Methyltrimethoxysilane (MTMS)-coupled mica substrate is reportedly suitable for fixing and straightening of DNA, but 3-aminopropyltriethoxysilane (APTES)-coupled mica substrate has been found less suitable. On MTMS-coupled mica substrate, the straightness of fixed DNA was sufficient, and the adsorption of contaminants was not observed using fluorescence microscopy and atomic force microscopy. For the APTES-coupled mica substrate, however, aggregated or curved DNA and adsorption of contaminants were observed. To clarify the surface factors that are responsible for this suitability, we analyzed the surface free energies of these substrates using the extended Fowkes theory. In each of the surface free energy components, the dispersion force component in the MTMS-coupled mica substrate was lower than that in the APTES-coupled mica substrate. The ratio of the polar force component on the MTMS-coupled mica substrate was about one order of magnitude on the APTES-coupled mica substrate. In addition, the ratio of the hydrogen-bonding force component for the MTMS-coupled mica substrate was about two times larger than that of the APTES-coupled mica substrate. These results suggest that the polar force and hydrogen-bonding force components are important factors for the fixation and straightening of DNA and that the dispersion force components influence the production and adsorption of contaminants. (C) 2009 Elsevier B.V. All rights reserved.