Experimental and Computational Studies of Ligated 3D DNA Crystals

这笔拨款将侧重于了解DNA晶体的基本物理性质。DNA是生命最重要的组成部分之一，因为它携带着遗传信息。最近的科学进展表明，DNA可以作为一种通用的工程构件。基于序列互补性，DNA分子可以自发自组装形成复杂的结构，这些结构可以通过计算机辅助设计编程。这种方法已经被用来创建具有亚纳米精度和精致可编程性的功能架构。尽管具有令人兴奋的潜力，但DNA自组装仅限于非常小的长度尺度，主要是100纳米或更小。大的DNA结构经常成为不需要的聚集体或遭受不稳定。本研究将研究DNA材料的结构特性和力学行为，为创建宏观DNA结构制定指导原则。这项工作将把先进的实验测量与建模和计算能力结合起来，以了解设计参数、组装结构和物理特性之间的基本关系。这项研究还将辅以一项教育和推广计划，以促进公众对生物分子纳米技术的理解。活动包括(i)为本科生提供基于研究的工程教育；（ii）为K-12学生开发一个说明DNA自组装原理的动手模块。该研究的中心目标是研究DNA的三维（3D）结构力学。该团队最近发现了一种将三角形DNA单元基序组装成宏观晶体的方法，这种晶体可以通过酶连接进一步加强。这个项目将使用结扎的3D晶体作为模型系统。研究目标包括：(1)从DNA中开发层状三维晶体；(2)了解设计和合成参数；(3)表征自组装结构；(4)阐明结构-性能关系。最先进的纳米压痕实验结果将辅以理论建模和分子动力学模拟，以深入了解结晶度、弹性和变形行为。本研究的基础知识将为合成具有结构稳定性、可控性和复杂性的宏观三维DNA材料奠定基础。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。

This grant will focus on understanding fundamental physical properties of DNA crystals. DNA is one of the most essential components of life as it carries genetic information. Recent scientific advances have shown that DNA may be used as a versatile engineering building block. Based on sequence complementarity, DNA molecules can spontaneously self-assemble to form complex structures, which can be programmed by computer-aided designs. This approach has been exploited to create functional architectures with sub-nanometer precision and exquisite programmability. Despite the exciting potential, DNA self-assembly has been limited to very small lengthscales, mostly 100 nm or less. Large DNA constructs often become unwanted aggregates or suffer from instability. This research will investigate structural properties and mechanical behaviors of DNA materials, in order to develop guiding principles for creating macroscopic DNA constructs. The effort will combine advanced experimental measurements with modeling and computational capabilities to understand the fundamental relationship between the design parameters, assembled structures, and physical properties. This research will also be complemented by an educational and outreach program to advance the public understanding of biomolecular nanotechnology. Activities include (i) research-based engineering education for undergraduate students and (ii) development of a hands-on module for K-12 students that illustrates the principles of DNA self-assembly.The central goal of the research is to study structural mechanics of three-dimensional (3D) architectures from DNA. The team recently discovered a route to assemble triangular DNA unit motifs into a macroscopic crystal which can be further strengthened via enzymatic ligation. This project will use ligated 3D crystals as a model system. The research objectives include: (1) development of layered 3D crystals from DNA, (2) understanding of design and synthesis parameters, (3) characterization of self-assembled structures, and (4) elucidation of the structure-property relationship. The results from state-of-the-art nanoindentation experiments will be complemented by theoretical modeling and molecular dynamics simulations to gain insights on the crystallinity, elasticity, and deformation behaviors. The fundamental knowledge from this study will lay the foundations for the synthesis of macroscopic 3D DNA materials with structural stability, controllability, and complexity.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.