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Identification of structural elements critical for inter–domain interactions in a group II self‐splicing intron
Author(s) -
Jestin JeanLuc,
Dème Elise,
Jacquier Alain
Publication year - 1997
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/16.10.2945
Subject(s) - biology , group ii intron , intron , rna splicing , computational biology , group i catalytic intron , identification (biology) , genetics , group (periodic table) , evolutionary biology , gene , rna , ecology , physics , quantum mechanics
Thus far, conventional biophysical techniques, such as NMR spectroscopy or X‐ray crystallography, allow the determination, at atomic resolution, of only structural domains of large RNA molecules such as group I introns. Determination of their overall spatial organization thus still relies on modeling. This requires that a relatively high number of tertiary interactions are defined in order to get sufficient topological constraints. Here, we report the use of a modification interference assay to identify structural elements involved in interdomain interactions. We used this technique, in a group II intron, to identify the elements involved in the interactions between domain V and the rest of the molecule. Domain V contains many of the active site components of these ribozymes. In addition to a previously identified 11 nucleotide motif involved in the binding of the domain V terminal GAAA tetraloop, a small number of elements were shown to be essential for domain V binding. In particular, we show that domain III is specifically required for the interaction with sequences encompassing the conserved 2 nucleotide bulge of domain V.