Functional DNA Nanostructures

功能性 DNA 纳米结构

• 批准号: 1827346
• 负责人: Aleksei Aksimentiev
• 金额: $ 35.53万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-09-01 至 2022-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1827346&HistoricalAwards=false
• 关键词: Functional; DNA; Nanostructures

NONTECHNICAL SUMMARYThis award supports theoretical and computational research and education on exploiting DNA self-assembly to develop a new class of functional materials that outperform their analogs in biological systems. Development of man-made systems that reproduce the functionality and outperform biological systems is one of the most challenging and intriguing aims of science and engineering. Miniature systems that perform practical tasks are in demand in all areas of modern technology, from protective clothing, filtration, and electronics to synthetic enzymes and artificial tissues. Self-assembly of DNA molecules programmed by the letters of the genetic alphabet has emerged as a practical method for building complex miniature objects. Driven by the complementary pairing of A and T and C and G DNA bases, such molecular self-assembly is robust and occurs in a massively parallel fashion. Using an arsenal of computational approaches, this project will develop man-made DNA systems capable of performing the functions of naturally occurring biological machines, including ones that alter the composition of biological membranes, use electricity to power rotary motors, harness the energy of light to generate thrust, and remain functional in the cellular environment. Products of the research will be used to educate the next generation of scientists and engineers through new graduate and undergraduate courses, annual hands-on workshops, interactive demonstrations of scientific concepts and lessons for middle school and high school students. Ultimately, this project will contribute to the development of synthetic systems capable of performing diverse functions of biological systems without the complexities required to sustain biological life.TECHNICAL SUMMARYThis award supports theoretical and computational research and education to investigate self-assembly of DNA as a way to develop a new class of functional nanostructures that reproduce and exceed the functionality of biological systems. All-atom, coarse-grained and continuum models of nanoscale interactions will be combined to obtain an accurate description of the electrostatic, optical, hydrodynamic and thermodynamic forces that give rise to the nanostructures with desired functionalities. The PI will focus on DNA nanostructures that can be inserted into lipid membranes in response to external stimuli to regulate the passage of nutrients and signals across cellular boundaries and to alter the composition of the biological membranes. DNA systems will be designed to convert light or an electric field into forces and torques to power nanoscale rotary motors and artificial muscles. The PI aims to elucidate the properties of self-assembled DNA systems in the crowded environment of a biological cell and to devise new methods to keep the DNA nanostructures functional in such an environment. New computational approaches for engineering matter at the nanoscale, enabling theoretical studies of systems that combine unfamiliar combinations of materials and physical interactions, will be developed in the course of the research. The research will advance understanding of the physics of assemblies that combine highly charged and hydrophobic objects, liquid flow in complex nanoscale structures, the effects of highly focused light on self-assembled DNA structures and the behavior of man-made systems inside biological cells. The methodological advances enabled through this project will be disseminated to the research community in the form of modules for well-used community software packages, including VMD, NAMD and ARBD; through self-study materials; and an annual hands-on workshop focused on modeling self-assembled nanostructures. The project outcomes will be integrated into graduate and undergraduate curricula in the form of topical modules that introduce microscopic simulations as a design and discovery tool and self-assembly as a new engineering paradigm. The project will engage K-12 students and their families through interactive demonstrations of scientific concepts and integration of research products into middle and high-school curricula.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.

