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 structural intermediates; At 1.5-3 mu M spermidine there are no interesting morphologies of the DNA, although there is a reduction of the apparent persistence length. At 7.5-15 mu M 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 mu M 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 mu M 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.