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

自组装三维DNA晶体的合理设计

• 批准号: 2004250
• 负责人: Hao Yan
• 金额: $ 45万
• 依托单位: Arizona State University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-01 至 2023-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2004250&HistoricalAwards=false
• 关键词: Rational; design; self; assembled; three

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.

大自然利用自组装将多个无生命的组件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的理想构建块，其目标是工程仿生和生物启发材料和设备。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，其应用包括定向材料组装、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。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三维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规定几何形状和定义腔和通道尺寸的新型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颖的、用户指定的晶体的计算模型。这些晶体特别适合在重复晶格中容纳其他物质（如蛋白质、小分子或纳米颗粒），用于结构测定、纯化、输送或具有新型光学或催化性能的材料。通过这种方式，该项目将使自组装的基础发现成为可能，并有助于解决依赖于高精度3D排列其他材料的实际应用。该项目将通过开发K-12教育和虚拟实验室研究的在线课程，对社会和教育产生重大影响。该计划将吸引本科生、研究生和少数族裔学生在科学、技术、工程和数学（STEM）领域获得知识和从事研究，并帮助开发纳米技术在线和远程教育的新范例。技术概述：该项目的目标是确定自组装的3D DNA晶体的设计规则，以便在纳米尺度上设计具有明确空腔的多孔可寻址支架。这些材料的分子控制和可调对称性将使客体物质的排列成为可能，如蛋白质、小分子或具有原子分辨率的纳米颗粒。本项目将系统地探测和测试影响合理设计的DNA晶体的参数，包括DNA Holliday结序列、双端和粘端长度和序列、实验组装途径。所得晶体的结构将通过x射线晶体学来确定它们的对称性，以及它们的通道和腔的大小。自组装的途径（如成核生长与分层纳米结构组装）也将在实验中进行探索，并用于为新型晶体设计的预测模拟提供晶体自组装的计算模型。序列对DNA双链和连接的影响将被建模，以及晶体的多尺度组装。全原子模拟将用于参数化粗粒度模型，以探测晶体的动力学组装途径和对称性，模型预测将有助于优化晶格组装的序列。最后，上述结果将用于设计具有非常大空腔（~40 nm）的晶体，以容纳客体物质，如纳米颗粒或中等大小的蛋白质。dna结合蛋白（及其融合物）将固定在这些空隙空间中，以创造功能材料，并在3D空间中定期展示客人。综上所述，这项工作将提供：(1)更好地科学理解DNA晶体设计；(2)为纳米技术社区提供一个理解DNA结构参数的工具包；(3)用于客体物种三维排列的具有可调对称性和腔大小的三维晶格库。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。

项目成果

A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail

具有可调腔尺寸和高分辨率结构细节的自组装菱面体 DNA 晶体支架

• DOI: 10.1002/anie.202005505
• 发表时间: 2020
• 期刊: Angewandte Chemie International Edition
• 作者: Simmons, Chad R.;MacCulloch, Tara;Zhang, Fei;Liu, Yan;Stephanopoulos, Nicholas;Yan, Hao
• 通讯作者: Yan, Hao