Abstract
Recently, deoxyribonucleic acid (DNA) has attracted much attention to be utilized for technological applications of its various functions. In our studies, self-assembled network patterns of poly(dA)-poly(dT) DNA on mica and highly oriented pyrolytic graphite (HOPG) surface were successfully observed by atomic force microscopy (AFM), which is preprocessed by a specific solution concentration of MgCl2. Focusing on the associated self-assembly mechanism, we develop and perform coarse-grained molecular dynamics simulations, in which 50 base-pairs (bp) long DNA fragments are modeled considering both intra- and inter-molecular interactions between the DNA and HOPG surface in aqueous solution. As a result, the network pattern formation, in which DNA fragments make bonds and bundle structures, are replicated. It is indicated that thermal fluctuations in solution work effectively to enhance the assembly process. Furthermore, characteristics of self-assembly of DNA can be classified by the fractal dimension.
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