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

Abstract

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.

Keywords:

• Cationic gemini surfactant
• DNA compaction
• kinetic intermediates
• surface trapping

Acknowledgements

The author is grateful for financial support from the Natural Science Foundation of Shandong Province of China (Grant No. ZR2009BQ003) and the Scientific Research Foundation of Qingdao Vocational and Technical College (Grant No. 11-A-9).