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Author ORCID Identifier


Campus-Only Access for Five (5) Years

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded


Month Degree Awarded


First Advisor

Mingxu You

Subject Categories

Analytical Chemistry | Bacteriology | Biochemistry | Bioimaging and Biomedical Optics | Biological Engineering | Biotechnology | Cell Biology | Chemistry | Microbiology | Molecular Biology | Nanotechnology


Fluorescence imaging of intracellular small molecules in live cells is crucial to understanding various biological pathways and disease-related phenomena. It enables researchers to learn more in-depth about how certain metabolisms and signal transducing pathways function, and it could provide valuable insights to the therapeutic and biomedical field. Fluorogenic RNA-based sensors have been recently developed and widely used in detecting small molecules in live cells. They exhibit general advantages over other traditional fluorescence imaging-based detection methods, such as being genetically encodable, highly modular, readily programmable, and able to develop specificity towards potentially any target of interest. These merits make fluorogenic RNA-based sensors a superior tool to discover the unexplored area in cell biology. In this thesis, we will show several examples of how these fluorogenic RNA sensors are developed and applied in live cells to study and reveal previously unknown information on the role of the target small molecules in the cellular systems.

First, in order to better understand the role of the alarmone, guanosine tetra-and pentaphosphate (p)ppGpp, in the stringent response in bacteria, we adapted the ppGpp recognition module from its naturally occurring riboswitch and engineered it into a fluorescent sensor by fusing it with a fluorogenic RNA aptamer, Broccoli. As a result, we were able to apply our sensor in E. coli and monitor the cellular dynamics of (p)ppGpp in live cells for the first time in over half a decade since its discovery. Second, it is hypothesized that (p)ppGpp and another bacterial second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) synergistically support certain physiological processes in bacteria. However, no direct correlation between the two has been proved or disproved. To further study the interactions between the two signaling molecules, we developed a multiplexed sensor to detect (p)ppGpp and c-di-GMP simultaneously. Third, to image beyond two or three targets in the same cells, one must overcome the challenge of lacking spectrally resolvable fluorophores that can be imaged simultaneously. Without further expanding the current imaging spectrum, we managed to circumvent the issue by exploring the possibility of sequential imaging. Here, we constructed the “sequential Fluorogenic RNA Imaging-Enabled Sensor” (seqFRIES) and adopted an “imaging-washing cycle” method to achieve multiplexed and orthogonal detection of small molecules, S-Adenosyl-L-methionine (SAM) and S-Adenosyl-L-homocysteine (SAH). Finally, to demonstrate the universal applicability of the fluorogenic RNA-based sensors in both prokaryotes and eukaryotes, we developed a (2’-5’, 3’-5’) cyclic guanosine monophosphate-adenosine monophosphate (2’,3’-cGAMP) sensor for its detection in live mammalian cells.


Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.

Available for download on Friday, March 01, 2024