Identification of structural elements critical for inter-domain interactions in a group II self-splicing intron

The EMBO Journal
J L JestinA Jacquier

Abstract

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.

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Citations

Jul 17, 1998·Current Opinion in Structural Biology·G L Conn, D E Draper
Jul 17, 1998·Current Opinion in Structural Biology·P Z Qin, A M Pyle
Nov 15, 2002·Methods : a Companion to Methods in Enzymology·Olga FedorovaAnna Marie Pyle
Jul 12, 2002·Nature·Jennifer A Doudna, Thomas R Cech
Apr 11, 2001·The EMBO Journal·J SwisherA M Pyle
Apr 29, 2008·RNA·Olga Fedorova, Anna Marie Pyle
Jan 15, 2014·PLoS Genetics·Nina SestoPascale Cossart
Jun 16, 2007·Biological Chemistry·Olga Fedorova, Nora Zingler
Jun 26, 2003·Journal of Molecular Biology·Olga FedorovaAnna Marie Pyle
May 8, 2010·Critical Reviews in Biochemistry and Molecular Biology·Anna Marie Pyle
Mar 21, 2009·Trends in Biochemical Sciences·François MichelEric Westhof
Oct 4, 2014·Molecular Cell·Anna Marie Pyle
Nov 13, 2012·PloS One·Liang-Fen YinChao-Xi Luo
May 10, 2000·The Journal of Biological Chemistry·F DucongéJ J Toulme
Jun 26, 1998·Journal of Molecular Biology·A R Ferré-D'AmaréJ A Doudna
Aug 10, 1999·Journal of Molecular Biology·P Z Qin, A M Pyle

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