Evidence map›Paper›PMID 39028520›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Tethered Particle Motion Analysis of DNA-Binding Properties of Architectural Proteins.

Ramon A van der Valk, Ilias Zarguit, Niels Laurens, Remus T Dame

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

4 authors.

Ramon A van der ValkLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
Ilias ZarguitLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
Niels LaurensLeiden Institute of Physics, Leiden University, Leiden, The Netherlands.
Remus T DameLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands. rtdame@chem.leidenuniv.nl.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Architectural DNA-binding proteins are key to the organization and compaction of genomic DNA inside cells. Tethered particle motion (TPM) permits analysis of DNA conformation and detection of changes in conformation induced by such proteins at the single molecule level in vitro. As many individual protein-DNA complexes can be investigated in parallel, these experiments have high throughput. TPM is therefore well suited for characterization of the effects of protein-DNA stoichiometry and changes in physicochemical conditions (pH, osmolarity, and temperature). Here, we describe in detail how to perform tethered particle motion experiments on complexes between DNA and architectural proteins to determine their structural and biochemical characteristics.

Indexed as

DNADNA-Binding ProteinsNucleic Acid ConformationMotionProtein BindingSingle Molecule ImagingDNADNA-Binding ProteinsDNA bendingDNA conformationDNA stiffeningDNA wrappingTethered particle motion

Identifiers

PMID39028520

What OpenQuestion holds

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Registered trials

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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.