Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron.
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.
Jestin
J L
JL
Laboratoire du Metabolisme des ARN, CNRS (URA 13CO) Département des Biotechnologies, Institut Pasteur, Paris, France.
Dème
E
E
Jacquier
A
A
D007438:Introns / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry; D010713:Phosphatidylcholines / Q000737:chemistry; D012326:RNA Splicing; D016337:RNA, Catalytic / Q000145:classification / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry*
D010710:Phosphates; D010713:Phosphatidylcholines; D016337:RNA, Catalytic; D012333:RNA, Messenger; C017251:1,2-oleoylphosphatidylcholine; C035638:thiophosphoric acid