Raman spectra and structure of a 25mer HCV RNA

We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1–25 nucleotides) in solution. The principal findings of this study are (1) the A‐form secondary structure involving C3′‐ endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2′‐ endo/anti and C3′‐ endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base‐paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs. Copyright © 2009 John Wiley & Sons, Ltd.