Quantitation of DNA Binding Affinity Using Tethered Particle Motion.

Bram Henneman, Amanda M Erkelens, Joost Heinsman, Julius Battjes, 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. Not yet cited in PubMed.

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0citing papers in PubMed

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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

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0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Bram HennemanLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Amanda M ErkelensLeiden Institute of Chemistry, Leiden University, Leiden, The Netherlands.

Joost HeinsmanLeiden Institute of Physics, Leiden University, Leiden, The Netherlands.

Julius BattjesLeiden 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

The binding constant is an important characteristic of a DNA-binding protein. A large number of methods exist to measure the binding constant, but many of those methods have intrinsic flaws that influence the outcome of the characterization. Tethered particle motion (TPM) is a simple, cheap, and high-throughput single-molecule method that can be used to measure binding constants of proteins binding to DNA reliably, provided that they distort DNA. In TPM, the motion of a bead tethered to a surface by DNA is tracked using light microscopy. A protein binding to the DNA will alter bead motion. This change in bead motion makes it possible to measure the DNA-binding properties of proteins. We use the bacterial protein integration host factor (IHF) and the archaeal histone HMfA as examples to show how specific binding to DNA can be measured. Moreover, we show how the end-to-end distance can provide structural insights into protein-DNA binding.

Indexed as

DNAProtein BindingDNA-Binding ProteinsHistonesIntegration Host FactorsMotionSingle Molecule ImagingDNADNA-Binding ProteinsHistonesIntegration Host FactorsDNA bindingNucleoid-associated protein, IHFRoot mean square displacementSingle moleculeTethered particle motion

Identifiers

PMID39028521

DOI10.1021/bi500344j

What Socratic 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 Socratic graph.