LS-4-P-1454 AFM study of DNA self-organization on molecular nanopatterns on graphite

DNA is one of the most important molecules for utilization in biological nanotechnologies, since it has unique recognition capabilities, high mechanical rigidity, physicochemical stability and possibility for repeated denaturation-hybridization cycles. Directed DNA immobilization on solid substrate through a "bottom-up" approach is one of the challenging tasks for bionanotechnology. In this work, peculiarities of DNA adsorption on modified highly oriented pyrolytic graphite (HOPG) were studied using atomic force microscopy (AFM). Three alkane derivatives with the same chain length (C₁₈) but different functional groups (-COOH, -OH and -NH₂) were used for HOPG modification: stearic acid (CH₃(CH₂)₁₆COOH), stearylamine (CH₃(CH₂)₁₆CH₂NH₂, octadecylamine) and stearyl alcohol (CH₃(CH₂)₁₆CH₂OH). All three modifiers form regular nanopatterns on its surface due to particular orientation of carbon chains along the crystallographic axes of graphite. We have shown that these molecular nanopatterns allowed immobilization of DNA in extended form. Moreover, DNA molecules self-organize on octadecylamine and stearyl alcohol nanopatterns along three directions, reflecting crystallographic axes of HOPG. The influence of the type of functional group in the nanopattern and its concentration on the shape of adsorbed DNA molecules was studied and analyzed using statistical analysis of fluctuations of the contours of biopolymers. Conformation of adsorbed DNA molecules were defined using the analysis of the scaling exponent ν, which relates mean squared end-to-end distance and contour length of the polymer. The persistence length of DNA adsorbed on molecular nanotemplates was determined from AFM images and compared to that of native DNA.