Fine DNA structure revealed by constant height frequency modulation AFM imaging

Few examples of sub nanometer resolution on biomolecules can be found in literature. In particular, AFM experiments on DNA mostly fail to show the double helical groove periodicity, and so far such a feat was only achieved in liquid. Here we describe a method that produces highly resolved images of DNA where contrast can be assigned to submolecular features such as DNA helix's grooves. Two types of AFM experiments are presented: (1) We started by imaging DNA with Frequency Modulation (FM) AFM, where a shift in resonance frequency is used as a feedback signal and maintained constant during imaging. With FM-AFM we performed experiments in the non-contact (NC) mode, with z-feedback on, where only gentle (few tens of pN) non compressive force is applied between the tip and the sample. (2) Then we switched off the z-feedback and scanned the DNA sample at constant height measuring frequency modulation in order to acquire frequency shift maps of the sample. This was done at several separations including the distances where the frequency feedback is not stable due to the non-monotonicity of the frequency shift curve. At this distance sub-molecular resolution was reached and a calculation of the tip-sample van der Wools interaction at constant height, as well as the periodicity of the observed features that ranges from 3 to 5 nm, suggest that these correspond to the DNA helix grooves. This is the first experimental study where submolecular features of single DNA molecules are observed in dry environment. The knowledge of DNA structure when dried and deposited on flat substrates is important for proper understanding of DNA's electronic behavior and its eventual nanotechnology applications. (C) 2013 Elsevier Ltd. All rights reserved.