AFM images of short oligonucleotides on a surface of supported lipid films

Atomic force microscopy (AFM) was used to study the topography of lipid films on a gold support with immobilized 19 mer single stranded DNA (ssDNA) chemically modified by oleylamine and after hybridization with complementary DNA. The topography of various surfaces was analyzed, including alkanethiol layer chemisorbed on a gold support, lipid films formed on alkanethiol layer without and with immobilized single or double stranded DNA (dsDNA). The value of root means square roughness (RMS) for each surface was determined. RMS value for sBLM with immobilized ssDNA was 2.98 nm, while slightly higher value of 3.37 nm was typical for dsDNA. The analysis of AFM images revealed that both ssDNA and dsDNA form clusters. The clusters formed by ssDNA are not uniform, but that formed by dsDNA are almost of circular shape with diameter of 13.6 ± 0.5 nm. Formation of the clusters could be consequence of lower hydration of lipids and DNA at an air. The water deficit and hence increased ion concentration probably facilitate the attraction between oligonucleotides.