Abstract
Here we describe a direct fluorescence method that reports real-time occupancies of the pre- and post-translocated state of multisubunit RNA polymerase. In a stopped-flow setup, this method is capable of resolving a single base-pair translocation motion of RNA polymerase in real time. In a conventional spectrofluorometer, this method can be employed for studies of the time-averaged distribution of RNA polymerase on the DNA template. This method utilizes commercially available base analogue fluorophores integrated into template DNA strand in place of natural bases. We describe two template DNA strand designs where translocation of RNA polymerase from a pre-translocation to a post-translocation state results in disruption of stacking interactions of fluorophore with neighboring bases, with a concomitant large increase in fluorescence intensity.
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Acknowledgements
This work was supported by the Academy of Finland grants 130581 and 263713 to G.A.B. Essential equipment was contributed by Walter and Lisi Wahl Foundation.
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Malinen, A.M., Turtola, M., Belogurov, G.A. (2015). Monitoring Translocation of Multisubunit RNA Polymerase Along the DNA with Fluorescent Base Analogues. In: Artsimovitch, I., Santangelo, T. (eds) Bacterial Transcriptional Control. Methods in Molecular Biology, vol 1276. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2392-2_3
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DOI: https://doi.org/10.1007/978-1-4939-2392-2_3
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