Sequence-dependent DNA condensation and the electrostatic zipper

Sequence-dependent configuration changes and condensation of double-stranded poly(dG-dC).(dG-dC) (GC-DNA) and ds poly(dA-dT).(dA-dT) (AT-DNA) were observed by atomic force microscopy in the presence of Ni(II). Less condensing agent was required to generate configuration changes in GC-DNA as compared to AT-DNA. In the presence of Ni(II) cations, GC-DNA adopted a Z-type conformation and underwent a stepwise condensation, starting with partial intramolecular folding, followed by intermolecular condensation of two to several molecules and ending with the formation of toroids, rods, and jumbles. GC-DNA condensates were unusual in that the most highly condensed regions were surrounded by loops of ds GC-DNA. In contrast, AT-DNA retained its B-type conformation and displayed only minor condensation even at high Ni(II) concentrations. The Ni(II)-dependent differences in condensation between GC-DNA and AT-DNA are predicted by an extension of the electrostatic zipper motif proposed by Kornyshev and Leikin, in which we account for shorter than Debye screening length surface separations between the DNA molecules and for the Ni(II)-induced conformation change of GC-DNA to Z-DNA.