Left-handed Z Form in Superhelical DNA: A Theoretical Study

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Abstract
This is a comprehensive statistical mechanical treatment of the Z form formation in purine- pyrimidine stretches of different length inserted into superhelical DNA. The B-Z transition for short inserts is shown to follow the “all-or-none” principle. Over some critical value of the insert length n, the B-Z transition in the insert proceeds in two stages. The flipping of m base pairs into the Z form is followed by a gradual growth of the Z-form stretch until it occupies the whole insert. By fitting the theoretical transition curves to experimental ones the fundamental thermodynamic parameters of the B-Z transition have been determined: the B-Z junction energy Fj = 4–5kcal•mol−1 and the free energy change ΔFB-Z = 0.5–0.7 kcal•mol−1 under standard salt conditions. Calculations show that the B-Z transition in short purine-pyrimidine inserts may be seriously affected by cruciform formation in the carrier DNA.