Print Email Facebook Twitter Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments Title Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments Author Kolbeck, Pauline J. (Universiteit Utrecht; Ludwig Maximilians University) Tišma, M. (TU Delft BN/Cees Dekker Lab) Analikwu, B.T. (TU Delft BN/Cees Dekker Lab) Vanderlinden, Willem (Ludwig Maximilians University) Dekker, C. (TU Delft BN/Cees Dekker Lab) Lipfert, Jan (Ludwig Maximilians University; Universiteit Utrecht) Date 2023 Abstract DNA stores our genetic information and is ubiquitous in applications, where it interacts with binding partners ranging from small molecules to large macromolecular complexes. Binding is modulated by mechanical strains in the molecule and can change local DNA structure. Frequently, DNA occurs in closed topological forms where topology and supercoiling add a global constraint to the interplay of binding-induced deformations and strain-modulated binding. Here, we present a quantitative model with a straight-forward numerical implementation of how the global constraints introduced by DNA topology modulate binding. We focus on fluorescent intercalators, which unwind DNA and enable direct quantification via fluorescence detection. Our model correctly describes bulk experiments using plasmids with different starting topologies, different intercalators, and over a broad range of intercalator and DNA concentrations. We demonstrate and quantitatively model supercoiling-dependent binding in a single-molecule assay, where we directly observe the different intercalator densities going from supercoiled to nicked DNA. The single-molecule assay provides direct access to binding kinetics and DNA supercoil dynamics. Our model has broad implications for the detection and quantification of DNA, including the use of psoralen for UV-induced DNA crosslinking to quantify torsional tension in vivo, and for the modulation of DNA binding in cellular contexts. To reference this document use: http://resolver.tudelft.nl/uuid:a9346733-a82d-4692-972f-4ac966078db0 DOI https://doi.org/10.1093/nar/gkad1055 ISSN 0305-1048 Source Nucleic acids research, 52 (1), 59-72 Part of collection Institutional Repository Document type journal article Rights © 2023 Pauline J. Kolbeck, M. Tišma, B.T. Analikwu, Willem Vanderlinden, C. Dekker, Jan Lipfert Files PDF gkad1055.pdf 2.53 MB Close viewer /islandora/object/uuid:a9346733-a82d-4692-972f-4ac966078db0/datastream/OBJ/view