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IBC 2012, vol. 4, article no. 10, pp. 1-12 | doi: 10.4051/ibc.2012.4.3.0010
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Reports on negative result (Synthetic biology, Biological computation/Database, Biomathematics/Mathematical Biology and Medicine )
Bacterial Logic Devices Reveal Unexpected Behavior of Frameshift Suppressor tRNAs
Eric M. Sawyer1,2, Cody Barta2, Romina Clemente1, Michel Conn2, Clif Davis2, Catherine Doyle1, Mary Gearing1, Olivia Ho-Shing1, Alyndria Mooney1,3, Jerrad Morton2, Shamita Punjabi1, Ashley Schnoor4, Siya Sun4, Shashank Suresh5, Bryce Szczepanik2, D. Leland Taylor1, Annie Temmink5, William Vernon2, A. Malcolm Campbell1, Laurie J. Heyer5, Jeffrey L. Poet4 and Todd Eckdahl2,*
1
Department of Biology, Davidson College, Davidson, NC 28035
2
Department of Biology, Missouri Western State University, St. Joseph, MO 64507
3
Department of Biology, University of Arkansas at Pine Bluff, Pine Bluff, AR 71601
4
Department of Computer Science, Math and Physics, Missouri Western State University, St. Joseph, MO 64507
5
Department of Mathematics, Davidson College, Davidson, NC 28035
*Corresponding author
received: September 10, 2012 ; accepted: September 18, 2012 ; published : September 19, 2012
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Synopsis

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.

Keywords : tRNA, frameshift suppression, DNA-based logic gates, synthetic biology
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Reviewed by
- Orr Yarkoni
- Lars F. Westblade
Edited by
- Hyun Joo
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