Probing DNA binding selectivity in SqrR through arginine side-chain dynamics

Understanding the molecular determinants of DNA-binding specificity in transcriptional regulators is central to current research, with direct implications for human disease, bacterial antibiotic resistance, and biosensor design. Here we present an NMR-based strategy to characterize protein–DNA interfaces in solution, applied to SqrR, a model member of the ubiquitous ArsR family of bacterial transcriptional regulators. Building on our previous structural and thermodynamic characterization of SqrR bound to a native-like operator, we focused on arginine side chains at the protein–DNA interface. We optimized a set of NMR pulse sequences to assign and track the dynamics of these positively charged side chains in free and DNA-bound SqrR. This approach confirms previous findings and provides a powerful, scalable strategy for dissecting the mechanistic basis of DNA-binding selectivity in this regulatory family.