A condensed form of (dG-dC)n.cntdot.(dG-dC)n as an intermediate between the B- and Z- conformations induced by sodium acetate

Abstract

Circular dichroism [CD] and laser Raman spectroscopy reveal that the synthetic DNA polymer (dG-dC)n .cntdot. (dG-dC)n undergoes a cooperative transition induced by sodium acetate from a right-handed B-form to a left-handed Z-type conformation with a midpoint at 2.05 M. However, at concentrations only slightly higher than the end point of this transition (above .apprx. 2.2 M) and up to .apprx. 2.65 M, the Z-form is not stable in solution but aggregates to form highly condensed DNA. A many-fold increase of positive ellipticity in the range 340-250 nm is observed which is indicative of a .psi. (+)-type structure. At even higher concentrations (.gtoreq. 2.7 M), the Z-form is stable without condensation, and there is no change in the inverted CD spectrum. All structural transitions are reversible except that it is not possible to redissolve the highly condensed .psi. (+)-form by further increasing the salt concentration to .gtoreq. 2.7 M. The very high cooperativity of these transitions enables the DNA polymer to adopt 3 distinctly different structures (B-, Z- and .psi.-forms) within a narrow range of sodium acetate concentration (.apprx. 200 mM). The Raman spectra of the condensed form and the Z-form in very concentrated sodium acetate show that the .psi.(+)-type state forms without substantial changes of the secondary conformation of the DNA. The left-handed Z-helix of (dG-dC)n .cntdot. (dG-dC)n can probably form .psi.-type aggregates with an ordered superstructure similar to those observed for natural right-handed DNA helices.