De novo designs of programmable toehold-mediated transcriptional attenuators
Embargo Date
2028-03-18
OA Version
Citation
Abstract
Engineered RNA-based genetic switches, such as riboregulators and riboswitches, are frequently utilized as translational and transcriptional regulatory elements to construct a diverse array of biological devices. RNA-only genetic circuitry provides several advantages over other types of genetic circuitry. While numerous transcriptional activation systems exist, there is a lack of tunable and orthogonal systems capable of transcriptionally attenuating signal propagation with a wide dynamic range. In this work, I developed a design blueprint for programmable toehold-mediated transcriptional attenuators that can transcriptionally repress gene expression via toehold-mediated strand displacement. My designs ensured the proper formation of the secondary terminator hairpin structure necessary for transcription attenuation and determined a subset of four functional toehold-mediated transcriptional attenuators demonstrating at least a 2-fold change in transcriptional repression. Extensive efforts were made to enhance these toehold-mediated transcriptional attenuators for a broader dynamic range. Potential improvements could involve extending and elongating the toehold region to further stabilize the secondary structure and incorporating necessary interior loops to facilitate the proper function of the attenuator hairpins.
Description
2024
License
Attribution-NonCommercial-NoDerivatives 4.0 International