More than one way to splice an RNA: branching without a bulge and splicing without branching in group II introns

RNA. 1998 Oct;4(10):1186-202. doi: 10.1017/s1355838298980724.


Domain 6 (D6) of group II introns contains a bulged adenosine that serves as the branch-site during self-splicing. In addition to this adenosine, other structural features in D6 are likely to contribute to the efficiency of branching. To understand their role in promoting self-splicing, the branch-site and surrounding nucleotides were mutagenized. Detailed kinetic analysis on the self-splicing efficiency of the mutants revealed several interesting features. First, elimination of the branch-site does not preclude efficient splicing, which takes place instead through a hydrolytic first step. Second, pairing of the branch-site does not eliminate branching, particularly if the adenosine is involved in a mispair. Third, the G-U pairs that often surround group II intron branch-points contribute to the efficiency of branching. These results suggest that there is a strong driving force for promoting self-splicing by group II introns, which employ a versatile set of different mechanisms for ensuring that splicing is successful. In addition, the behavior of these mutants indicates that a bulged adenosine per se is not the important determinant for branch-site recognition in group II introns. Rather, the data suggest that the branch-site adenosine is recognized as a flipped base, a conformation that can be promoted by a variety of different substructures in RNA and DNA.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenosine / genetics
  • Base Sequence
  • Endoribonucleases
  • Introns*
  • Kinetics
  • Models, Genetic
  • Nucleic Acid Conformation*
  • Point Mutation
  • RNA / chemistry*
  • RNA / genetics
  • RNA Splicing / genetics*
  • Sequence Analysis, RNA
  • Sequence Deletion


  • RNA
  • Endoribonucleases
  • Adenosine