Left-handed Z form in superhelical DNA: a theoretical study

Journal of Biomolecular Structure & Dynamics
A V Vologodskii, M D Frank-Kamenetskii

Abstract

This is a comprehensive statistical mechanical treatment of the Z form formation in purinepyrimidine 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 delta FBZ = 0.5-7.0 kcal.mol-1 under standard salt conditions. Calculations show that the B-Z transition in short purinepyrimidine inserts may be seriously affected by cruciform formation in the carrier DNA.

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Citations

Dec 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·M J EllisonA Rich
Sep 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·R J KelleherA Rich
Sep 27, 1994·Proceedings of the National Academy of Sciences of the United States of America·P S Ho
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Feb 2, 2011·PLoS Computational Biology·Dina Zhabinskaya, Craig J Benham
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