Slow exchanging protons in the Z-form of G-C and A-C alternating polymers by using a rapid dialysis method

Using a dialysis method we have measured the hydrogen exchange (HX) kinetics in poly(dG-dC).poly(dG-dC), poly(dG-m5dC).poly(dG-m5dC), poly(dG-br5dC).poly(dG-br5dC) and platinated poly(dA-br5dC).poly(dG-dT) under experimental conditions in which these polymers adopt the Z-conformation. The latter polymer has one slow exchanging proton with a half-time of about 2 h, whereas the other G-C alternating polymers display a slow class of two protons with exchange half-time of about 6 h. These exchange half-times are independent of ionic strength and of the nature of the salt for all these polymers in the Z-form. The slow proton exchange appears to be strongly correlated to the Z-conformation but rather independent of the Z-DNA sequence. The comparison of the proton exchange rates with the corresponding B in equilibrium Z transition rates is not in favour of the same rate limiting step for both processes.