Engineering a robust DNA split proximity circuit with minimized circuit leakage.
Engineering a robust DNA split proximity circuit with minimized circuit leakage.
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DOI：
10.1093/nar/gkw447
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发表时间：
2016-08-19
影响因子：
14.9
通讯作者：
Yung LY
中科院分区：
文献类型：
--
作者：
Ang YS;Tong R;Yung LY
DNA电路是一个多功能的、高度可编程的工具箱，可以潜在地用于动态事件的自主感知，如生物分子相互作用。然而，硅电路设计的实验实施一直受到电路泄漏问题的阻碍。在这里，我们系统地分析了分离接近电路中各种类型泄漏的来源和特征，该电路被设计用于空间探测距离较近的目标位置。直接证据表明，3 ' -截断寡核苷酸是导致电路泄漏的主要杂质。更重要的是，引入了一种独特的在结构域之间转移单个核苷酸的策略，称为“结构域间桥接”，以消除与支点无关的泄漏，同时增强跨三向结的链位移动力学。我们还分析了电路计算中涉及的中间复合物的动力学，以便分别定义报告点和关联区域的域长度的工作范围。最终电路设计成功地在链亲和素-生物素模型系统上实现，并被证明具有抗电路泄漏和生物干扰的鲁棒性。我们期望这种简单的信号转导策略可以用来探测不同的生物分子相互作用，当与特定的目标识别部分结合使用时。
DNA circuit is a versatile and highly-programmable toolbox which can potentially be used for the autonomous sensing of dynamic events, such as biomolecular interactions. However, the experimental implementation of in silico circuit designs has been hindered by the problem of circuit leakage. Here, we systematically analyzed the sources and characteristics of various types of leakage in a split proximity circuit which was engineered to spatially probe for target sites held within close proximity. Direct evidence that 3′-truncated oligonucleotides were the major impurity contributing to circuit leakage was presented. More importantly, a unique strategy of translocating a single nucleotide between domains, termed ‘inter-domain bridging’, was introduced to eliminate toehold-independent leakages while enhancing the strand displacement kinetics across a three-way junction. We also analyzed the dynamics of intermediate complexes involved in the circuit computation in order to define the working range of domain lengths for the reporter toehold and association region respectively. The final circuit design was successfully implemented on a model streptavidin-biotin system and demonstrated to be robust against both circuit leakage and biological interferences. We anticipate that this simple signal transduction strategy can be used to probe for diverse biomolecular interactions when used in conjunction with specific target recognition moieties.
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影响因子：
38.3
作者：
通讯作者：
--
无酶DNA电路对多种检测方法的有理模块化适应。
影响因子：
14.9
作者：
Li B;Ellington AD;Chen X
通讯作者：
Chen X
DOI：
10.1073/pnas.0407024101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Dirks, RM;Pierce, NA
通讯作者：
Pierce, NA
影响因子：
14.9
作者：
Ang YS;Yung LY
通讯作者：
Yung LY
影响因子：
15
作者：
Chen, Xi
通讯作者：
Chen, Xi