Atomic Force Microscopy Visualization of NC:NA Complexes

NC:NA complexes were assembled under conditions used for EMSA with 1 ng/ $$\mathsf{\mu }$$ L of M13 ssDNA and in a binding solution containing 10 mM TrisAcetate pH 7.0, 50 mM sodium acetate, 2.5 to 5 mM magnesium diacetate, and 0.5 mM TCEP. A freshly cleaved muscovite mica surface was pre-treated for 2 min with a fresh dilution of spermidine (50 $$\mathsf{\mu }$$ M), extensively rinsed with water and dried under a nitrogen flow [96 (link)]. A 5 $$\mathsf{\mu }$$ L drop of the NP complexes was deposited on the surface and incubated for 3–5 min and dried with nitrogen gas. AFM images were carried out in air with a multimode scanning probe microscope (Bruker, USA) operating with a Nanoscope IIIa or V controller (Bruker, USA) and silicon AC160TS cantilevers (Olympus, Japan) using the tapping mode at their resonant frequency. The scan frequency was typically 1.0 Hz per line and the modulation amplitude was a few nanometers. A second-order polynomial function was used to remove the background with the AFM software (Bruker, USA).