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化过程，这被称为化学反应网络(CRN)。利用DNA分子上的反应合成CRN可以被系统地设计成近似复杂的生化过程。然而，以前大多数CRN的实验方案要么依赖于DNA链置换杂交，要么依赖于酶反应，由此产生的合成系统通常要么速度慢，要么反应泄漏。相比之下，DNA酶链置换聚合酶(PSD)可以获得更高的反应速度。该项目仅使用DNA杂交和PSD反应来研究各种快速和强大的CRN。该项目包括设计、模拟和实验实施。此外，该项目高度跨学科，对本科生和研究生的跨学科教育产生了影响。该项目让来自多个学科的不同学术水平的学生(重点是妇女和代表性不足的少数群体)参与指导和教学。正在为杜克大学和当地高中的外展项目设计DNA计算和CRN的动手演示。讲习班和讲座正在向本科生和研究生受众传播先进的基于PSD的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化过程，这被称为化学反应网络(CRN)。利用DNA分子上的反应合成CRN可以被系统地设计成近似复杂的生化过程。然而，以前大多数CRN的实验方案要么依赖于DNA链置换杂交，要么依赖于酶反应，由此产生的合成系统通常要么速度慢，要么反应泄漏。相比之下，DNA酶链置换聚合酶(PSD)可以获得更高的反应速度。该项目仅使用DNA杂交和PSD反应来研究各种快速和强大的CRN。该项目包括设计、模拟和实验实施。本项目中研究的关键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，和(Iv)线性控制系统。所有这些CRN都有重要的实际应用。该项目已经完成了使用PSD的一些简单CRN的设计、模拟和初步实验，包括使用PSD的动态CRN的电子演示，它提供了对这些简单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，使用PSD来确定循环次数、循环精度、对初始浓度的敏感性和对单位速率的近似等。该项目目前正在完善上面列出的关键CRN的初步设计。这些都在进行模拟和优化。正在对每个CRN进行实验演示。由于速度的加快，该项目可能会对DNA CRN的研究产生革命性的影响。速度的加快也显著影响了基于PSD的CRN的许多应用：(A)扩增CRN允许快速的核酸检测用于医学诊断和检测用于法医，(B)共识CRN允许多个分子设备投票，(C)振荡CRN允许同步多个重复的分子规模的操作，以及(D)线性控制CRN允许调节分子浓度，用于控制多种合成和天然生化系统。该项目正在调查这些应用程序(a-d)，并计划至少实验证明其中之一。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势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.