Comparison between shear force and tapping mode AFM - High resolution imaging of DNA

An improved shear force microscope (ShFM) is presented, where the oscillation of the probe can be excited and quantitatively detected in two orthogonal directions in the sample plane. This set-up allows a complete control of the dynamic behaviour of the probe that is necessary in order to obtain reproducible results. Increasing evidence has been collected confirming that the shear force mechanism is due to the water layer confined between the tip and the sample and that, therefore, ShFM is a true non-contact technique. To confirm the reduced tip-sample interaction with respect to conventional scanning probe techniques, the height and the width of more than 100 double stranded DNA fragments (4.3 kbp) were measured in air using different ShFM probes. The measurements were then compared with tapping mode atomic force microscopy (TMAFM) on a similar number of DNA fragments. From the statistical analysis of the data consistently higher profiles were obtained using ShFM: (1.1+/-0.2) nm instead of (0.6+/-0.1) nm that is the expected DNA height when using TMAFM in air. When acquiring high resolution images of DNA, the lower force of interaction of the shear force technique allowed the observation of a higher order periodic structure, which may reflect a conformational aspect of DNA peculiar to its interaction with mica. By improving the shear force technique, we have shown that important intrinsic advantages, such as non-contact interaction, can be fully exploited and the ShFM can become a very useful tool in the study of biomolecules