Figure 4.

MBD4_MBD exchanges between molecules of DNA on the slow NMR timescale. (a) 2D ¹H-¹⁵N HSQC spectra of MBD4_MBD bound to wild-type (black) and inverted (red) DNA sequences show that the chemical shifts for Arg¹⁰⁵ and Phe¹⁰⁶ differ between the two complexes. (b) 2D ¹H-¹⁵N N_z-exchange spectra of MBD4_MBD bound to a 1:1 mixture of wild-type and inverted (10 bp) sequences shows two distinct peaks for Arg¹⁰⁵ and Phe¹⁰⁶ which represent between binding to the different DNA sequences. The exchange crosspeaks, AB and BA, increase in intensity with increasing exchange delay (2.5 and 25 ms) and represent intermolecular exchange between DNA molecules. (c) The intensities for auto (AA and BB) and exchange (AB and BA) crosspeaks for Arg¹⁰⁵ (upper panels) and Phe¹⁰⁶ (lower panels) were fit to four coupled equations to determine the rate of intermolecular exchange at 200 μM (left panels) and 333 μM (right panels) MBD4_MBD concentration.