Abstract
We report analysis of the NaCl-induced B- Z transition in a 16 base-pair duplex DNA with sequence designed such that when NaCl is increased the left half of the molecule undergoes the B- Z transition while the right half remains in the B-form. An equilibrium thermodynamic model based on the body of available published experimental data and the recent theoretical work of Soumpasis, which indicate, in the salt range above ~0.9 m-NaCl, the transition free-energy of B- Z conversion in DNA is a linear function of the NaCl concentration, is employed. Analysis of the B- Z transition of the junction-containing molecule indicates the B- Z junction formed in this 16 base-pair DNA is composed of approximately three base-pairs and has a free energy of formation of ~4.7 kcal/mol junction. These values for the junction are in excellent agreement with published estimates of B- Z junction size and energy derived from much longer DNA pieces.
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