Complementary sets of noncanonical base pairs mediate RNA helix packing in the group I intron active site
Scott A. Strobel1, 2, Lori Ortoleva-Donnelly1, Sean P. Ryder1, Jamie H. Cate1
& Eileen Moncoeur1
1Department of Molecular Biophysics and Biochemistry, 260 Whitney Avenue, Yale University, New Haven, Connecticut 06520, USA.
2email: strobel@csb.yale.edu
Helix packing is critical for RNA tertiary structure formation, although the rules for helix−helix association within structured RNAs are largely unknown. Docking of the substrate helix into the active site of the Tetrahymena group I ribozyme provides a model system to study this question. Using a novel chemogenetic method to analyze RNA structure in atomic detail, we report that complementary sets of noncanonical base pairs (a GU wobble pair and two consecutively stacked sheared AA pairs) create an RNA helix packing motif that is essential for 5'-splice site selection in the group I intron. This is likely to be a general motif for helix−helix interaction within the tertiary structures of many large RNAs.
U wobble pair and two consecutively stacked sheared A
