Breaking the speed limit with multimode fast scanning of DNA by Endonuclease V

Arash Ahmadi, Ida Rosnes, Pernille Blicher, Robin Diekmann, Mark Schüttpelz, Kyrre Glette, Jim Tørresen, Magnar Bjørås, Bjørn Dalhus () and Alexander D. Rowe ()
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Arash Ahmadi: University of Oslo
Ida Rosnes: University of Oslo
Pernille Blicher: University of Oslo
Robin Diekmann: University of Bielefeld
Mark Schüttpelz: University of Bielefeld
Kyrre Glette: University of Oslo
Jim Tørresen: University of Oslo
Magnar Bjørås: Rikshospitalet and University of Oslo
Bjørn Dalhus: University of Oslo
Alexander D. Rowe: University of Oslo

Nature Communications, 2018, vol. 9, issue 1, 1-9

Abstract: Abstract In order to preserve genomic stability, cells rely on various repair pathways for removing DNA damage. The mechanisms how enzymes scan DNA and recognize their target sites are incompletely understood. Here, by using high-localization precision microscopy along with 133 Hz high sampling rate, we have recorded EndoV and OGG1 interacting with 12-kbp elongated λ-DNA in an optical trap. EndoV switches between three distinct scanning modes, each with a clear range of activation energy barriers. These results concur with average diffusion rate and occupancy of states determined by a hidden Markov model, allowing us to infer that EndoV confinement occurs when the intercalating wedge motif is involved in rigorous probing of the DNA, while highly mobile EndoV may disengage from a strictly 1D helical diffusion mode and hop along the DNA. This makes EndoV the first example of a monomeric, single-conformation and single-binding-site protein demonstrating the ability to switch between three scanning modes.

Date: 2018
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DOI: 10.1038/s41467-018-07797-4

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