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.
University of Heidelberg, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
Richard
R
Wombacher
Andres
A
Jäschke
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