Evidence map›Paper›PMID 30568191›Full record

ArticleNature communications2018

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, Alexander D Rowe

Erratum issuedAbstract read
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In one paragraph

Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

14 citing papers in PubMed.

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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Arash AhmadiDepartment of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway.ORCID http://orcid.org/0000-0001-5566-7775
Ida RosnesDepartment of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway.
Pernille BlicherDepartment of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway.
Robin DiekmannBiomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany.ORCID http://orcid.org/0000-0002-5290-9123
Mark SchüttpelzBiomolecular Photonics, Department of Physics, University of Bielefeld, Universitätsstraße 25, DE-33615, Bielefeld, Germany.ORCID http://orcid.org/0000-0001-5338-1706
Kyrre GletteDepartment of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.ORCID http://orcid.org/0000-0003-3550-3225
Jim TørresenDepartment of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.ORCID http://orcid.org/0000-0003-0556-0288
Magnar BjøråsDepartment of Microbiology, Oslo University Hospital HF, Rikshospitalet and University of Oslo, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
Bjørn DalhusDepartment of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. bjornda@medisin.uio.no.ORCID http://orcid.org/0000-0002-9867-8391
Alexander D RoweDepartment of Medical Biochemistry, Institute for Clinical Medicine, University of Oslo, NO-0372, Oslo, Norway. alerow@ous-hf.no.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Deoxyribonuclease (Pyrimidine Dimer)DNA GlycosylasesEscherichia coliMarkov ChainsSingle Molecule ImagingThermotoga maritimaDeoxyribonuclease (Pyrimidine Dimer)DNA Glycosylasesoxoguanine glycosylase 1, human

Identifiers

PMID30568191
PMCPMC6300609

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.