Diverse and robust molecular algorithms using reprogrammable DNA self-assembly
Diverse and robust molecular algorithms using reprogrammable DNA self-assembly
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DOI：
10.1038/s41586-019-1014-9
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发表时间：
2019-03-21
期刊：
影响因子：
64.8
通讯作者：
Winfree, Erik
中科院分区：
文献类型：
--
作者：
Woods, Damien;Doty, David;Winfree, Erik
分子生物学提供了一个鼓舞人心的原理证明，即化学系统可以存储和处理信息，以指导分子活动，例如从分子组分制造复杂结构。为了发展信息化学作为一种编程物质以生物系统中看不到的方式发挥作用的技术，有必要了解分子相互作用如何编码和执行算法。将相对简单的单元自组装成复杂的产品（1）特别适合于这种研究。结合数学平铺和分子结晶的物理力学模型的理论表明，算法行为可以嵌入分子自组装过程中（2，3），并且这已经使用DNA纳米技术（4）通过多达22种平铺类型（5-11）进行了实验证明。然而，许多信息技术都有一个复杂性阈值，如通用计算机所需的最小晶体管数量，超过这个阈值，可重编程系统的功率就会定性地增加，目前还不清楚DNA自组装的生物物理学是否允许超过这个阈值。在这里，我们报告的设计和实验验证的DNA瓦片集，包含355单链瓦片，可以通过简单的瓦片选择，重新编程，以实现各种各样的6位算法。我们使用这个集合来构建21个电路，这些电路执行算法，包括复制，排序，识别回文和3的倍数，随机行走，从有偏的随机源中获得无偏的选择，选举领导者，模拟细胞自动机，生成确定性和随机模式，并计数到63，整体每瓦片错误率小于1/3，000。这些发现表明，分子自组装可能是可编程化学系统中可靠的算法组件。分子机器的发展是可重编程的在高抽象层次上，因此不需要基础物理学的知识将建立一个创造性的空间，分子程序员可以蓬勃发展。
Molecular biology provides an inspiring proof-of-principle that chemical systems can store and process information to direct molecular activities such as the fabrication of complex structures from molecular components. To develop information-based chemistry as a technology for programming matter to function in ways not seen in biological systems, it is necessary to understand how molecular interactions can encode and execute algorithms. The self-assembly of relatively simple units into complex products(1) is particularly well suited for such investigations. Theory that combines mathematical tiling and statistical-mechanical models of molecular crystallization has shown that algorithmic behaviour can be embedded within molecular self-assembly processes(2,3), and this has been experimentally demonstrated using DNA nanotechnology(4) with up to 22 tile types(5-11). However, many information technologies exhibit a complexity threshold-such as the minimum transistor count needed for a general-purpose computer-beyond which the power of a reprogrammable system increases qualitatively, and it has been unclear whether the biophysics of DNA self-assembly allows that threshold to be exceeded. Here we report the design and experimental validation of a DNA tile set that contains 355 single-stranded tiles and can, through simple tile selection, be reprogrammed to implement a wide variety of 6-bit algorithms. We use this set to construct 21 circuits that execute algorithms including copying, sorting, recognizing palindromes and multiples of 3, random walking, obtaining an unbiased choice from a biased random source, electing a leader, simulating cellular automata, generating deterministic and randomized patterns, and counting to 63, with an overall per-tile error rate of less than 1 in 3,000. These findings suggest that molecular self-assembly could be a reliable algorithmic component within programmable chemical systems. The development of molecular machines that are reprogrammable-at a high level of abstraction and thus without requiring knowledge of the underlying physics-will establish a creative space in which molecular programmers can flourish.