A map of the binding site for catalytic domain 5 in the core of a group IIintron ribozyme

Group II introns are ribozymes with a complex tertiary architecture that is of great interest as a model for RNA folding, Domain 5 (D5) is a highly co nserved region of the intron that is considered one of the most critical st ructures in the catalytic core. Despite its central importance, the means b y which D5 interacts with other core elements is unclear, To obtain a map o f potential interaction sites, dimethyl sulfate was used to footprint regio ns of the intron that are involved in D5 binding, These studies were comple mented by measurements of D5 binding to a series of truncated intron deriva tives. In this way, the minimal region of the intron required for strong D5 association was defined and the sites most likely to represent thermodynam ically significant positions of tertiary contact were identified, These stu dies shaw that ground-state D5 binding is mediated by tertiary contacts to specific regions of D1, including a tetraloop receptor and an adjacent thre e-way junction. In contrast, D2 and D3 are not found to stabilize D5 associ ation. These data highlight the significance of D1-D5 interactions and sill facilitate the identification of specific tertiary contacts between them.