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Speaker: Thomas Visser BSc (PCC)

Title: Quantifying in vitro transcription

Abstract: Gene expression if one of the most important topics in biochemistry, at the root of gene expression lies transcription, the production of RNA from a DNA template by RNA polymerase. Transcription of DNA to mRNA has been studied extensively, but quantifying the rate of transcription often remains a challenge. We explore a new method to study in vitro transcription by using a specific DNA sequence. This sequence called “Broccoli” transcribes to a mRNA sequence that is able to form a complex with a fluorescent dye. The fluorescence of this mRNA complex can be measured directly and the transcription rate can easily be determined, for multiple processes at once. We compare the data obtained with this method with a thermodynamic model. The model predicts the relative transcription rate by calculating the occupation of transcription sites at determined concentrations of polymerase and DNA. We propose that in future experiments more complex systems with additional transcription factors, such as lacl suppressor, can also be studied. Being able to quantitatively study in vitro transcription opens up a versatile test ground for models of gene regulation.