Influence of Silicon Surface Structure on Long Deoxyribonucleic Acid Molecule Alignment

Abstract

We investigated the effects of silicon surface structure on the alignment of double-stranded lambda deoxyribonucleic acid (λ-DNA) molecules using atomic force microscopy (AFM). It has been found that the reproducible λ-DNA alignment strongly depends on the nature of the silicon surface charge, uniform distribution of positive charge sites and the roughness of silicon surface. AFM experiments demonstrate that it is difficult for λ-DNA molecules to adsorb on a bare SiO2/Si substrate, but it is easy for the λ-DNA molecules to be well aligned on the aminosilanized SiO2/Si surface. Compared with mica, the SiO2/Si substrate offers a significant advantage in providing a well-defined amino-terminated self-assembled monolayer silane film. Our AFM experiments also show that the rough SiO2/Si surface has a negative effect on λ-DNA alignment.