Rational design of self-assembled, three-dimensional DNA crystals

非技术SUMMARY大自然利用自我组装将多个非生命成分组织成有生命的系统。信息编码聚合物，如DNA、RNA和蛋白质，已被用作设计纳米结构组装的理想构建块，目标是设计仿生和生物启发的材料和设备。基于DNA的纳米技术利用DNA分子的可编程性来精确定位功能分子，应用于定向材料组装、结构生物学、生物催化、人工光合作用、分子计算、纳米机器人、疾病诊断和药物输送等应用。DNA纳米技术的一个重要目标是合理地设计、构建和表征自组装的3D DNA晶格作为宿主，以原子精度组织其他客体分子。该项目旨在揭示设计具有指定几何形状、指定腔和通道大小的新型DNA晶体的科学原理和规则。它还将阐明3D晶体组装的途径，并创建一个可广泛用于设计新的、用户指定的晶体的计算模型。这些晶体特别适合于在重复晶格中容纳其他物种(如蛋白质、小分子或纳米颗粒)，用于结构确定、纯化、传递或具有新的光学或催化性能的材料。通过这种方式，该项目将使自组装方面的基础发现成为可能，并有助于解决依赖于以高精度排列3D其他材料的实际应用。该项目将通过为K-12教育和虚拟实验室研究开发在线课程，产生重大的社会和教育影响。该计划将吸引本科生、研究生和未被充分代表的少数族裔学生在科学、技术、工程和数学(STEM)领域获得知识和进行研究，并帮助开发纳米技术在线和远程教育的新范式。技术总结该项目的目标是确定自组装3D DNA晶体的设计规则，以便在纳米级设计具有明确空洞的多孔、可寻址的支架。这些材料可获得的分子控制和可调对称性将使客体物种的排列成为可能，例如蛋白质、小分子或纳米粒子具有原子分辨率。本项目将系统地探索和测试影响DNA晶体合理设计的参数，包括DNA Holliday连接序列、双链和粘端长度和序列以及实验组装路径。所得到的晶体的结构将通过X射线结晶学来解决，以确定它们的对称性，以及它们的通道大小和腔大小。自组装的途径(例如，成核-生长与层次化纳米结构组装)也将在实验上被探索，并被用来提供晶体自组装的计算模型，用于预测新的晶体设计。将模拟DNA双链和连接中序列的影响，以及晶体的多尺度组装。全原子模拟将被用来对粗晶模型进行参数化，以探索晶体的动力学组装路径和对称性，而模型预测将有助于优化晶格组装的序列。最后，上述结果将被用来设计具有非常大的空腔(~40 nm)的晶体，以便容纳客体物种，如纳米颗粒或中等大小的蛋白质。DNA结合蛋白(及其融合)将被固定在这些空隙中，以创建具有常规展示客人在3D空间中的功能材料。综上所述，这项工作将提供：(1)对DNA晶体设计的更好的科学理解；(2)为整个纳米技术社区了解DNA结构参数的工具包；以及(3)具有可调对称性和腔大小的3D晶格库，用于客户物种的3D安排。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。

NONTECHNICAL SUMMARYNature uses self-assembly in order to organize multiple nonliving components into living systems. Information-coding polymers such as DNA, RNA, and proteins have been used as ideal building blocks in the assembly of designer nano-architectures, with the goal of engineering biomimetic and bioinspired materials and devices. DNA based nanotechnology exploits the programmability of DNA molecules to accurately position functional molecules for applications including directed material assembly, structural biology, biocatalysis, artificial photosynthesis, molecular computing, nanorobotics, disease diagnosis, and drug delivery. An important goal of DNA nanotechnology is to rationally design, construct, and characterize self-assembling 3D DNA lattices as hosts to organize other guest molecules with atomic precision. This project aims to reveal the scientific principles and rules for designing novel DNA crystals with prescribed geometries, and with defined cavity and channel sizes. It will also elucidate the pathway for 3D crystal assembly and create a computational model that can be used broadly to design novel, user-specified crystals. These crystals are especially well suited for hosting other species (like proteins, small molecules, or nanoparticles) in a repeating lattice, for applications that include structural determination, purification, delivery, or materials with novel optical or catalytic properties. In this way, this project will enable both fundamental discoveries on self-assembly, and help address practical applications that rely on arranging other materials in 3D with high precision. The project will have significant societal and educational impact by developing an online curriculum for K-12 education and virtual lab research. This program will engage undergraduate, graduate, and underrepresented minority students to gain knowledge and pursue research in the science, technology, engineering, and math (STEM) fields, and help develop a new paradigm for online and distance education in nanotechnology.TECHNICAL SUMMARYThe goal of this project is to determine the design rules for self-assembled, 3D DNA crystals in order to engineer porous, addressable scaffolds with well-defined cavities at the nanometer scale. The molecular control and tunable symmetries attainable with these materials will enable the arrangement of guest species, such as proteins, small molecules, or nanoparticles with atomic resolution. This project will systematically probe and test the parameters that affect rationally designed DNA crystals, including DNA Holliday junction sequence, duplex and sticky end length and sequence, and experimental assembly pathway. The structures of the resulting crystals will be solved by X-ray crystallography to determine their symmetry, and the size of their channels and cavity size. The pathway of self-assembly (e.g. nucleation-growth vs. hierarchical nanostructure assembly) will also be probed experimentally and used to inform a computational model of crystal self-assembly for predictive simulation of novel crystal designs. The effect of sequence in DNA duplexes and junctions will be modeled, as well as the multi-scale assembly of the crystals. Fully atomistic simulations will be used to parameterize coarse-grained models to probe the kinetic assembly pathway and symmetry of the crystals, and the model predictions will help optimize sequences for the lattice assembly. Finally, the above results will be used to design crystals with very large cavities (~40 nm) in order to accommodate guest species such as nanoparticles or mid-sized proteins. DNA-binding proteins (and fusions thereof) will be immobilized in these void spaces to create functional materials with a regular presentation of the guests in 3D space. Taken together, the work will provide: (1) a better scientific understanding of DNA crystal design; (2) a toolkit for understanding DNA structural parameters for the nanotechnology community at large; and (3) a library of 3D lattices with tunable symmetries and cavity sizes for the 3D arrangement of guest species.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.