Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins.

Ramon A van der Valk, Bert van Erp, Liang Qin, Geri F Moolenaar, Remus T Dame

Abstract read

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. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing 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

1 citing paper in PubMed.

Selective targeting of a histone-like silencer Sfx to the R6K conjugal transfer operon.Nucleic acids research · 2026
Article

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

5 authors.

Ramon A van der ValkLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Bert van ErpLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Liang QinLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Geri F MoolenaarLeiden Institute of Chemistry, 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

DNA looping is important for genome organization in all domains of life. The basis of DNA loop formation is the bridging of two separate DNA double helices. Detecting DNA bridge formation generally involves the use of complex single-molecule techniques (atomic force microscopy, magnetic or optical tweezers). Although DNA bridging can be qualitatively described, quantification of DNA bridging and bridging dynamics using these techniques is challenging. Here we describe a biochemical assay capable of not only detecting DNA bridge formation but also allowing for quantification of DNA bridging efficiency and the quantification of the effects of physicochemical conditions or protein interaction partners on DNA bridge formation.

Indexed as

ChromatinDNAHumansMicroscopy, Atomic ForceNucleic Acid ConformationOptical TweezersChromatinDNADNA bridgingDNA bridging proteinsDNA-DNA cross-linkingDNA-DNA interactionsDNA loopingPull-down assay

Identifiers

PMID39028518

DOI10.1093/NAR/GKZ1226

What OpenQuestion holds

Textmetadata

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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.