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Bacterial Logic Devices Reveal Unexpected Behavior of Frameshift Suppressor tRNAs

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Author(s): Eric M. Sawyer | Cody Barta | Romina Clemente | Michel Conn | Clif Davis | Catherine Doyle | Mary Gearing | Olivia Ho-Shing | Alyndria Mooney | Jerrad Morton | Shamita Punjabi | Ashley Schnoor | Siya Sun | Shashank Suresh | Bryce Szczepanik | D. Leland Taylor | Annie Temmink | William Vernon | A. Malcolm Campbell | Laurie J. Heyer | Jeffrey L. Poet | Todd Eckdahl

Journal: Interdisciplinary Bio Central
ISSN 2005-8543

Volume: 4;
Date: 2012;
Original page

Keywords: tRNA | frameshift suppression | DNA-based logic gates | synthetic biology

ABSTRACT
Introduction: We investigated frameshift suppressor tRNAs previously reported to use five-base anticodon-codon interactions in order to provide a collection of frameshift suppressor tRNAs to the synthetic biology community and to develop modular frameshift suppressor logic devices for use in synthetic biology applications. Results and Discussion: We adapted eleven previously described frameshift suppressor tRNAs to the BioBrick cloning format, and built three genetic logic circuits to detect frameshift suppression. The three circuits employed three different mechanisms: direct frameshift suppression of reporter gene mutations, frameshift suppression leading to positive feedback via quorum sensing, and enzymatic amplification of frameshift suppression signals. In the course of testing frameshift suppressor logic, we uncovered unexpected behavior in the frameshift suppressor tRNAs. The results led us to posit a four-base binding hypothesis for the frameshift suppressor tRNA interactions with mRNA as an alternative to the published five-base binding model. Conclusion and Prospects: The published five-base anticodon/codon rule explained only 17 of the 58 frameshift suppression experiments we conducted. Our deduced four-base binding rule successfully explained 56 out of our 58 frameshift suppression results. In the process of applying biological knowledge about frameshift suppressor tRNAs to the engineering application of frameshift suppressor logic, we discovered new biological knowledge. This knowledge leads to a redesign of the original engineering application and encourages new ones. Our study reinforces the concept that synthetic biology is often a winding path from science to engineering and back again; scientific investigations spark engineering applications, the implementation of which suggests new scientific investigations.

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