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| The EMBO Journal
(1998) 17, 7105–7117, doi:10.1093/emboj/17.23.7105 |
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| A map of the binding site for catalytic domain 5 in the core of a group II intron ribozyme |
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| Boyana B. Konforti1, 3, Qiaolian Liu1, 3 and Anna Marie Pyle2 |
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1 Department of Biochemistry and Molecular Biophysics, Columbia University, 701 W. 168th Street, Room 616, Hammer Health Sciences Center, New York, NY 10032, USA 2 Howard Hughes Medical Institute, Columbia University, 701 W. 168th Street, Room 616, Hammer Health Sciences Center, New York, NY 10032, USA 3 B.B.Konforti and Q.Liu contributed equally to this work To whom correspondence should be addressed Anna Marie Pyle, amp11@columbia.edu Boyana B. Konforti, bbk8@columbia.edu Received 28 August 1998; Revised 6 October 1998; Accepted 7 October 1998. |
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| Abstract |
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| 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 conserved region of the intron that is considered one of the most critical structures in the catalytic core. Despite its central importance, the means by which D5 interacts with other core elements is unclear. To obtain a map of potential interaction sites, dimethyl sulfate was used to footprint regions of the intron that are involved in D5 binding. These studies were complemented by measurements of D5 binding to a series of truncated intron derivatives. In this way, the minimal region of the intron required for strong D5 association was defined and the sites most likely to represent thermodynamically significant positions of tertiary contact were identified. These studies show that ground-state D5 binding is mediated by tertiary contacts to specific regions of D1, including a tetraloop receptor and an adjacent three-way junction. In contrast, D2 and D3 are not found to stabilize D5 association. These data highlight the significance of D1–D5 interactions and will facilitate the identification of specific tertiary contacts between them. |
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| Keywords: catalysis, folding, RNA, splicing, tertiary structure |
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