title: A folding control element for tertiary collapse of a group II intron ribozyme.
abstract: Ribozymes derived from the group II intron ai5gamma collapse to a compact intermediate, folding to the native state through a slow, direct pathway that is unperturbed by kinetic traps. Molecular collapse of ribozyme D135 requires high magnesium concentrations and is thought to involve a structural element in domain 1 (D1). We used nucleotide analog interference mapping, in combination with nondenaturing gel electrophoresis, to identify RNA substructures and functional groups that are essential for D135 tertiary collapse. This revealed that the most crucial atoms for compaction are located within a small section of D1 that includes the kappa and zeta elements. This small substructure controls specific collapse of the molecule and, in later steps of the folding pathway, it forms the docking site for catalytic D5. In this way, the stage is set for proper active site formation during the earliest steps of ribozyme folding.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Yale University New Haven, Connecticut 06520, USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Waldsich
authors.forename: Anna Marie
authors.initials: AM
authors.lastname: Pyle
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D007438:Introns; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009710:Nucleotide Mapping; D012331:RNA, Fungal / Q000737:chemistry*; D044563:RNA, Ribosomal, Self-Splicing / Q000737:chemistry*; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000235:genetics*
chemical_list: C506264:D135 ribozyme, S cerevisiae; D012331:RNA, Fungal; D044563:RNA, Ribosomal, Self-Splicing