The affinity, association and dissociation between the drug and the DNA duplexes were measured using a BIAcore 3000A surface plasmon resonance (SPR) instrument (Pharmacia, Uppsala, Sweden) with a SensorChip SA5 from Pharmacia by monitoring the refractive index change of the sensor chip surface [41, 42, 43] . These changes are proportional to the amount of bound analyte. The SPR angle change is reported as resonance units (RU). Five fragments of 59 biotinylated oligonucleotides probes purified by PAGE were purchased from MDBio Inc. (Taiwan). Activation buffer (100 mM NaCl, 50 mM NaOH) was injected for 1 min (20 ml) to remove any unbound streptavidin from the sensor chip. To control the amount of the DNA bound to the SA chip surface, 200 nM of the biotinated oligonucleotides were immobilized manually onto the surface of a streptavidin chip until 120 RU was reached in the first cell. The chip surface was then washed with 10 ml of 10 mM HCl to eliminate non-specific binding. The second flow cell was unmodified and served as a control. Different concentration of TcaR, IcaR, and SAR2349 proteins were injected at a flow rate of 30 ml/min in 50 mM Tris, 150 mM NaCl, pH 7.5 for 170 s to reach equilibrium. Blank buffer solution was then passed over the chip to initiate the dissociation reaction. At the end of each cycle, the surface was recovered with two 30 s injections of 0.025% SDS. SPR-binding constant is analyzed as described previously [44] . Sensorgrams for the interactions between DNA and TcaR were analyzed using BIA evaluation software to determine the association and dissociation rate constant (k a /k d ). In the assay analyzing the effect of antibiotics on the interaction between TcaR and ssDNA, TcaR protein with 640 nM kanamycin or ampicillin in 50 mM Tris, 150 mM NaCl, pH 7.5 was injected on to the sensor chip.