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Gel shift assay of CodY affinity for nupN DNA fragments. Different labeled nupNp+ DNA fragments were incubated with increasing amounts of purified CodY in the presence of 10 mM ILV and 2 mM GTP. The CodY concentrations used (nanomolar concentrations of monomers) are indicated below each lane. KD, the apparent equilibrium dissociation constant, was estimated as the protein concentration needed to shift 50% of DNA fragments under conditions of vast protein excess over DNA.