该奖项支持理论和计算研究以及利用DNA自组装开发一类新的功能材料的教育，这些材料在生物系统中的性能优于其类似物。人造系统的发展，复制的功能和优于生物系统是科学和工程的最具挑战性和最有趣的目标之一。执行实际任务的微型系统在现代技术的所有领域都有需求，从防护服，过滤和电子到合成酶和人造组织。由遗传字母表的字母编程的DNA分子的自组装已经成为建造复杂微型物体的实用方法。在A和T以及C和G DNA碱基的互补配对的驱动下，这种分子自组装是稳健的，并且以大规模平行的方式发生。利用计算方法的军火库，该项目将开发能够执行自然发生的生物机器功能的人造DNA系统，包括改变生物膜的组成，使用电力为旋转电机提供动力，利用光能产生推力，并在细胞环境中保持功能。研究成果将用于通过新的研究生和本科生课程，年度实践研讨会，科学概念的互动演示和中学和高中学生的课程来教育下一代科学家和工程师。最终，该项目将有助于开发能够执行生物系统的各种功能的合成系统，而不需要维持生物生命所需的复杂性。技术总结该奖项支持理论和计算研究和教育，以调查DNA的自组装，作为开发一类新的功能纳米结构的方式，复制和超越生物系统的功能。 纳米级相互作用的全原子，粗粒和连续模型将被结合起来，以获得静电，光学，流体动力学和热力学力的准确描述，从而产生具有所需功能的纳米结构。PI将专注于DNA纳米结构，这些纳米结构可以插入脂质膜中以响应外部刺激，以调节营养物质和信号穿过细胞边界的通道，并改变生物膜的组成。DNA系统将被设计成将光或电场转化为力和扭矩，为纳米级旋转马达和人造肌肉提供动力。PI旨在阐明自组装DNA系统在生物细胞拥挤环境中的特性，并设计新的方法来保持DNA纳米结构在这种环境中的功能。 在研究过程中，将开发纳米级工程物质的新计算方法，从而能够对联合收割机不熟悉的材料组合和物理相互作用的系统进行理论研究。这项研究将促进对组装物理学的理解，这些组装物理学结合了联合收割机高电荷和疏水物体，复杂纳米结构中的液体流动，高度聚焦的光对自组装DNA结构的影响以及生物细胞内人造系统的行为。通过该项目实现的方法学进步将以广泛使用的社区软件包（包括VMD，NAMD和ARBD）的模块形式传播给研究界;通过自学材料;以及专注于自组装纳米结构建模的年度实践研讨会。项目成果将以专题模块的形式纳入研究生和本科生课程，介绍微观模拟作为设计和发现工具以及自组装作为新的工程范式。该项目将通过科学概念的互动演示和将研究产品融入初中和高中课程来吸引K-12学生及其家庭。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

项目成果

Dynamic Interactions between Lipid-Tethered DNA and Phospholipid Membranes.

• DOI: 10.1021/acs.langmuir.8b02271
• 发表时间: 2018-12-11
• 期刊: Langmuir : the ACS journal of surfaces and colloids
• 作者: Arnott PM;Joshi H;Aksimentiev A;Howorka S
• 通讯作者: Howorka S

High-Fidelity Capture, Threading, and Infinite-Depth Sequencing of Single DNA Molecules with a Double-Nanopore System.

• DOI: 10.1021/acsnano.0c06191
• 发表时间: 2020-11-24
• 期刊: ACS nano
• 影响因子: 17.1
• 作者: Choudhary A;Joshi H;Chou HY;Sarthak K;Wilson J;Maffeo C;Aksimentiev A
• 通讯作者: Aksimentiev A

Single molecule analysis of structural fluctuations in DNA nanostructures

• DOI: 10.1039/c9nr03826d
• 发表时间: 2019-10-21
• 期刊: NANOSCALE
• 影响因子: 6.7
• 作者: Jepsen, Mette D. E.;Sorensen, Rasmus Scholer;Birkedal, Victoria
• 通讯作者: Birkedal, Victoria

Synthetic Macrocycle Nanopore for Potassium-Selective Transmembrane Transport

• DOI: 10.1021/jacs.1c04910
• 发表时间: 2021-08-17
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Qiao, Dan;Joshi, Himanshu;Feng, Jiandong
• 通讯作者: Feng, Jiandong

Artificial water channels enable fast and selective water permeation through water-wire networks

• DOI: 10.1038/s41565-019-0586-8
• 发表时间: 2019-12
• 期刊: Nature Nanotechnology
• 影响因子: 38.3
• 作者: Woochul Song;Himanshu Joshi;Ratul Chowdhury;Joseph S. Najem;Yue-xiao Shen;Chao Lang;Codey B. Henderson;Yu-Ming Tu;Megan Farell;Megan E. Pitz;C. Maranas;P. Cremer;R. Hickey;Stephen A. Sarles;Jun‐Li Hou;A. Aksimentiev;Manish Kumar