Figure 5

RNase probing data for SBL ribozyme were projected on 3D model of HDV ribozyme. (a) RNase probing data for pre-cleaved SBL ribozyme were projected on 3D model of pre-cleaved genomic HDV ribozyme; (b) RNase probing data for post-cleaved SBL ribozyme were projected on 3D model of the post-cleaved genomic HDV ribozyme; (c) RNase probing data for pre-cleaved SBL ribozyme projected on 3D model of the pre-cleaved SBL ribozyme. Red balls indicate cut sites for single-strand-specific nucleases, orange balls for double-strand-specific nuclease. Ball size is roughly proportional to the intensity of the corresponding lines on the electrophoregram. Green ball indicates the cut site for the self-cleavage reaction. Blue sticks denote nucleotide bases of stem P2 in (a) and (b) and stem P2' composed of nt 16–18 and nt 11–13 in (c). Cyan sticks nucleotide bases of stem P4, brown of stem and loop P3–l3, lilac of stem P1.1 and CPK of stem P1. Dark green sticks in (a) and (c) denote the f region of the SBL ribozyme. This region is absent from structure depicted in (b). Two exclamation marks indicate a doublet at nt C18. Black circle in (a) and (b) surrounds the RNAse cleavage sites that are to be fully hindered by other parts of the molecule from any nuclease attack. The nucleotide numbers in (a) and (b) are for the genomic and in (c) for the antigenomic ribozyme. Secondary structure homology between antigenomic and genomic HDV ribozymes [11] was used to project antigenomic RNase cleavage pattern on the structure of genomic ribozyme according to the table shown in Figure 6.