Evidence map›Paper›PMID 39028523›Full record

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

Unravelling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers.

Thomas B Brouwer, Artur Kaczmarczyk, Ilias Zarguit, Chi Pham, Remus T Dame, John van Noort

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. 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.

  1. 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.

Thomas B BrouwerLeiden Institute of Physics, Leiden University, Leiden, The Netherlands.
Artur KaczmarczykLeiden Institute of Physics, Leiden University, Leiden, The Netherlands.
Ilias ZarguitLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
Chi PhamLeiden Institute of Physics, Leiden University, Leiden, The Netherlands.
Remus T DameLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.
John van NoortLeiden Institute of Physics, Leiden University, Leiden, The Netherlands. noort@physics.leidenuniv.nl.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers, in particular, have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA-organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to a magnetic bead inside a flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleoprotein filaments can be extracted from the data.

Indexed as

DNASingle Molecule ImagingMagneticsMicroscopy, Atomic ForceNucleic Acid ConformationOptical TweezersDNAArchaeal chromatinBacterial chromatinDNA compactionDNA mechanicsEukaryotic chromatinForce spectroscopyMagnetic tweezersRotational spectroscopySingle molecule

Identifiers

PMID39028523

What OpenQuestion holds

Textmetadata
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.