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Article

Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription

1
Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Korea
2
Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
3
Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
*
Authors to whom correspondence should be addressed.
Academic Editors: Carlos Penedo and Grzegorz Wegrzyn
Int. J. Mol. Sci. 2021, 22(5), 2398; https://doi.org/10.3390/ijms22052398
Received: 21 January 2021 / Revised: 8 February 2021 / Accepted: 24 February 2021 / Published: 27 February 2021
Two different molecular mechanisms, sliding and hopping, are employed by DNA-binding proteins for their one-dimensional facilitated diffusion on nonspecific DNA regions until reaching their specific target sequences. While it has been controversial whether RNA polymerases (RNAPs) use one-dimensional diffusion in targeting their promoters for transcription initiation, two recent single-molecule studies discovered that post-terminational RNAPs use one-dimensional diffusion for their reinitiation on the same DNA molecules. Escherichia coli RNAP, after synthesizing and releasing product RNA at intrinsic termination, mostly remains bound on DNA and diffuses in both forward and backward directions for recycling, which facilitates reinitiation on nearby promoters. However, it has remained unsolved which mechanism of one-dimensional diffusion is employed by recycling RNAP between termination and reinitiation. Single-molecule fluorescence measurements in this study reveal that post-terminational RNAPs undergo hopping diffusion during recycling on DNA, as their one-dimensional diffusion coefficients increase with rising salt concentrations. We additionally find that reinitiation can occur on promoters positioned in sense and antisense orientations with comparable efficiencies, so reinitiation efficiency depends primarily on distance rather than direction of recycling diffusion. This additional finding confirms that orientation change or flipping of RNAP with respect to DNA efficiently occurs as expected from hopping diffusion. View Full-Text
Keywords: Cy3; Cy5; Escherichia coli; fluorescent labeling; fluorescent transcription complex; one-dimensional facilitated diffusion; protein-induced fluorescence enhancement; single-molecule fluorescence; transcription termination Cy3; Cy5; Escherichia coli; fluorescent labeling; fluorescent transcription complex; one-dimensional facilitated diffusion; protein-induced fluorescence enhancement; single-molecule fluorescence; transcription termination
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MDPI and ACS Style

Kang, W.; Hwang, S.; Kang, J.Y.; Kang, C.; Hohng, S. Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription. Int. J. Mol. Sci. 2021, 22, 2398. https://doi.org/10.3390/ijms22052398

AMA Style

Kang W, Hwang S, Kang JY, Kang C, Hohng S. Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription. International Journal of Molecular Sciences. 2021; 22(5):2398. https://doi.org/10.3390/ijms22052398

Chicago/Turabian Style

Kang, Wooyoung, Seungha Hwang, Jin Y. Kang, Changwon Kang, and Sungchul Hohng. 2021. "Hopping and Flipping of RNA Polymerase on DNA during Recycling for Reinitiation after Intrinsic Termination in Bacterial Transcription" International Journal of Molecular Sciences 22, no. 5: 2398. https://doi.org/10.3390/ijms22052398

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