Design of theophylline-dependent Diels-Alderase ribozymes

Copyright information:Taken from "Controlling the rate of organic reactions: rational design of allosteric Diels-Alderase ribozymes"Nucleic Acids Research 2006;34(18):5032-5038.Published online 20 Sep 2006PMCID:PMC1636424.© 2006 The Author(s) () The Diels-Alderase ribozyme (left) and the theophylline aptamer (right) are fused after removing the upper and lower helix, respectively, leading to the starting design Theo 1. Colored boxes indicate interactions that stabilize the inactive structure. Colored letters show interactions that stabilize the active structure. Colored arrows indicate positions of mutations leading to molecules Theo 2 to Theo 7. () Systematic investigation of interactions that stabilize or destabilize the active (left, colored letters) or inactive (right, colored boxes) structures. The colored arrows indicate the positions of mutations and correspond to (a). Black circle, inactive molecule; green circle, constitutively active molecules; red circle, allosteric molecule; two red circles, good allostericity. Numbers indicate the allosteric switching factor, defined as the initial rate in the presence of effector divided by the initial rate in the absence of effector. () Fluorescence–time curve for Theo 5 in the presence (red) and absence (green) of theophylline. NFS (%) is normalized fluorescence signal.