Kinetics measurements of G-quadruplex binding and unfolding by helicases.

• Many helicases accelerate G-quadruplex unfolding, commonly with topology preferences and flanking sequence requirements. • Simple biochemical techniques such as electrophoretic mobility shift assays are useful for probing helicase mediated G-quadruplex unfolding. • We detail specific methods for measuring the kinetics of helicase-mediated G-quadruplex binding, dissociation, and unfolding, and we outline practical tips and potential pitfalls. G-quadruplex structures (G4s) form readily in DNA and RNA and play diverse roles in gene expression and other processes, and their inappropriate formation and stabilization are linked to human diseases. G4s are inherently long-lived, such that their timely unfolding depends on a suite of DNA and RNA helicase proteins. Biochemical analysis of G4 binding and unfolding by individual helicase proteins is important for establishing their levels of activity, affinity, and specificity for G4s, including individual G4s of varying sequence and structure. Here we describe a set of simple, accessible methods in which electrophoretic mobility shift assays (EMSA) are used to measure the kinetics of G4 binding, dissociation, and unfolding by helicase proteins. We focus on practical considerations and the pitfalls that are most likely to arise when these methods are used to study the activities of helicases on G4s. [ABSTRACT FROM AUTHOR]