Core protein-nucleic acid interactions in hepatitis C virus as revealed by Raman and circular dichroism spectroscopy

Molecular interactions required for hepatitis C virus (HCV) assembly are not well known and are poorly understood. The 5' untranslated region (5'UTR) of the RNA genome is highly conserved and has extensive secondary structure, and the highly basic core protein is rich in arginine residues. Using Raman and circular dichroism (CD) spectroscopies, specific interactions have been demonstrated here between the 5'UTR sequence and the core protein that may be important for the specific encapsidation of the viral genome during HCV replication. These interactions can be described as follows: (1) hydrogen bonding of arginine with unpaired guanine and/or with wobble GU base pairs, and arginine-phosphate electrostatic contacts; (2) although the percentage of base pairs in the A-form is maintained in 5'UTR, the HCVc-120 protein is beta-sheet and alpha-helix enriched upon formation of protein-5'UTR macromolecular assemblies; (3) protein-5'UTR interactions resulting in protein alpha-helix formation involve guanine bases in duplex segments. The mentioned interactions may represent novel targets for antiviral strategies against this important virus.