You are studying the function of phosphorylation of TFIIH with extracts from yeast. You can add these extracts to dsDNA and have transcription occur in vitro (if you also add rNTPs). Your research team has created an inhibitor that specifically prevents TFIIH from phosphorylating the CTD of RNA pol II. You decide to measure the size of the transcription bubble with and without the inhibitor. Develop or find an assay that would measure the size of the bubble and describe it, with controls. How big would the bubble be with and without the inhibitor?
Single-molecule nanomanipulation was a method developed by Prof. Terence Strick. We have used this method to characterize transcription kinetics (including the transcription bubble size) for both prokaryotes and eukaryotes. Take a look if that fits your request.
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