Structural characterization of the 5′ untranslated RNA of hepatitis C virus by vibrational spectroscopy

Raman and FTIR spectroscopy have been used to characterize the structure of 5′untranslated region (5′UTR, 342-mer RNA) of the HCV genome. The study of the 750-850 cm− 1 Raman spectral domain of the ribose-phosphate backbone reveals that the percentage of nucleobases involved in double helix-loop junctions is 19 ± 1%, which is very close to that of a theoretical secondary structure model (18.7%) proposed on the basis of comparative sequence analysis and thermodynamic modelling. In addition, about 68 ± 2% of the bases are helically ordered having C(3′)-endo ribofuranose pucker. FTIR-monitored H/D exchange provides the following results: (a) base-paired guanine and cytosine nucleobases show the lowest rate of isotopic exchange, and some synchronous intensity changes of marker bands of A·U pair and single stranded adenine are consistent with the presence of A⁎A·U triplets; (b) the vibrational coupling between the ribose ether C-O stretching and 2′OH bending motions reveals that helical regions of 5′UTR RNA are characterized by hydrogen bonding between the 2′OH ribose groups and the ether oxygen atoms of neighbouring ribose residues.