DNA nanofilm thickness measurement on microarray in air and in liquid using an atomic force microscope

The measurement of the thickness of DNA films on microarray as a function of the medium (liquid, air) is gaining importance for understanding the signal response of biosensors. Thiol group has been used to attach DNA strands to gold micropads deposited on silicon surface. Atomic force microscopy (AFM) was employed in its height mode to measure the change in the pad thickness and in its force mode to measure the indentation depth of the nanofilm. A good coherence between the height and force modes is observed for the film thickness in air. The adhesion force was found to be an alternative way to measure the surface coverage of the biolayer at nanoscopic scale. However the force analysis (compression, steric and electrostatic) provides baseline information necessary to interpret the AFM height image in liquid. Analysis of the film thickness distribution shows that the height of the DNA strands depends on both the DNA strand length (15-35 base pairs) and the environment (air, liquid). In air, longer strands lay down onto gold surface whereas the charge reversal of gold in liquid causes a repulsion of longer strands, which stand up.