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A detailed molecular model for alkali-denatured duplex circular DNA (“Form IV”) is proposed. The illustrative biological example used is the replicative form of fx174, a 5 kb duplex circular chromosome. The model explains all of Form IV’s known and peculiar features. In a sedimentation coefficient vs. pH titration, Form IV begins to appear at pH 12.3, at which point it can be persuasively argued that no further supertwists can be added to the already-highly-supertwisted chromosome. Therefore a new structure must appear. The sedimentation coefficient s then undergoes a massive, but initially reversible increase as the pH is raised further, culminating at pH 12.8 with a 250% increase. This degree of compactness can only be explained by a 4-stranded tetraplex structure, consisting of a pair of duplexes whose base pairs are mutually intercalated. Above pH 12.8, the structural changes become irreversible, suggesting a further conformational change. It is proposed that this involves an axial rotation of the component duplex strands, so that the bases now stack on the outside, and the phosphate groups lie in the core, where they bond ionically by means of salt bridges. When the irreversibly denatured compact structure is neutralized at moderate-to-high salt concentrations, a third novel structure appears, which has a sedimentation coefficient midway between the native 21 s and the denatured 50 s. It is proposed that this is a hybrid structure; part tetraplex, part duplex. To return to a fully-duplex form, it is necessary to both neutralize the solution, and also to greatly reduce the ionic strength, i.e., to the range 0.001-0.01 M. Since the DNA, under those conditions, cannot possibly have normal complementary base-pairing, the duplex structure must either be tautomerically base-paired, or else stabilized solely by base-stacking, with no base-pairing at all.

The Probable Structure of “Form IV” (Alkali-Denatured Circular DNA)