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It is shown that temperature-controlled ordered layers of dodecylamine, self-assembled on highly oriented pyrolytic graphite (HOPG), are an appropriate substrate for aligning individual DNA molecules. High resolution atomic force microscopy (AFM) permits visualization of the lamellar structure of dodecylamine on HOPG. The DNA adsorbed on ordered dodecylamine layers is stretched and oriented along the lamellae, while DNA on disordered dodecylamine layers is found to be in a random conformation. Small DNA bubbles appear in the case of partially denaturated linear double stranded DNA (dsDNA) adsorbed on ordered layers of dodecylamine.

Interaction of the atomic force microscopy (AFM) tip with the sample can be invasive for soft samples. Frequency Modulation (FM) AFM is gentler because it allows scanning in the non-contact regime where only attractive forces exist between the tip and the sample, and there is no sample compression. Recently, FM-AFM was used to resolve the atomic structure of single molecules of pentacene and of carbon nanotubes. We are testing similar FM-AFM-based approaches to study biological samples. We present FM-AFM experiments on dsDNA deposited on 3-aminopropyltriethoxysilane modified mica in ultra high vacuum. With flexible samples such as DNA, the substrate flatness is a sub-molecular resolution limiting factor. Non-contact topographic images of DNA show variations that have the periodicity of the right handed helix of B-form DNA - this is an unexpected result as dehydrated DNA is thought to assume the A-form structure. Frequency shift maps at constant height allow working in the non-monotonic frequency shift range, show a rich contrast that changes significantly with the tip-sample separation, and show 0.2 to 0.4 nm size details on DNA. Frequency shift versus distance curves acquired on DNA molecules and converted in force curves show that for small molecules (height < 2.5 nm), there is a contribution to the interaction force from the substrate when the tip is on top of the molecules. Our data shine a new light on dehydrated and adsorbed DNA behavior. They show a longer tip-sample interaction distance. These experiments may have an impact on nanotechnological DNA applications in non-physiological environments such as DNA based nanoelectronics and nanotemplating. Copyright © 2012 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]