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 language | English |
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Title of host publication | Bacterial Chromatin |
Subtitle of host publication | Methods and Protocols |
Editors | Remus T. Dame |
Place of Publication | New York, NY |
Publisher | Springer |
Pages | 443-454 |
Number of pages | 12 |
Edition | 2 |
ISBN (Electronic) | 978-1-0716-3930-6 |
ISBN (Print) | 978-1-0716-3929-0 |
DOIs | |
Publication status | Published - 2024 |
Publication series
Name | Methods in Molecular Biology |
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Publisher | Springer |
Volume | 2819 |
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-careOtherwise 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