Probing the active site of a diels-alderase ribozyme by photoaffinity cross-linking.
The active site of a Diels-Alderase ribozyme is located in solution by photoaffinity cross-linking using a productlike azidobenzyl probe. Two key nucleotides are identified that contact the Diels-Alder product in a conformation-dependent fashion. The design of such probes does not require knowledge of the three-dimensional structure of the ribozyme, and the technique yields both static and dynamic structural information. This work establishes photoaffinity cross-linking as an empirical approach that is applied here for the first time to an artificial ribozyme.
Wombacher
Richard
R
University of Heidelberg, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
Jäschke
Andres
A
D001386:Azides / Q000737:chemistry*; D001665:Binding Sites; D003432:Cross-Linking Reagents / Q000138:chemical synthesis / Q000737:chemistry*; D018360:Crystallography, X-Ray; D008027:Light; D009690:Nucleic Acid Conformation; D019920:Photoaffinity Labels / Q000138:chemical synthesis / Q000737:chemistry*; D010777:Photochemistry; D016337:RNA, Catalytic / Q000737:chemistry*
D001386:Azides; D003432:Cross-Linking Reagents; C518747:Diels-Alder ribozyme; D019920:Photoaffinity Labels; D016337:RNA, Catalytic; C014747:phenylazide