Thermodynamics of the B-Z transition in superhelical DNA

Abstract

One of the most exciting events in recent years in molecular biology was the discovery of the left-handed Z form of the DNA double helix. Originally found in linear self-complementary d(GC)x . d(GC)x polymers and oligomers in non-physiological conditions (a rather high salt concentration), it was recently shown to be easily enough adopted in physiological conditions when purine-pyrimidine sequences are inserted into superhelical DNA. From such a system, superhelical DNA carrying an artificial purine-pyrimidine insert, we can obtain data allowing the determination of the energy of the junction between the B and Z stretches, Fj, and the free energy change delta FBZ per base pair (bp). We present here a simple thermodynamic consideration of the B-Z transition in such a system. By applying the results to experimental data we have shown that the thermodynamic parameters for both sequences studied so far (d(GC)x . d(GC)x and d(GT)x . d(AC)x) are similar and equal to Fj = 4-5 kcal per mol per junction and delta FBZ = 0.5 divided by 0.7 kcal per mol per bp.