Open Access Peer-reviewed Research Article

Simulation of gene regulatory elements for biosensing

Main Article Content

Mallory Bates
Svetlana Harbough
Tarun Goswami corresponding author


Gene regulatory studies are of significant importance in many scenarios such as mental illness. 21% of U.S adults experience mental illnesses including 1 in 4 active-duty military personnel. Mental health can be identified in the body by different biomarkers. These biomarkers potentially controlled by riboswitches, which are located in mRNA and switch “ON” or “OFF” depending on the concentration of a biomarker. In this research, a known riboswitch reengineered and its response in the presence of a biomarker investigated. We changed computationally PreQ1, a known riboswitch that has the smallest aptamer, and then experimentally tested against biomarkers, dehydroepiandrosterone-sulfate (DHEA-S), Serotonin, Cortisol, Dopamine, Epinephrine, and Norepinephrine. A total of 7 variant riboswitches were tested in this research, 4 created computationally discussed here and 3 experimentally not covered in this paper. The results from these variants showed that variants 1 and 2 had different responses to DHEA-S then the expected PreQ1 response. A dose response showed downward trend as DHEA-S concentration increased. In conclusion of this research, riboswitches can be re-engineered to have a different response to biomarkers at the same time keeping the same structure.

riboswitches, biomarkers, protein, regulation, PreQ1, computer simulations

Article Details

How to Cite
Bates, M., Harbough, S., & Goswami, T. (2022). Simulation of gene regulatory elements for biosensing. Advances in Biochips, 3(1), 35-49.


  1. Pavlova N, Kaloudas D and Penchovsky R. Riboswitch distribution, structure, and function in bacteria. Gene, 2019, 708: 38-48.
  2. Breaker RR. Riboswitches and the RNA World. Cold Spring Harbor Perspectives in Biology, 2012, 4(2): 441-441.
  3. Mayeux R. Biomarkers: potential uses and limitations. Neurorx, 2004, 1(2): 182-188.
  4. Jenkins JL, Krucinska J, Mccarty RM, et al. Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation. Journal of Biological Chemistry, 2011, 286(28): 24626-24637.
  5. Menezes KD, Peixoto C, Nardi AE, et al. Dehydroepiandrosterone, Its Sulfate and Cognitive Functions. Clinical Practice and Epidemiology in Mental Health, 2016, 12(1): 24-37.
  6. Steckl AJ and Ray P. Stress Biomarkers in Biological Fluids and Their Point-of-Use Detection. Acs Sensors, 2018, 3(10): 2025-2044.
  7. Mental health by the numbers, NAMI. [Online] Available: [Accessed: 06-Jan- 2022]
  8. Amin EB, Mishler DM, Wang J, et al. Automated physics-based design of synthetic riboswitches from diverse RNA aptamers. Nucleic Acids Research, 2016, 4(1): 1-13.
  9. Peselis A and Serganov A. Themes and variations in riboswitch structure and function. Biochimica Et Biophysica Acta, 2014, 1839(10): 908-918.
  10. Auslnder S and Fussenegger M. Synthetic RNA-based switches for mammalian gene expression control. Current Opinion in Biotechnology, 2017, 48: 54-60.
  11. Wu MC, Lowe PT, Robinson CJ, et al. Rational Re-engineering of a Transcriptional Silencing PreQ1 Riboswitch. Journal of the American Chemical Society, 2015, 137(28): 9015-9021.