• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Journal of the Korean Chemical Society
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• v.38 no.8
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• pp.539-546
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• 1994

The critical micelle concentration(CMC) and the counterion binding $constant(\beta)$ at the CMC of cetyltrimethylammonium bromide(CTAB) in a series of aqueous solutions containing medium chain-length n-alcohols(Propanol, Butanol, Pentanol and Hexanol) have been determined from the concentration dependence of electrical conductance at serveral temperature from $17^{\circ}C\;to\;41^{\circ}C.$ Thermodynamic parameters $({\Delta}G^o_m,\;{\Delta}H^o_m,\;{\Delta}S^o_m,\;and\;{\Delta}C_p)$ associated with micelle formation of CTAB have been also estimated from the temperature dependence of CMC and $\beta$ values, and the significance of these parameters and their relation to the theory of micelle formation have been considered. The results show that an enthalpy-entropy compensation effect is usually observed for the micellization of CTAB. The effects of n-alcohols on the micellar properties (CMC and $\beta$) of CTAB solutions have been also investigated. The addition of n-alcohol to the CTAB solution in a small quantity decreases the CMC value and the counterion binding constant $(\beta)$ at the CMC, but the addition of n-alcohol in an excessive quantity increases the CMC values on the conterary. These results have been explained in terms of the effect of the micelle-solubilized alcohol on the micellar surface charge density.