Early intermediates in spermidine-induced DNA condensation on the surface of mica

The folding pathway of spermidine-induced DNA condensation on the surface of mica was examined by varying the concentration of spermidine in a dilute DNA solution and visualizing intermediates by atomic force microscopy (AFM). Images reveal that spermidine-induced DNA condensation on mica involves multiple well-defined intermediates. At 1.5-3 μM spermidine there are no interesting morphologies of the DNA, although there is a reduction of the apparent persistence length. At 7.5-15 μM spermidine, intramolecular loops (mean diameter 40 ± 15 nm) form. Loops initially appear to form independently of each other, but individual molecules with multiple loops tend to crossover at the same point producing 'flower'-shaped structures. At 30 μM spermidine, the tendency to form single crossover points increases and multimolecular flowers form. After initial flower formation disklike condensates appear, sometimes as apparent outgrowths from flowers. The resolvable strands in the disks are thicker than double-stranded DNA, suggesting a close association of two or more DNA strands and, thus, a stabilization of strand-strand interactions along the length of the DNA. This strand-strand stabilization is further indicated by the formation of very large (>500 nm) multimolecular aggregates, at 150 μM spermidine, composed predominantly of flowers and disks. These aggregates are initially planar with a monomolecular thickness and few crossover points. At the highest spermidine concentrations examined growth in the third dimension is seen as additional layers of condensates formed. These results suggest that there are several intermediates early in spermidine-induced DNA condensation on mica, with well-defined characteristics. Some of these intermediates have novel intra- and intermolecular contacts.