Intramolecular secondary structure rearrangement by the kissing interaction of the Neurospora VS ribozyme

Kissing interactions in RNA are formed when bases between two hairpin loops pair. Intra- and intermolecular kissing interactions are important in form ing the tertiary or quaternary structure of many RNAs, Self-cleavage of the wild-type Varkud satellite (VS) ribozyme requires a kissing interaction be tween the hairpin loops of stem-loops I and V, In addition, self-cleavage r equires a rearrangement of several base pairs at the base of stem I. We sho w that the kissing interaction is necessary for the secondary structure rea rrangement of wild-type stem-loop I. Surprisingly, isolated stem-loop V in the absence of the rest of the ribozyme is sufficient to rearrange the seco ndary structure of isolated stem-loop I. In contrast to kissing interaction s in other RNAs that are either confined to the loops or culminate in an ex tended intermolecular duplex, the VS kissing interaction causes changes in intramolecular base pairs within the target stem-loop.