SHF: Small: High-speed DNA polymerase CRNs for signal amplification, oscillation, consensus, and linear control

细胞和分子过程的调节通常涉及复杂的生物化学过程，其被称为化学反应网络（CRN）。利用DNA分子上的反应合成的CRN可以系统地设计成近似复杂的生化过程。然而，大多数先前的CRN实验方案依赖于DNA链置换杂交或酶促反应，并且所得的合成系统通常遭受缓慢速率或泄漏反应。相反，通过DNA酶链置换聚合酶（PSD）可以获得高得多的反应速率。该项目正在研究仅使用DNA杂交和PSD反应的各种快速且强大的CRN。 该项目包括设计，仿真和实验实施。此外，该项目是高度跨学科的，影响本科和研究生水平的跨学科教育。该项目让来自多个学科不同学术水平的学生（重点是妇女和代表性不足的少数民族）参与辅导和教学。DNA计算和CRN的实践演示正在为杜克和当地高中的推广计划而设计。讲习班和讲座正在向本科生和研究生受众传播先进的PSD纳米科学概念的知识。细胞和分子过程的调节通常涉及复杂的生物化学过程，其被称为化学反应网络（CRN）。利用DNA分子上的反应合成的CRN可以系统地设计成近似复杂的生化过程。然而，大多数先前的CRN实验方案依赖于DNA链置换杂交或酶促反应，并且所得的合成系统通常遭受缓慢速率或泄漏反应。相反，通过DNA酶链置换聚合酶（PSD）可以获得高得多的反应速率。该项目正在研究仅使用DNA杂交和PSD反应的各种快速且强大的CRN。 该项目包括设计，仿真和实验实施。在这个项目中研究的关键CRN包括（i）一个自催化放大器，（ii）一个动态振荡系统，（iii）一个分子尺度的共识协议，和（iv）一个线性控制系统。所有这些CRN都有重要的实际应用。该项目已经使用PSD完成了一些简单CRN的设计，模拟和初步实验，包括使用PSD的动态CRN的计算机演示，其中提供了这些简单CRN的反应速率，泄漏和假阳性的估计。此外，该项目已经完成了使用PSD的动态振荡CRN系统的设计和模拟实验演示，以确定循环次数，循环精度，对初始浓度的敏感性和单位速率的近似值等。这些都是模拟和优化。目前正在对每一个CRN进行实验演示。由于速度加快，该项目可能对DNA CRN研究产生变革性影响。速度提升也显著影响了基于PSD的CRN的许多应用：（a）扩增CRN允许用于医学诊断用途和法医学检测用途的快速核酸检测，（B）共有CRN允许多个分子装置投票，（c）振荡CRN允许多个重复分子尺度操作的同步，和（d）线性对照CRN允许调节分子浓度，用于控制各种合成和天然生化系统。该项目正在研究这些应用（a-d），并计划对其中至少一个进行实验性演示。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

The regulation of cellular and molecular processes typically involves complex biochemical processes, which are termed chemical reaction networks (CRNs). Synthetic CRNs using reactions on DNA molecules can be systematically designed to approximate sophisticated biochemical processes. However, most of the prior experimental protocols for CRNs relied on either DNA strand-displacement hybridization or enzymatic reactions, and the resulting synthetic systems usually suffer from either slow rates or leaky reactions. In contrast, much higher reaction rates can be obtained by the DNA enzyme strand-displacement polymerase (PSD). This project is investigating a wide variety of fast and robust CRNs using only DNA hybridization and PSD reactions. The project includes design, simulation, and experimental implementations. Further, the project is highly interdisciplinary and impacts interdisciplinary education at undergraduate and graduate levels. The project engages students (with emphasis on women and under-represented minorities) from different academic levels across multiple disciplines in mentoring and teaching. Hands-on demonstrations of DNA computing and CRNs are being designed for outreach programs at Duke and local high schools. Workshops and lectures are disseminating knowledge of advanced PSD-based nanoscience concepts to undergraduate and graduate student audiences. The regulation of cellular and molecular processes typically involves complex biochemical processes, which are termed chemical reaction networks (CRNs). Synthetic CRNs using reactions on DNA molecules can be systematically designed to approximate sophisticated biochemical processes. However, most of the prior experimental protocols for CRNs relied on either DNA strand-displacement hybridization or enzymatic reactions, and the resulting synthetic systems usually suffer from either slow rates or leaky reactions. In contrast, much higher reactions rates can be obtained by the DNA enzyme strand-displacement polymerase (PSD). This project is investigating a wide variety of fast and robust CRNs using only DNA hybridization and PSD reactions. The project includes design, simulation, and experimental implementations. The key CRNs investigated in this project include (i) an autocatalytic amplifier, (ii) a dynamic oscillatory system, (iii) a molecular-scale consensus protocol, and (iv) a linear control system. All of these CRNs have important practical applications. The project has already completed the design, simulation and preliminary experiments of some simple CRNs using PSD, including in silico demonstration of dynamic CRNs using PSD, which provided estimates of reaction rate, leak, and false positives for these simple CRNs. Further, the project has already completed the design, simulation & experimental demonstration of dynamic oscillatory CRN systems using PSD to identify the number of cycles, precision of cycles, sensitivity to initial concentrations and approximation to unit rates, etc. The project is now refining its initial designs for the key CRNs listed above. These are being simulated and optimized. Experimental demonstrations are being made of each CRN. The project has potentially a transformative impact on research in DNA CRNs due to the speed-ups. The speed-ups also significantly impact many applications of PSD-based CRNs: (a) the amplification CRNs allow speedy nucleic acid detection for diagnostic use in medicine and detection use for forensics, (b) the consensus CRNs allow multiple molecular-device voting, (c) the oscillation CRNs allow for synchronization of multiple repeated molecular-scale operations, and (d) the linear control CRNs allow for regulation of molecular concentrations, for control of a large variety of synthetic and natural biochemical systems. The project is investigating these applications (a-d) and plans to experimentally demonstrate at least one of them.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.