Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks
Availability-Driven Design of Hairpin Fuels and Small Interfering Strands for Leakage Reduction in Autocatalytic Networks
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DOI：
10.1021/acs.jpcb.0c01229
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发表时间：
2020-04-23
影响因子：
3.3
通讯作者：
Graugnard, Elton
中科院分区：
文献类型：
--
作者：
Lysne, Drew;Jones, Kailee;Graugnard, Elton
基于DNA的电路和计算工具为先进的生物医学和技术应用提供了巨大的潜力。然而，DNA网络中普遍存在泄漏，即在没有输入的情况下产生输出。作为一种减少泄漏的新方法，本研究利用可用性来减少熵驱动的自催化DNA反应网络中的泄漏。在这里，我们报告了通过两种新的方法直接定制燃料链可用性所产生的性能改进：(1)在燃料链上添加干扰区域，(2)引入单独的小干扰链。性能最好的燃料设计使性能比提高了高达22%。使用小干扰链(5-12个核苷酸(NT))可将性能比提高高达21%。此外，无论采用哪种减少泄漏的方法，网络的稳定性都与计算的可用性和实验结果相吻合，实验结果显示，对于改进的燃料串，Spearman相关系数为-0.84，对于小干扰串，Spearman相关系数为-0.92。
DNA-based circuits and computational tools offer great potential for advanced biomedical and technological applications. However, leakage, which is the production of an output in the absence of an input, widely exists in DNA network. As a new approach to leakage reduction, this study utilizes availability to reduce leakage in an entropy-driven autocatalytic DNA reaction networks. Here, we report the performance improvements resulting from direct tailoring of fuel strand availability through two novel approaches: (1) the addition of interfering domains to fuel strands, and (2) the introduction of separate small interfering strands. The best performing fuel designs resulted in increased performance ratios of up to 22%. Employing small interfering strands (5-12 nucleotides (nt)) improved the performance ratios by up to 21%. Furthermore, the stability of the network using either leakage reduction method matched well with computed availability and experimental results showing Spearman correlation coefficients of -0.84 for modified fuel strands and -0.92 for small interfering strands.