Evidence map›Paper›PMID 28334870›Full record

ArticleNucleic acids research2017

Annealing helicase HARP closes RPA-stabilized DNA bubbles non-processively.

Daniel R Burnham, Bas Nijholt, Iwijn De Vlaminck, Jinhua Quan, Timur Yusufzai, Cees Dekker

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.2field-weighted citation impact, top 39% of its field
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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 2 countries.

Daniel R BurnhamDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands.
Bas NijholtDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands.
Iwijn De VlaminckDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands.
Jinhua QuanBiological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Timur YusufzaiBiological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA.
Cees DekkerDepartment of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, 2629 HZ, The Netherlands.
Delft University of Technology · NLHarvard University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

We investigate the mechanistic nature of the Snf2 family protein HARP, mutations of which are responsible for Schimke immuno-osseous dysplasia. Using a single-molecule magnetic tweezers assay, we construct RPA-stabilized DNA bubbles within torsionally constrained DNA to investigate the annealing action of HARP on a physiologically relevant substrate. We find that HARP closes RPA-stabilized bubbles in a slow reaction, taking on the order of tens of minutes for ∼600 bp of DNA to be re-annealed. The data indicate that DNA re-anneals through the removal of RPA, which is observed as clear steps in the bubble-closing traces. The dependence of the closing rate on both ionic strength and HARP concentration indicates that removal of RPA occurs via an association-dissociation mechanism where HARP does not remain associated with the DNA. The enzyme exhibits classical Michaelis-Menten kinetics and acts cooperatively with a Hill coefficient of 3 ± 1. Our work also allows the determination of some important features of RPA-bubble structures at low supercoiling, including the existence of multiple bubbles and that RPA molecules are mis-registered on the two strands.

Indexed as

Bacteriophage lambdaBiomechanical PhenomenaDNA HelicasesDNA, SuperhelicalHumansKineticsMagnetic FieldsOptical TweezersOsmolar ConcentrationPlasmidsProtein BindingRecombinant ProteinsReplication Protein ADNA HelicasesDNA, SuperhelicalRecombinant ProteinsReplication Protein ASMARCAL1 protein, human

Identifiers

PMID28334870
PMCPMC5416776
OpenAlexW2594916129

What OpenQuestion holds

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LicenceCC BY-NC
Read underepoch 390

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.