Electrophoretic mobility shift assay (EMSA) and microscale thermophoresis

Electrophoretic mobility shift assays (EMSA) were performed using binding buffer containing 10 mM sodium phosphate pH8, 50 mM NaCl, 0.5 mM EDTA, 5 mM MgCl₂, 1 mM DTT, 20 μg/ml BSA, 6% glycerol and 2 nM IRD₇₀₀-labeled dsDNA oligonucleotides and increasing protein concentrations (10 nM to 20 μM) in dark and blue light illuminated states (see Supplementary Methods). Thermophoresis binding experiments were performed in a binding buffer containing 10 mM Tris-HCl pH8, 300 mM NaCl and 0.1% (w/v) Tween-20. Dark state experiments were performed under safe light (λ_max ≈ 650 nm). A total of 66.7 nM of fluorescently labeled protein was titrated at steady state with increasing concentrations of unlabeled interaction partners (see Supplementary Methods).