It is shown that temperature-control led 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.