Fig. 2.

Kinetics of intermolecular translocation between nonspecific DNA duplexes. (a) Overlay of three ¹H-¹⁵N HSQC spectra measured on nonspecific complexes comprising Nhb (black) and Zhb (magenta) duplexes and their 1:1 mixture (green). (b) Amide ¹H_N-R₂ rates for Leu-26 as a function of free DNA concentration measured by Lorentzian line-shape-fitting in the ¹H dimension of the ¹H-¹⁵N HSQC spectra. HoxD9 was ²H,¹⁵N-labeled, yielding a pure Lorentzian line shape without ³J_HNHα splitting. In processing, a 5-Hz, line-broadening exponential window function was applied in the ¹H-dimension and then subtracted from the fitted value of R₂. (c) Overall apparent intermolecular translocation rate k_ex^inter plotted as function of [DNA]_free{[Nhb + Zhb]_free for the mixture with [Nhb]:[Zhb] = 1:1}. The value of k_ex^inter was obtained by fitting all of the data for residues with ∣δ_Nhb − δ_Zhb∣ > 20 Hz (at a ¹H frequency of 500 MHz) simultaneously, minimizing a χ² function defined as Σ(R_ex,calc^inter − R_ex,obs^inter)²/σ², where σ is the experimental error and R_ex,calc^inter is given by Eq. 1). Values of R_ex,obs^inter were obtained from the experimental values of R₂^Nhb, R₂^Zhb, and R₂^mixture.