Fig. 1.

Schematic and tertiary structure of the hatchet ribozyme. (A) The predicted secondary structure of the env10 hatchet ribozyme. The sequence is color coded according to helical segments observed in the tertiary structure. The highly conserved residues are shown in red rectangles. (B) A schematic representation of hatchet ribozyme product secondary structure highlighting long-range interactions. (C) The tertiary fold of the HT-GAAA hatchet ribozyme product dimer. The red thick dashed line divided the dimer structure as two new monomer molecules termed A′ and B′. (D) A schematic representation of the tertiary structure of HT-GAAA hatchet ribozyme product dimer. Two hatchet ribozyme product molecules form a dimer through swapping of the 3′ ends of the pairing strand. Long-range interactions observed in the tertiary structure are labeled with solid lines. The cleavage site is indicated by a yellow star. To simplify the structural analysis, we swapped the 3′ end of the pairing strand of the two molecules in the dimer and termed them as the new monomer molecules A′ and B′ as shown in the dashed rectangles. (E) The tertiary fold of molecule A′ of the HT-GAAA ribozyme product structure. The color coding is similar to that in Fig. 1A. The cleavage site is labeled with a yellow star. (F) The residues G8, A9, and G10 from stem-loop L1 are stacked on each other on the top of stem P1, while U39 extruded from loop L3 forms extensive interaction with L1 and stabilizes the long-range interaction. (G) U7 and A11 formed a trans-Watson–Crick Hoogsteen pair in L1. The sugar pucker of A11 adopts a C2′-endo conformation, whereas U7 adopts a C3′-endo conformation. (H) Two consecutive canonical base pairs A36-U58 and U37-A57 form on zippering-up L3; A12 and U13 that are extruded from L1 interact with the minor groove edge of A36-U58 and U37-A57, thereby forming two stacked base triples involving long-range interactions. (I) The compounds 1-NH and 2-NH₂ of G8 form hydrogen bonds with the phosphate oxygen of A11 in L1; 2′-OH of G8 hydrogen bonds with the Hoogsteen side of G10; the extruded residue U39 from L3 intercalates between G10 and A11, and its Watson–Crick edge pairs with the minor groove edge of G8; the Watson–Crick edge of G10 and the Watson–Crick edge of A11 are also involved in the stacking interaction of the long helix H12. (J) U59 formed a stable base triple with the Watson–Crick A3-U17 pair aligned along the major groove edge of stem P1, with the sugar pucker of U59 adopting a 2′-endo conformation. Note that the dashed lines indicate distances <3.5 Å and their number can exceed the possible number of hydrogen bonds formed by an atom.