VISCOUS DRAG EFFECT ON IMAGING OF LINEARIZED PLASMID DEOXYRIBONUCLEIC-ACID IN LIQUID-MEDIUM WITH THE ATOMIC-FORCE MICROSCOPE

In many attempts to image biomolecules like deoxyribonucleic acid with the atomic force microscope, the apparent width of the molecules exce eds the expected width as obtained by x-ray diffraction. This increase in size was explained by a geometrical tip convolution, but the incre ased width seems to persist despite improvements to the tip. Experimen tal evidence is shown that part of this increase is due to the liquid drag force when molecules are imaged under liquid. The liquid drag for ce 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 con figuration is smaller than 1, characterizing a laminar flow and the ca lculated drag force is 80 pN, which is in agreement with the experimen tally measured force for ethanol and relative tip velocity of 100 mu m /s. Both the viscous drag force and the apparent width increase may be modeled by a v(k) 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 inc rease of similar to 30 nm for a similar to 2 nm diam molecule for a 15 0 mu m/s scanning velocity was observed. (C) 1997 American Institute o f Physics.