title: Sequence and structural analysis of the 5' noncoding region of hepatitis C virus in patients with chronic infection.
abstract: Hepatitis C virus (HCV), exhibits considerable genetic diversity, but presents a relatively well conserved 5' noncoding region (5' NCR) among all genotypes. In this study, the structural features and translational efficiency of the HCV 5' NCR sequences were analyzed using the programs RNAfold, RNAshapes and RNApdist and with a bicistronic dual luciferase expression system, respectively. RNA structure prediction software indicated that base substitutions will alter potentially the 5' NCR structure. The heterogeneous sequence observed on 5' NCR led to important changes in their translation efficiency in different cell culture lines. Interactions of the viral RNA with cellular transacting factors may vary according to the cell type and viral genome polymorphisms that may result in the translational efficiency observed.
authors.affiliation: Instituto René Rachou/FIOCRUZ. Av. Augusto de Lima, Minas Gerais, Brazil. araujo@cpqrr.fiocruz.br
authors.forename: Flávio Marcos Gomes
authors.initials: FM
authors.lastname: Araújo
authors.forename: Ariane
authors.initials: A
authors.lastname: Machado-Lima
authors.forename: Alan Mitchell
authors.initials: AM
authors.lastname: Durham
authors.forename: Rosangela
authors.initials: R
authors.lastname: Teixeira
authors.forename: Guilherme
authors.initials: G
authors.lastname: Oliveira
mesh_terms: D020121:5' Untranslated Regions; D000368:Aged; D001483:Base Sequence; D002460:Cell Line; D005260:Female; D017930:Genes, Reporter; D016174:Hepacivirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D019698:Hepatitis C, Chronic / Q000821:virology*; D006801:Humans; D008156:Luciferases / Q000378:metabolism; D008297:Male; D008875:Middle Aged; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis; D012367:RNA, Viral / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral; D008156:Luciferases