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

Research output: Chapter in Book/Conference proceedings/Edited volumeChapterScientificpeer-review

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.
Original languageEnglish
Title of host publicationBacterial Chromatin
Subtitle of host publicationMethods and Protocols
EditorsRemus T. Dame
Place of PublicationNew York, NY
PublisherSpringer
Pages443-454
Number of pages12
Edition2
ISBN (Electronic)978-1-0716-3930-6
ISBN (Print)978-1-0716-3929-0
DOIs
Publication statusPublished - 2024

Publication series

NameMethods in Molecular Biology
PublisherSpringer
Volume2819
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Bibliographical note

Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care
Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.

Keywords

  • DNA bridging
  • DNA bridging proteins
  • DNA looping
  • DNA-DNA cross-linking
  • DNA-DNA interactions
  • Pull-down assay

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