Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments
Algorithmic Self-Assembly of DNA: Theoretical Motivations and 2D Assembly Experiments
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DOI：
10.1080/07391102.2000.10506630
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发表时间：
2000-01
影响因子：
4.4
通讯作者：
E. Winfree
中科院分区：
文献类型：
--
作者：
E. Winfree
生物学使事物比人类工程学所产生的任何东西都要小得多，也要复杂得多。生物技术革命第一次为我们提供了在分子水平上考虑工程所需的工具。由Len Adleman发起的DNA计算研究为可编程生化反应的实验研究打开了大门。在这里，我们专注于一个单一的生化机制，DNA结构的自组装，这是理论上足够的图灵通用计算。该理论结合了王浩的纯数学平铺问题和Ned Seeman的分支DNA结构。在数学逻辑的背景下，王展示了如何设计拼图形状的瓷砖来模拟任何图灵机的操作。对于一个生化的实现，我们将需要分子王瓷砖。DNA分子结构和分子间的相互作用特别适合设计，足以创造复杂的分子物体。单个分子的结构可以通过最大化期望的和最小化不期望的沃森-克里克互补性来设计。分子间的相互作用是通过粘性末端的设计来编程的，粘性末端决定了哪些分子缔合以及如何缔合。该理论已经通过使用合成DNA双交叉分子系统进行实验证明，该系统自组装成二维晶体，这些晶体已经通过原子力显微镜可视化。该实验系统为探索计算与分子自组装之间的关系提供了一个很好的平台，因此代表了对分子反应和分子结构进行编程的能力的第一步。
Abstract Biology makes things far smaller and more complex than anything produced by human engineering. The biotechnology revolution has for the first time given us the tools necessary to consider engineering on the molecular level. Research in DNA computation, launched by Len Adleman, has opened the door for experimental study of programmable biochemical reactions. Here we focus on a single biochemical mechanism, the self-assembly of DNA structures, that is theoretically sufficient for Turing-universal computation. The theory combines Hao Wang's purely mathematical Tiling Problem with the branched DNA constructions of Ned Seeman. In the context of mathematical logic, Wang showed how jigsaw-shaped tiles can be designed to simulate the operation of any Turing Machine. For a biochemical implementation, we will need molecular Wang tiles. DNA molecular structures and intermolecular interactions are particularly amenable to design and are sufficient for the creation of complex molecular objects. The structure of individual molecules can be designed by maximizing desired and minimizing undesired Watson-Crick complementarity. Intermolecular interactions are programmed by the design of sticky ends that determine which molecules associate, and how. The theory has been demonstrated experimentally using a system of synthetic DNA double-crossover molecules that self-assemble into two-dimensional crystals that have been visualized by atomic force microscopy. This experimental system provides an excellent platform for exploring the relationship between computation and molecular self-assembly, and thus represents a first step toward the ability to program molecular reactions and molecular structures.