NMR-based conformational analysis of DNA G-quadruplex guides mapping essential structure–function relationship in protein chaperoning

Abstract

G-quadruplexes (G4s) are increasingly recognized to chaperone proteins, warranting studies of structure–function relationships. In this study, we apply solution NMR methods to determine the topology and base-level resolution structure of a G-rich DNA sequence with protein chaperoning activity (referred to as Seq576) without chemical shift assignments. Seq576 samples two conformations, in the slow exchange timescale, arising from a G-register shift. Using the structural insights of Seq576, we then perform structure–function studies via mutation and chaperone assays to investigate the G4 properties essential for chaperoning protein aggregation and folding. These studies highlight the possibility of using a construct design to perform in-depth nucleic acid structural biology investigation using inexpensive and fast NMR experiments to obtain and analyze function, such as the residue-level investigation of chaperone activity.