Figure 3

Schematic diagrams of the interaction networks maintaining the three-dimensional architecture of two different ribozymes. (a) The HDV ribozyme [7,93]; (b) the active hammerhead ribozyme [42]. The HDV ribozyme has a convoluted pseudoknotted topology: the color lines indicate the path of the sugar-phosphate backbone. The nomenclature is as follows [75]. Each nucleotide has three edges with hydrogen bonding possibilities: the Watson-Crick edge (denoted by a circle), the Hoogsteen edge (denoted by a square) and the sugar edge (denoted by a triangle). A pairwise base-base interaction can be formed either with the attached sugar moieties on the same side of the line of approach (cis-configuration, the symbols are closed) or with the sugars on either sides of the line of approach (the trans-configuration, the symbols are open). To avoid ambiguities, when annotating tertiary contacts, the nucleotides that are involved have been boxed. When the base of a nucleotide is in the syn-conformation with respect to the sugar it is marked in bold. The rectangles indicate the position actually occupied in space by a nucleotide. In (b), the cleavage occurs 3' of the red C.