During my PhD in the lab of Eric Galburt, I became interested in how one could use kinetics to make predictions regarding transcriptional activity. To phrase it differently, how does DNA sequence (which encodes for the basal transcription kinetics) lead to gene regulation? Using a simplified mathematical model (https://doi.org/10.1073/pnas.1809454115) I illustrated how individual DNA sequence motifs can affect the steady-state rate of RNA production via changes in the initiation kinetics and drew caution in using an isolated sequence motif or rate constant when trying to predict transcriptional activity. To ultimately test these predictions, I described methods for a fluorescent-based readout of steady-state transcription. This facile method can be used for any DNA-dependent RNA polymerase and can be scaled up to make high-throughput, genome-wide kinetic measurements.
Publications
Drake Jensen, Ana Ruiz Manzano, Maxwell Rector, Eric J Tomko, M. Thomas Record, Eric A. Galburt
Nucleic Acids Research, vol. 51(19), 2023
Drake Jensen, Eric A. Galburt
Journal of Bacteriology, vol. 203(8), 2021