Experimental and Computational Studies of Ligated 3D DNA Crystals

连接 3D DNA 晶体的实验和计算研究

• 批准号: 2025187
• 负责人: Jong Hyun Choi
• 金额: $ 49.23万
• 依托单位: Purdue 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: 2020-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2025187&HistoricalAwards=false
• 关键词: Experimental; Computational; Studies; Ligated; 3D

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.

该基金将专注于了解DNA晶体的基本物理特性。DNA是生命最重要的组成部分之一，因为它携带遗传信息。最近的科学进展表明，DNA可以用作通用的工程构建块。基于序列互补性，DNA分子可以自发地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进行编程。这种方法已被用于创建具有亚纳米精度和精致可编程性的功能架构。尽管DNA自组装具有令人兴奋的潜力，但其长度仅限于非常小的尺度，大多数为100 nm或更小。本研究将研究DNA材料的结构特性和力学行为，以制定创建宏观DNA构建体的指导原则。这项工作将联合收割机先进的实验测量与建模和计算能力相结合，以了解设计参数，组装结构和物理性能之间的基本关系。这项研究还将辅之以教育和推广计划，以促进公众对生物分子纳米技术的理解。活动包括（i）为本科生提供以研究为基础的工程教育;（ii）为K-12学生开发一个实践模块，说明DNA自组装的原理。研究的中心目标是从DNA研究三维（3D）结构的结构力学。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，该晶体可以通过酶连接进一步加强。该项目将使用连接的3D晶体作为模型系统。研究目标包括：（1）从DNA开发层状3D晶体，（2）理解设计和合成参数，（3）表征自组装结构，以及（4）阐明结构-性质关系。来自最先进的纳米压痕实验的结果将通过理论建模和分子动力学模拟来补充，以获得对结晶度，弹性和变形行为的见解。该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3D DNA材料奠定基础。该奖项反映了NSF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

Engineering DNA Crystals toward Studying DNA-Guest Molecule Interactions.

• DOI: 10.1021/jacs.3c00081
• 发表时间: 2023-02
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Cuizheng Zhang;Jiemin Zhao;Brandon Lu;N. Seeman;R. Sha;N. Noinaj;C. Mao

Implementing Logic Gates by DNA Crystal Engineering

• DOI: 10.1002/adma.202302345
• 发表时间: 2023-07-10
• 期刊: ADVANCED MATERIALS
• 影响因子: 29.4
• 作者: Zhang，Cuizheng;Paluzzi，Victoria E.;Mao，Chengde
• 通讯作者: Mao，Chengde

Mechanical deformation behaviors and structural properties of ligated DNA crystals

• DOI: 10.1016/j.bpj.2022.09.036
• 发表时间: 2022-11-01
• 期刊: BIOPHYSICAL JOURNAL
• 影响因子: 3.4
• 作者: Li, Ruixi;Zheng, Mengxi;Choi, Jong Hyun
• 通讯作者: Choi, Jong Hyun

Surface-assisted self-assembly of 2D, DNA binary crystals

二维 DNA 二元晶体的表面辅助自组装

• DOI: 10.1039/d3nr01187a
• 发表时间: 2023
• 期刊: Nanoscale
• 影响因子: 6.7
• 作者: Liu, Longfei;Mao, Dake;Li, Zhe;Zheng, Mengxi;He, Kai;Mao, Chengde
• 通讯作者: Mao, Chengde

Structure-Guided Designing Pre-Organization in Bivalent Aptamers

• DOI: 10.1021/jacs.1c12593
• 发表时间: 2022-03-16
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Hu, Xiaoli;Tang, Linlin;Zuo, Hua
• 通讯作者: Zuo, Hua