense constructs was evaluated by RNase H cleavage mapping in the presence of combinatorial oligodeoxynucleotide libraries. The mapping results facilitated identification of antisense oligodeoxynucleotides and a 10-23 deoxyribozyme active against the positive-strand 3'-X region RNA in vitro.

* Corresponding author. Mailing address: University of Connecticut Health Center, 263 Farmington Ave., Farmington, CT 06030. Phone: (860) 679-3158. Fax: (860) 679-3159. E-mail: wu{at}nso.uchc.edu.

Journal of Virology, October 2002, p. 9563-9574, Vol. 76, No. 19
0022-538X/02/$04.00+0     DOI: 10.1128/JVI.76.19.9563-9574.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Friebe, P., Bartenschlager, R. (2009). Role of RNA Structures in Genome Terminal Sequences of the Hepatitis C Virus for Replication and Assembly. J. Virol. 83: 11989-11995 [Abstract] [Full Text]  
  • Kauffmann, A. D., Campagna, R. J., Bartels, C. B., Childs-Disney, J. L. (2009). Improvement of RNA secondary structure prediction using RNase H cleavage and randomized oligonucleotides. Nucleic Acids Res 37: e121-e121 [Abstract] [Full Text]  
  • Masante, C., Mahias, K., Lourenco, S., Dumas, E., Cahour, A., Trimoulet, P., Fleury, H., Astier-Gin, T., Ventura, M. (2008). Seven nucleotide changes characteristic of the hepatitis C virus genotype 3 5' untranslated region: correlation with reduced in vitro replication. J. Gen. Virol. 89: 212-221 [Abstract] [Full Text]  
  • Tellinghuisen, T. L., Evans, M. J., von Hahn, T., You, S., Rice, C. M. (2007). Studying Hepatitis C Virus: Making the Best of a Bad Virus. J. Virol. 81: 8853-8867 [Full Text]  
  • Binder, M., Quinkert, D., Bochkarova, O., Klein, R., Kezmic, N., Bartenschlager, R., Lohmann, V. (2007). Identification of Determinants Involved in Initiation of Hepatitis C Virus RNA Synthesis by Using Intergenotypic Replicase Chimeras. J. Virol. 81: 5270-5283 [Abstract] [Full Text]  
  • Ivanyi-Nagy, R., Kanevsky, I., Gabus, C., Lavergne, J.-P., Ficheux, D., Penin, F., Fosse, P., Darlix, J.-L. (2006). Analysis of hepatitis C virus RNA dimerization and core-RNA interactions.. Nucleic Acids Res 34: 2618-2633 [Abstract] [Full Text]  
  • Kierzek, E., Ciesielska, A., Pasternak, K., Mathews, D. H., Turner, D. H., Kierzek, R. (2005). The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 33: 5082-5093 [Abstract] [Full Text]  
  • Dutkiewicz, M., Ciesiolka, J. (2005). Structural characterization of the highly conserved 98-base sequence at the 3' end of HCV RNA genome and the complementary sequence located at the 5' end of the replicative viral strand. Nucleic Acids Res 33: 693-703 [Abstract] [Full Text]  
  • van Leeuwen, H. C., Reusken, C. B. E. M., Roeten, M., Dalebout, T. J., Riezu-Boj, J. I., Ruiz, J., Spaan, W. J. M. (2004). Evolution of naturally occurring 5' non-translated region variants of hepatitis C virus genotype 1b in selectable replicons. J. Gen. Virol. 85: 1859-1866 [Abstract] [Full Text]  
  • Reusken, C. B. E. M., Dalebout, T. J., Eerligh, P., Bredenbeek, P. J., Spaan, W. J. M. (2003). Analysis of hepatitis C virus/classical swine fever virus chimeric 5'NTRs: sequences within the hepatitis C virus IRES are required for viral RNA replication. J. Gen. Virol. 84: 1761-1769 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»