CAREER: Robust heterochiral molecular computing in mammalian cells

DNA双螺旋结构是最具标志性和知名度的分子结构之一。所有自然产生的DNA双螺旋都向同一个方向扭曲：向右。这些被称为D-DNA。由D-DNA制成的分子装置可以直接与自然发生的核酸相互作用，但这种装置很容易被识别自然发生的D-DNA的细胞防御系统识别和降解。近年来，许多D-DNA分子传感器、电路和执行器已经开发出来，但它们在活细胞和生物体中的应用受到这个问题的限制。这个CAREER项目将通过包含镜像“左旋”DNA （L-DNA）的工程系统来增强基于DNA的分子器件的实际应用。L-DNA的双螺旋与D-DNA的方向相反，因此可以抵抗细胞环境中的降解。特别是，该项目将研究在这些新型电路设计中L-DNA和D-DNA之间的分子信息传递，结合实验和计算研究来优化这些系统的行为，并展示它们在生物系统的传感和控制中的应用。该CAREER项目还将通过与“探索”合作，加强新墨西哥州的生物技术教育管道。这是一家位于新墨西哥州阿尔伯克基的动手科学博物馆。这项合作将为当地高中学生开发生物技术迷你课程，重点关注代表性不足的群体成员。因此，该项目将加强新墨西哥州的科学和工程培训基础设施。这个跨学科的职业项目将研究新的分子电路设计，利用DNA手性来产生强大的分子电路，可以在活的哺乳动物细胞内执行计算。该项目将开发在混合系统中L-DNA和D-DNA组分之间有效信号传导的设计规则，其中L-DNA组分用于信息处理，D-DNA组分用于与周围生物环境连接。它还将研究这种系统在活细胞中对退化的鲁棒性。最后，将开发基于分子计算输出的创新机制来控制细胞行为，这些机制将用于基于特定生物标志物组合的感知的特定细胞类型的靶向控制。这些结果将推动分子电路设计的发展，增强基于dna的分子器件在生物医学和生物技术工业中的实际应用。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 DNA double helix is one of the most iconic and well-known molecular structures. All naturally occurring DNA double helices twist in the same direction: to the right. These are called D-DNA. Molecular devices made from D-DNA can interact directly with naturally occurring nucleic acids, but such devices are easily recognized and degraded by cellular defenses that recognize naturally occurring D-DNA. A wide range of D-DNA molecular sensors, circuits and actuators have been developed in recent years, but their utility in living cells and organisms is limited by this issue. This CAREER project will enhance the practical utility of DNA-based molecular devices by engineering systems that include mirror-image “left-handed” DNA (L-DNA). The L-DNA double helix twists in the opposite direction to D-DNA and can therefore resist degradation in the cellular environment. In particular, this project will study the transmission of molecular information between L-DNA and D-DNA in these novel circuit designs, combining experimental and computational research to optimize the behavior of these systems and to demonstrate their use for sensing and control of biological systems. This CAREER project will also strengthen the biotechnology educational pipeline in New Mexico via a collaboration with ¡Explora!, a hands-on science museum in Albuquerque, NM. This collaboration will develop biotechnology minicourses for local high school students, with a focus on members of underrepresented groups. This project will thus enhance the scientific and engineering training infrastructure in the state of New Mexico.This interdisciplinary CAREER project will study novel molecular circuit designs that exploit DNA chirality to produce robust molecular circuits that can execute computations within living mammalian cells. The project will develop design rules for efficient signaling between L-DNA and D-DNA components in a mixed system where the L-DNA components are used for information processing and the D-DNA components are used for interfacing with the surrounding biological environment. It will also study the robustness to degradation of such systems in living cells. Finally, innovative mechanisms will be developed to control cell behavior based on the output from a molecular computation, and these will be used for targeted control of specific cell types based on sensing of specific biomarker combinations. These results will advance the state of molecular circuit design and enhance the utility of DNA-based molecular devices for practical applications in biomedicine and biotechnological industry.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.