Reaction–diffusion wave model for self-assembled network formation of poly(dA)·poly(dT) DNA on mica and HOPG surfaces

Abstract

Deoxyribonucleic acid (DNA) is a vital molecule for life since it contains genetic information. However, DNA has recently been reported to have unique properties that make it suitable for bionanoelectronic applications, such as the possibility of electrical conductivity and self-organisation. Self-assembled DNA network structures have been observed on several substrates, but the detailed self-assembly mechanism has yet to be determined. The present study investigates self-assembled structures of DNA both theoretically and experimentally. We developed a reaction-diffusion model and used it to investigate pattern formations observed by atomic force microscopy. The computational results qualitatively replicate the network patterns of DNA molecules based on a quantitative agreement with the surface size and timescale. The model can account for the effect of the DNA concentration on pattern formation. Furthermore, peculiar geometric patterns are simulated for mica and highly oriented pyrolytic graphite surfaces.

1205 Dynamics of self-assembled network formation of poly(dA)poly(dT) DNA fragments

“…遺伝情報を担う生体高分子として知られる deoxyribonucleic acid (DNA)は，その工学的応用についても注目を集めている． DNA は，塩基対相補性，電気伝導性，自己集合化などの特徴 を示すことが知られており，その多彩な物性の利用を可能とする ための一分子操作技術に関する研究開発も盛んに行われてい る． (1) 二重鎖 DNA は，マイカ， (2) 銅， (3) さらには高配向焼結グ ラファイト(Highly oriented pyrolytic graphite: HOPG) (4)- (6) の清浄 表面において特徴的な自己集合化パターンを形成することが知 られている．川野 (2) (11) MD シミュレーションで解 析できる時間スケールを超越している．そこで，長時間の現象を 解析するために DNA 分子をばねと質点で粗視化し，Langevin 方程式に基づき溶媒分子の影響をランダム力として長時間のシ ミュレーションを行った． (7) (8) その結果，電場存在下における電 気泳動現象 (7) や二重鎖 DNA の融解過程 (8) に関する定量的な解 析に成功した．さらに多角的に，ヒューリスティックな方法として知 られる反応拡散モデルを用いて自己集合化パターン形成のシ ミュレーションを行った．Turing のパターン形成モデルに基づい て，吸着と脱離の二状態に着目し，空間的な拡散と反応による二 状態間の遷移を考慮した数値解析を行った． (10) The Japan Society of Mechanical Engineers…”

DNA rearrangement on the octadecylamine modified graphite surface by heating and ultrasonic treatment

“…DNA is one of the ideal molecules for investigation, since it has sequences of genetic information, 5 Authors to whom any correspondence should be addressed. high mechanical rigidity, conformational flexibility, as well as physicochemical stability [5,6]. Recently, obtaining different types of DNA architectures has received particular attentions with regard to their potential application in logical computation, novel materials design, biosensors, and nanomedicine [7][8][9][10].…”

Theoretical Study of the Transpore Velocity Control of Single-Stranded DNA

“…Herein, focusing on the multiply-connected nanofluidic channels, the retardation process and its advantage are discussed from a theoretical point of view. As part of this work, we develop a coarse-grained ssDNA model [ 16 , 45 , 46 ] and perform Langevin dynamics simulations of ssDNA transport under nonuniform electric fields in a rectangular nanochannel containing a nanopore with various cross-sections [ 47 , 48 , 49 , 50 , 51 ], where the electric fields are calculated for the cross-sections, ranging from 20 × 20 to 50 × 50 nm 2 . The results allow a visual analysis of the electrokinetic transport dynamics of ssDNA chains and allow us to determine the most suitable morphology for nanofluidic flow channels for single molecule detection.…”