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 polymers¹ and oligomers² 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^3–9. 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, F_j, and the free energy change ΔF_BZ 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^3–9 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 F_j = 4–5 kcal per mol per junction and ΔF_BZ = 0.5÷0.7 kcal per mol per bp.