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

细胞和分子过程的调控通常涉及复杂的生化过程，这些过程被称为化学反应网络（crn）。利用DNA分子上的反应合成crn可以系统地设计成近似复杂的生化过程。然而，大多数crn的先前实验方案依赖于DNA链置换杂交或酶促反应，并且所得到的合成系统通常遭受缓慢或泄漏反应的影响。相比之下，DNA链置换聚合酶（PSD）可以获得更高的反应速率。该项目仅使用DNA杂交和PSD反应来研究各种快速和健壮的crn。该项目包括设计、仿真和实验实现。此外，该项目是高度跨学科的，影响了本科和研究生水平的跨学科教育。该项目让来自不同学科、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）参与指导和教学。DNA计算和crn的实际演示正在为杜克大学和当地高中的推广项目设计。研讨会和讲座正在向本科生和研究生传播基于psd的先进纳米科学概念的知识。细胞和分子过程的调控通常涉及复杂的生化过程，这些过程被称为化学反应网络（crn）。利用DNA分子上的反应合成crn可以系统地设计成近似复杂的生化过程。然而，大多数crn的先前实验方案依赖于DNA链置换杂交或酶促反应，并且所得到的合成系统通常遭受缓慢或泄漏反应的影响。相比之下，DNA链置换聚合酶（PSD）可以获得更高的反应速率。该项目仅使用DNA杂交和PSD反应来研究各种快速和健壮的crn。该项目包括设计、仿真和实验实现。本项目研究的关键crn包括(i)自催化放大器，（ii）动态振荡系统，（iii）分子尺度共识协议，以及（iv）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进行动态crn的硅演示，提供了这些简单crn的反应速率、泄漏和假阳性的估计。此外，该项目已经完成了动态振荡CRN系统的设计、模拟和实验演示，该系统使用PSD来识别周期数、周期精度、对初始浓度的敏感性和单位速率的近似值等。该项目目前正在完善上面列出的关键crn的初始设计。这些都在进行模拟和优化。目前正在对每个CRN进行实验演示。由于加速，该项目可能对DNA crn的研究产生变革性影响。加速也显著影响了基于psd的crn的许多应用：(a)扩增crn允许快速核酸检测用于医学诊断和法医检测，(b)共识crn允许多个分子设备投票，(c)振荡crn允许多个重复分子尺度操作的同步，(d)线性控制crn允许调节分子浓度，用于控制各种合成和自然生化系统。该项目正在研究这些应用（a-d），并计划对其中至少一种进行实验演示。该奖项反映了美国国家科学基金会的法定使命，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.