Precision mapping of NF-κB-DNA binding: high-resolution insights via dynamic UV-laser footprinting

Abstract

Sequence-specific binding is at the core of all DNA-templated processes, including the initiation of DNA replication, gene expression and DNA repair. Yet the kinetics and precision of these interactions remain difficult to capture at high resolution. Here, we present Dynamic UV Laser Footprinting (DULF), a novel technique that integrates UV laser footprinting with stopped-flow mixing to probe transcription factor (TF)-DNA interactions at millisecond temporal and single base-pair spatial resolution. Using NF-κB as a model TF, we demonstrate the feasibility of DULF in visualizing the spatiotemporal details of a sequence-specific TF-DNA interaction. The high temporal resolution of our data reveals that TF-DNA binding proceeds through a rapid recognition step and a subsequent slower stabilization phase. DULF also revealed that the p50 homodimer binds specifically to DNA outside the canonical binding site, emphasizing the role of flanking sequences in these interactions. All-atom molecular dynamics simulations confirmed that DNA sequence context, including flanking base pairs, modulates NF-κB binding stability and induces local structural changes such as bending, groove widening, and base unstacking. DULF offers a unique opportunity to study DNA-protein interactions at unprecedented resolution, providing insights into the mechanism of sequence-specific binding and stabilization of chromatin interactors.

Keywords: Dynamic UV laser footprinting; Molecular dynamics; NF-κB, transcription factor; UV Laser footprinting.