The interaction of the in vitro Nuclear Aggregates of Polyamines with the genomic DNA: an AFM characterization

Polyamines self-assemble in vitro with phosphate ions generating three different supra-molecular aggregates named in vitro Nuclear Aggregates of Polyamines (iv-NAPs). These compounds share structure and functions with the naturally occurring homologues NAPs. They interacts with DNA phosphate groups and influence, more efficaciously than single polyamines, both the conformation and the protection of the DNA, thus playing crucial functions. We report on the morphological AFM characterization of the iv-NAPs and their interactions with the genomic DNA. A hierarchical multi-step process of supra-molecular assembly for each one of the three iv-NAPs in cyclic like structures was highlighted. Moreover, the track of the iv-NAPs coating the DNA was visualized by phase imaging, highly sensitive to the height changes of the samples. We show that iv-NAPs interact with genomic DNA disposing around its longitudinal axis and wrapping it in a helical tunnel like structure. Our images prove that such a molecular organization represents the sole strategy by which polyamines efficiently protect genomic DNA while maintaining its dynamic structure.