Direct resolution of the pitch of DNA on positively charged lipid bilayers by frequency-modulation AFM

High resolution structural studies of DNA and DNA binding proteins by atomic force microscopy (AFM) require well-bound samples on suitably flat substrates. Adsorbing the DNA onto a positively charged supported lipid bilayer has previously been shown to be a potentially effective strategy for structural studies with AFM. Here, using our home-built frequency-modulation AFM (FM-AFM), we show that these bilayer substrates are only maximally effective for high resolution AFM when the samples are short, linear DNA, compared with circular plasmid DNA. We find that, with the former sample, the measured width of the DNA is about 2 nm, the known DNA diameter, and there is a clear height modulation along the length of the DNA with a periodicity of about 3.4 nm, in excellent agreement with the known pitch of the double helix. This sample preparation strategy is expected to enable higher resolution studies of DNA and DNA binding proteins with FM-AFM than that can presently be achieved.