Kinetics of binding of Antp homeodomain to DNA analyzed by measurements of surface plasmon resonance.

The kinetics of binding of the Antp homeodomain to three kinds of DNA fragment were analyzed by measurements of surface plasmon resonance at various temperatures. Non-specific and specific binding of the homeodomain to DNA was examined. In the case of non-specific binding, the association rate constant (k(ass)) was estimated to be 1.41-2.62 x 10(5) M(-1) s(-1) and the dissociation rate constant (k(diss)) was 1.36-3.10 x 10(-2) s(-1), thus, the dissociation constant (KD) was 0.847-1.72 x 10(-7) M. The association seemed to be driven by entropy. In the case of specific binding, by contrast, the enthalpy term seemed to contribute more to the binding than did the entropy term. The k(ass) was 2.04-2.59 x 10(5) M(-1) s(-1) and the k(diss) was 0.759-1.16 x 10(-3) s(-1), thus, the KD was 2.93-5.69 X 10(-9) M. These values were measured under the condition of 150 mM NaCl. Both interactions were strongly dependent on the concentration of NaCl. The KD at 50 mM NaCl became several tens of times smaller than those at 150 mM. Possible reasons for the differences between non-specific and specific interactions are discussed.