Viscous drag effect on imaging of linearized plasmid deoxyribonucleic acid in liquid medium with the atomic force microscope

Abstract

In many attempts to image biomolecules like deoxyribonucleic acid with the atomic force microscope, the apparent width of the molecules exceeds the expected width as obtained by x-ray diffraction. This increase in size was explained by a geometrical tip convolution, but the increased width seems to persist despite improvements to the tip. Experimental evidence is shown that part of this increase is due to the liquid drag force when molecules are imaged under liquid. The liquid drag force is calculated using standard fluid dynamics where the tip motion in the liquid is modeled by the relative motion of a cylinder through a constant velocity fluid. The Reynold’s number for the experimental configuration is smaller than 1, characterizing a laminar flow and the calculated drag force is 80 pN, which is in agreement with the experimentally measured force for ethanol and relative tip velocity of 100 μm/s. Both the viscous drag force and the apparent width increase may be modeled by a vk dependence, where v is the sample velocity relative to the tip, and k is a constant independent of the liquid and the tip–sample geometry and is equal to 0.53. An apparent molecular width increase of ∼30 nm for a ∼2 nm diam molecule for a 150 μm/s scanning velocity was observed.