Secondary structures of HDV genome segment and HDV ribozyme. (A) Portion of the HDV genome illustrating rod-like (top) and alternative cruciform (bottom) structures (Branch and Robertson 1991; Diegelman-Parente and Bevilacqua 2002). Color-coding represents two strands that either base pair in the ribozyme (colors match those in B) or in the upstream P(−1) region between −54 and −1 (Chadalavada et al. 2000). (B) Secondary structure for 1/99 WT and alterations in the 1/99 P4 variants, Δ3 bp and +3 bp. Variant 1/99 Δ3 bp was prepared by removing the following six nucleotides: G50, A51, G52, C64, U65, and C66 (all six nucleotides boxed), while 1/99 + 3 bp was prepared by adding the six nucleotides at the position shown.
