Fractal Dimension of Self-assembled 50 bp Poly(dA).Poly(dT) DNA on HOPG Surface

Abstract

Deoxyribonucleic acid (DNA) has attracted much attention to be utilized for technological applications of its various cellular functions and possibility to fabricate nanoscaled patterns on various substrate surfaces. Several techniques have also been applied to manipulate biomacromolecules. In our previous studies, self-assembled network patterns of poly(dA).poly(dT) DNA on mica and highly oriented pyrolytic graphite (HOPG) surface could be fabricated and observed by atomic force microscopy (AFM), which is preprocessed by a specific solution concentration of MgCl2. Although negatively charged DNA molecules repulsively interact with negatively polarized HOPG surfaces, we built our fabrication techniques to produce self-assembled DNA. 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. Using this model, we carry out Langevin dynamics simulations. As a result, the network pattern formations, in which DNA fragments make bonds and bundle structures, are replicated. Our results also indicate that thermal fluctuations in solution work effectively to enhance the assembly process. In this study, characteristics of self-assembly of DNA are classified by the fractal dimension, which is associated with various time and spatial scales.