Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states
Quantitative design and experimental validation for a single-molecule DNA nanodevice transformable among three structural states
复制标题
DOI：
10.1093/nar/gkq250
复制
发表时间：
2010-07-01
影响因子：
14.9
通讯作者：
Rose, John A.
中科院分区：
文献类型：
--
作者：
Komiya, Ken;Yamamura, Masayuki;Rose, John A.
在这项工作中，我们报告了一个耦合的统计热力学模型的开发和实验验证，该模型允许预测一个新的DNA纳米器件执行的结构转变，用于定量操作设计。这种纳米设备用一个双稳态DNA分子实现，可以在三个不同的结构之间转换，通过耦合各个结构的孤立平衡模型来模拟这种纳米设备形成目标结构的效率。预测了这种纳米器件的特殊行为，它通过感应热变化在有限的温度范围内形成目标结构。然后，通过荧光测量验证预测的热响应，以定量评估纳米设备是否如设计的那样发挥作用。预测与实验之间的一致性很大，在30 http://www.w3.org/1999C.的较大温度范围内，总体曲线形状的相关性为0.95%所获得的精确度可与传统的分离DNA双链熔融行为预测相媲美，确保了耦合模型适用于描述包含竞争性双链形成的一般DNA反应体系。最后，提出了利用电流模型对纳米器件进行调谐，以设计热带通滤光器来控制化学电路，作为DNA纳米器件的一种新功能。
In this work, we report the development and experimental validation of a coupled statistical thermodynamic model allowing prediction of the structural transitions executed by a novel DNA nanodevice, for quantitative operational design. The efficiency of target structure formation by this nanodevice, implemented with a bistable DNA molecule designed to transform between three distinct structures, is modeled by coupling the isolated equilibrium models for the individual structures. A peculiar behavior is predicted for this nanodevice, which forms the target structure within a limited temperature range by sensing thermal variations. The predicted thermal response is then validated via fluorescence measurements to quantitatively assess whether the nanodevice performs as designed. Agreement between predictions and experiment was substantial, with a 0.95 correlation for overall curve shape over a wide temperature range, from 30 http://www.w3.org/1999C. The obtained accuracy, which is comparable to that of conventional melting behavior prediction for DNA duplexes in isolation, ensures the applicability of the coupled model for illustrating general DNA reaction systems involving competitive duplex formation. Finally, tuning of the nanodevice using the current model towards design of a thermal band pass filter to control chemical circuits, as a novel function of DNA nanodevices is proposed.