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• W2147029256 abstract "Engineered “aptazymes” fuse in vitro selected aptamers with ribozymes to create allosteric enzymes as biosensing components and artificial gene regulatory switches through ligand-induced conformational rearrangement and activation. By contrast, activating ligand is employed as an enzymatic cofactor in the only known natural aptazyme, the glmS ribozyme, which is devoid of any detectable conformational rearrangements. To better understand this difference in biosensing strategy, we monitored by single molecule fluorescence resonance energy transfer (FRET) and 2-aminopurine (AP) fluorescence the global conformational dynamics and local base (un)stacking, respectively, of a prototypical drug-sensing aptazyme, built from a theophylline aptamer and the hammerhead ribozyme. Single molecule FRET reveals that a catalytically active state with distal Stems I and III of the hammerhead ribozyme is accessed both in the theophylline-bound and, if less frequently, in the ligand-free state. The resultant residual activity (leakage) in the absence of theophylline contributes to a limited dynamic range of the aptazyme. In addition, site-specific AP labeling shows that rapid local theophylline binding to the aptamer domain leads to only slow allosteric signal transduction into the ribozyme core. Our findings allow us to rationalize the suboptimal biosensing performance of the engineered compared to the natural aptazyme and to suggest improvement strategies. Our single molecule FRET approach also monitors in real time the previously elusive equilibrium docking dynamics of the hammerhead ribozyme between several inactive conformations and the active, long-lived, Y-shaped conformer." @default.
• W2147029256 created "2016-06-24" @default.
• W2147029256 creator A5016259851 @default.
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• W2147029256 date "2008-11-24" @default.
• W2147029256 modified "2023-09-24" @default.
• W2147029256 title "Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme" @default.
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• W2147029256 doi "https://doi.org/10.1261/rna.1346609" @default.
• W2147029256 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/2612772" @default.
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• W2147029256 hasPublicationYear "2008" @default.
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