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Ion‐induced folding of the hammerhead ribozyme: a fluorescence resonance energy transfer study
Author(s) -
Bassi Gurminder S.,
Murchie Alastair I. H.,
Walter Frank,
Clegg Robert M.,
Lilley David M. J.
Publication year - 1997
Publication title -
the embo journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 7.484
H-Index - 392
eISSN - 1460-2075
pISSN - 0261-4189
DOI - 10.1093/emboj/16.24.7481
Subject(s) - hammerhead ribozyme , hairpin ribozyme , ribozyme , förster resonance energy transfer , folding (dsp implementation) , vs ribozyme , biology , ion , biophysics , stacking , crystallography , rna , chemistry , physics , biochemistry , fluorescence , nuclear magnetic resonance , organic chemistry , quantum mechanics , gene , electrical engineering , engineering
The ion‐induced folding transitions of the hammerhead ribozyme have been analysed by fluorescence resonance energy transfer. The hammerhead ribozyme may be regarded as a special example of a three‐way RNA junction, the global structure of which has been studied by comparing the distances (as energy transfer efficiencies) between the ends of pairs of labelled arms for the three possible end‐to‐end vectors as a function of magnesium ion concentration. The data support two sequential ion‐dependent transitions, which can be interpreted in the light of the crystal structures of the hammerhead ribozyme. The first transition corresponds to the formation of a coaxial stacking between helices II and III; the data can be fully explained by a model in which the transition is induced by a single magnesium ion which binds with an apparent association constant of 8000–10 000 M −1 . The second structural transition corresponds to the formation of the catalytic domain of the ribozyme, induced by a single magnesium ion with an apparent association constant of ∼1100 M −1 . The hammerhead ribozyme provides a well‐defined example of ion‐dependent folding in RNA.