Protocol for detecting interactions between intrinsically disordered proteins and long DNA substrates by electrophoretic mobility shift assay

Intrinsically disordered regions (IDRs) of proteins leverage their structural flexibility to play important roles in numerous cellular processes including molecular recognition. Many IDRs interact with DNA, and characterizing these interactions is crucial for understanding their biological impact. Here, we present a protocol for the in vitro detection of IDR-DNA interactions using an electrophoretic mobility shift assay. We describe a radioactive-free procedure using long DNA substrates and define steps for data analysis. Altogether, this protocol facilitates reproducible and sensitive quantification of IDR-DNA interactions. For complete details on the use and execution of this protocol, please refer to Pastic et al.(1).