Relative Stabilities and Transitions of DNA Conformations in 1:1 Electrolytes: A Theoretical Study

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Abstract
We use a recently developed formalism (1) to calculate the salt dependent part of the free energy determining DNA conformational stability in 1:1 electrolytes. The conformations studied are the A,B,C and alternating-B right-handed forms and the Z1ZII left-handed forms of DNA. In the case of the B-Z1 transition of d(G-C) · d(G-C) helices in NaCl solution, the free energy contribution considered suffices to describe the transition in a quantitative manner. The theory also predicts the occurrence of salt-induced B-A transitions which have been recently observed with poly[d(n2A-T)| and poly[d(G-C)|. In other cases, additional terms in the free energy balance, particularly due to hydration effects, must be at least as important as salt effects in determining conformational stability and structural transitions in solution. If diffuse ionic cloud electrostatic effects alone would dominate in all cases, the relative helical stabilities at 0.2 M monovalent salt would decrease in the order C > B > A > ZII > Z1 > alternating-B. At high salt concentrations (2.0 M - 5.0 M), the order would be alternating-B > Z, > A > ZII > B > C.