Modeling Kinetic Competition Between Ribozyme Cleavage and RNA Termination in Living Cells
Additional Funding Sources
Our work is funded by the National Institutes of General Medical Science through grants 2R15GM123446-02A1 and 3R15GM123446-02A1S1.
Abstract
Introduction: Understanding the complex spatiotemporal relationships between different processes at an active gene requires careful measurement and complex modeling. Methods: In our current work, we attempt to model preliminary single-molecule experiments of transcription, termination, and ribozyme cleavage of RNA in living cells using a stochastic Gillespie simulation. Results: By modeling the binding of MCP-GFP to RNA, transcription, termination, and ribozyme cleavage we hope to discriminate between a deterministic and kinetic competition model of termination and ribozyme cleavage in our 3D Orbital tracking data. Discussion: In the future, this type of experiment and model can be extended to the study of the regulation of transcription and splicing of RNA and the spatiotemporal dynamics of the genome in living cells.
- Roberts, J., Kunz, G., Hayden, E., Ferguson, M.L. Kinetic competition between theophylline sensitive ribozyme cleavage and termination in living cells by 3D orbital tracking-fluorescent cross-correlation spectroscopy. Biophys J 2023;122:428a.
Modeling Kinetic Competition Between Ribozyme Cleavage and RNA Termination in Living Cells
Introduction: Understanding the complex spatiotemporal relationships between different processes at an active gene requires careful measurement and complex modeling. Methods: In our current work, we attempt to model preliminary single-molecule experiments of transcription, termination, and ribozyme cleavage of RNA in living cells using a stochastic Gillespie simulation. Results: By modeling the binding of MCP-GFP to RNA, transcription, termination, and ribozyme cleavage we hope to discriminate between a deterministic and kinetic competition model of termination and ribozyme cleavage in our 3D Orbital tracking data. Discussion: In the future, this type of experiment and model can be extended to the study of the regulation of transcription and splicing of RNA and the spatiotemporal dynamics of the genome in living cells.
- Roberts, J., Kunz, G., Hayden, E., Ferguson, M.L. Kinetic competition between theophylline sensitive ribozyme cleavage and termination in living cells by 3D orbital tracking-fluorescent cross-correlation spectroscopy. Biophys J 2023;122:428a.