Atomic Force Microscopy of spermidine-induced DNA condensates on silicon surfaces

In the present work, we show that oxidized silicon may be successfully used to image multivalent cation-induced DNA condensates under the Atomic Force Microscope (AFM). The images thus obtained are good enough, allowing us to distinguish between different condensate forms and to perform nanometer-sized measurements. Qualitative results previously obtained using mica as a substrate are recovered here. We additionally show that the interactions between the cation spermidine (the condensing agent) and the DNA molecules are not significantly disturbed by the silicon surface, since the phase behavior of an ensemble of DNA molecules deposited on the silicon substrate as a function of the cation concentration is very similar to that found in solution.

► We developed a protocol do deposit condensed DNA on oxidized silicon substrates.
► We measured the sizes of the spermidine-induced DNA condensates under the AFM.
► We sketch the phase diagram of an ensemble of DNA molecules in a spermidine solution.