Department of Physics, Institute of Basic Science, and Sungkyunkwan Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Korea.
Core Facility Management Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea.
ACS Appl Bio Mater. 2022 Jan 17;5(1):97-104. doi: 10.1021/acsabm.1c00455. Epub 2021 Dec 12.
Multiple models and simulations have been proposed and performed to understand the mechanism of the various pattern formations existing in nature. However, the logical implementation of those patterns through efficient building blocks such as nanomaterials and biological molecules is rarely discussed. This study adopts a cellular automata model to generate simulation patterns (SPs) and experimental patterns (EPs) obtained from DNA lattices similar to the discrete horizontal brown-color line-like patterns on the bark of the Zelkova serrata tree, known as lenticels [observation patterns (OPs)]. SPs and EPs are generated through the implementation of six representative rules (i.e., R004, R105, R108, R110, R126, and R218) in three-input/one-output algorithmic logic gates. The EPs obtained through DNA algorithmic self-assembly are visualized by atomic force microscopy. Three different modules (A, B, and C) are introduced to analyze the similarities between the SPs, EPs, and OPs of Zelkova serrata lenticels. Each module has unique configurations with specific orientations allowing the calculation of the deviation of the SPs and the EPs with respect to the OPs within each module. The findings show that both the SP and the EP generated under R105 and R126 and analyzed with module B provide a higher similarity of Zelkova serrata lenticel-like patterns than the other four rules. This study provides a perspective regarding the use of DNA algorithmic self-assembly for the construction of various complex natural patterns.
已经提出并执行了多种模型和模拟，以了解自然界中存在的各种模式形成的机制。然而，通过纳米材料和生物分子等高效构建块来实现这些模式的逻辑实现很少被讨论。本研究采用元胞自动机模型生成模拟模式 (SP) 和实验模式 (EP)，这些模式类似于榉树树皮上离散的水平棕色线状图案，称为皮孔 [观察模式 (OP)]。SP 和 EP 通过在三输入/一输出算法逻辑门中实现六个代表性规则 (即 R004、R105、R108、R110、R126 和 R218) 来生成。通过 DNA 算法自组装获得的 EP 通过原子力显微镜可视化。引入了三个不同的模块 (A、B 和 C) 来分析榉树皮孔的 SP、EP 和 OP 之间的相似性。每个模块都具有独特的配置和特定的方向，允许计算每个模块中 SP 和 EP 相对于 OP 的偏差。研究结果表明，在 R105 和 R126 下生成的 SP 和 EP 以及使用模块 B 进行分析，提供了比其他四个规则更高的榉树皮孔状图案的相似性。本研究为使用 DNA 算法自组装构建各种复杂的自然图案提供了一个视角。
