Gemini Surfactant-Induced DNA Compaction with Process Similar to Chromatin Assembly and the Kinetic Intermediates Captured by Surface Trapping

The intrachain DNA compaction induced by a cationic gemini surfactant hexyl-α,ω-bisdodecyldimethylammonium bromide (C₁₂C₆C₁₂Br₂) shows a process with high similarity to that of chromatin formation. The kinetic topological intermediates during compaction were successfully captured by surface trapping method. Further atomic force microscopy (AFM) characterization revealed that a phase-segregated state with the coexistence of compacted beadlike structures and elongated regions within a single DNA chain was generated at the first stage. Then more beadlike structures were formed to result in the necklace-like structures, which further assembled into closely packed higher-order structures while maintaining independence of each bead. The cooperative binding of the C₁₂C₆C₁₂Br₂ molecules onto the DNA chain should play crucial roles in such a compaction mode. Moreover, the structures obtained were found to be highly dependent on the sample preparation method.