Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments.

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 wit

SUBMITTER: Kolbeck PJ 

PROVIDER: S-EPMC10783501 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature