Riboswitch-based sensor in low optical background

Svetlana V. Harbaugh; Molly E. Davidson; Yaroslav G. Chushak; Nancy Kelley-Loughnane; Morley O. Stone

doi:10.1117/12.796122

9 September 2008 Riboswitch-based sensor in low optical background

Svetlana V. Harbaugh, Molly E. Davidson, Yaroslav G. Chushak, Nancy Kelley-Loughnane, Morley O. Stone

Proceedings Volume 7040, Nanobiosystems: Processing, Characterization, and Applications; 70400C (2008) https://doi.org/10.1117/12.796122
Event: NanoScience + Engineering, 2008, San Diego, California, United States

Abstract

Riboswitches are a type of natural genetic control element that use untranslated sequence in the RNA to recognize and bind to small molecules that regulate expression of that gene. Creation of synthetic riboswitches to novel ligands depends on the ability to screen for analyte binding sensitivity and specificity. In our work, we have coupled a synthetic riboswitch to an optical reporter assay based on fluorescence resonance energy transfer (FRET) between two genetically-coded fluorescent proteins. Specifically, a theophylline-sensitive riboswitch was placed upstream of the Tobacco Etch Virus (TEV) protease coding sequence, and a FRET-based construct, BFP-eGFP or eGFP-REACh, was linked by a peptide encoding the recognition sequence for TEV protease. Cells expressing the riboswitch showed a marked optical difference in fluorescence emission in the presence of theophylline. However, the BFP-eGFP FRET pair posses significant optical background that reduces the sensitivity of a FRET-based assay. To improve the optical assay, we designed a nonfluorescent yellow fluorescent protein (YFP) mutant called REACh (for Resonance Energy-Accepting Chromoprotein) as the FRET acceptor for eGFP. The advantage of using an eGFP-REACh pair is the elimination of acceptor fluorescence which leads to an improved detection of FRET via better signal-to-noise ratio. The EGFP-REACh fusion protein was constructed with the TEV protease cleavage site; thus upon TEV translation, cleavage occurs diminishing REACh quenching and increasing eGFP emission resulting in a 4.5-fold improvement in assay sensitivity.

Citation Download Citation

Svetlana V. Harbaugh, Molly E. Davidson, Yaroslav G. Chushak, Nancy Kelley-Loughnane, and Morley O. Stone "Riboswitch-based sensor in low optical background", Proc. SPIE 7040, Nanobiosystems: Processing, Characterization, and Applications, 70400C (9 September 2008); https://doi.org/10.1117/12.796122

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