FIG. 1.

Alternative predictions of secondary RNA structure within domain II of the 5′NTR of HCV (N strain, genotype Ib). (A) Structure suggested by a recent comparison of the HCV and GBV-B sequences, comprising a complex stem-loop extending from nt 44 to 118, with two internal hairpin loops, IIa (nt 50 to 64) and IIb (nt 65 to 102), and a large, internal single-stranded bulge loop (nt 103 to 114) (9). Predicted ΔG = −8.6 kcal/mol. (B) Structure predicted by MFOLD when folding is constrained to include base pairing between nt 44 to 47 and nt 115 to 118, as suggested by the GBV-B sequence comparison. ΔG = −18.2 kcal/mol.