Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker
Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker
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DOI：
10.1021/nn3058483
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发表时间：
2013-03-01
期刊：
影响因子：
17.1
通讯作者：
Turberfield, Andrew J.
中科院分区：
文献类型：
--
作者：
Ouldridge, Thomas E.;Hoare, Rollo L.;Turberfield, Andrew J.
DNA作为一种可编程材料，具有巨大的潜力，可用于制造人工纳米结构和设备。然而，对于更复杂的系统，合理的设计和优化可能变得困难。我们最近提出了一个粗粒度的DNA模型，它捕获了与DNA纳米技术中的大部分基本过程相关的基本热力学，结构和机械变化，即从单链形成双链体。在这篇文章中，我们证明了该模型可以提供强大的洞察复杂的纳米技术系统的操作，通过详细调查的双脚DNA步行者，旨在一步沿着一个可重复使用的轨道，从而提供优化设计的可能性，这样的系统。我们发现，施加适度的张力的轨道可以有一个很大的影响，步行者的操作，提供了一个偏见，向前迈进，并帮助步行者从不可取的过度状态恢复。此外，我们表明，从步行者分离乏燃料的过程可以有一个显着的影响重新绑定的步行者的轨道，强烈影响步行者的效率和速度。最后，使用模拟的结果，我们提出了一些修改的步行者，以改善其操作。
DNA has enormous potential as a programmable material for creating artificial nanoscale structures and devices. For more complex systems, however, rational design and optimization can become difficult. We have recently proposed a coarse-grained model of DNA that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of DNA nanotechnology, the formation of duplexes from single strands. In this article, we demonstrate that the model can provide powerful insight into the operation of complex nanotechnological systems through a detailed investigation of a two-footed DNA walker that is designed to step along a reusable track, thereby offering the possibility of optimizing the design of such systems. We find that applying moderate tension to the track can have a large influence on the operation of the walker, providing a bias for stepping forward and helping the walker to recover from undesirable overstepped states. Further, we show that the process by which spent fuel detaches from the walker can have a significant impact on the rebinding of the walker to the track, strongly influencing walker efficiency and speed. Finally, using the results of the simulations, we propose a number of modifications to the walker to improve its operation.