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Nat Commun. 2018 Dec 19;9(1):5381. doi: 10.1038/s41467-018-07797-4.

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

Author information

1
Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway.
2
Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
3
Biomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany.
4
European Molecular Biology Laboratory (EMBL), Cell Biology and Biophysics Unit, Meyerhofstraße 1, DE-69117, Heidelberg, Germany.
5
Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.
6
Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU), PO Box 8905, NO-7491, Trondheim, Norway.
7
Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. bjornda@medisin.uio.no.
8
Department of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway. bjornda@medisin.uio.no.
9
Department of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. alerow@ous-hf.no.
10
Department of Newborn Screening, Division of Child and Adolescent Medicine, Oslo University Hospital, PO Box 4950 Nydalen, NO-0424, Oslo, Norway. alerow@ous-hf.no.

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.

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