SI2-SSE: Collaborative Research: Integrated Tools for DNA Nanostructure Design and Simulation

SI2-SSE：合作研究：DNA 纳米结构设计和模拟的集成工具

• 批准号: 1740212
• 负责人: Aleksei Aksimentiev
• 金额: $ 25万
• 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: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2020-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1740212&HistoricalAwards=false
• 关键词: SI2; SSE; Collaborative; Research; Integrated

Nanotechnology could one day revolutionize several activities of great importance to our national interest, including how we manufacture consumer products, how we diagnose and treat disease, and how we detect and neutralize threats to our defense. One promising approach to atomically precise construction is adapting molecular building blocks from living organisms such as DNA, RNA, and proteins, and repurposing them to self-assemble into prescribed shapes, devices, and materials. A key bottleneck to progress is the complexity of designing, building, and testing nanostructures comprised of thousands or millions of atoms. The goal of this project is to accelerate development of bio-inspired nanostructures by integrating two widely adopted software tools used in bio-nanostructure design and physics-based molecular simulation. The products of this effort will enhance our fundamental capability to understand and precisely engineer self-assembled biomolecular nanostructures, which, when coupled with experimental validation in the laboratory, will enable future demand-meeting applications of bionanotechnology.Toward realizing the goal of programming matter with nanoscale precision, this project will develop software interfaces between two classes of molecular design programs that, until now, have been evolving independently from one another. A widely adopted DNA structure design program, Cadnano, will be extended to utilize the results of physics-based microscopic simulations, enabling an iterative structure design process. A leading molecular graphics program, VMD (Visual Molecular Dynamics), will be developed to seamlessly visualize Cadnano designs, provide their structural interpretation, and enable further modification of the structures using an arsenal of computational structural biology and nanotechnology tools. Both developments will utilize recent advances in cloud computing technologies, making the DNA structure design software available anywhere and to anyone in a platform-independent manner.This project is supported by the Office of Advanced Cyberinfrastructure in the Directorate for Computer & Information Science & Engineering and the Division of Civil, Mechanical and Manufacturing Innovation in the Directorate of Engineering.

纳米技术有一天可能会彻底改变对我们国家利益非常重要的几项活动，包括我们如何制造消费品，我们如何诊断和治疗疾病，以及我们如何检测和消除对我们国防的威胁。一种很有前途的原子精确构建方法是从生物体（如DNA，RNA和蛋白质）中改造分子构建块，并将其重新利用以自组装成指定的形状，设备和材料。进展的一个关键瓶颈是设计、构建和测试由数千或数百万个原子组成的纳米结构的复杂性。该项目的目标是通过整合生物纳米结构设计和基于物理的分子模拟中广泛采用的两种软件工具来加速生物启发纳米结构的开发。这一努力的成果将提高我们理解和精确设计自组装生物分子纳米结构的基本能力，当与实验室中的实验验证相结合时，将使生物纳米技术的未来需求满足应用成为可能。为了实现以纳米级精度编程物质的目标，该项目将开发两类分子设计程序之间的软件接口，到目前为止，都是相互独立地进化的广泛采用的DNA结构设计程序Cadnano将扩展到利用基于物理的微观模拟结果，从而实现迭代结构设计过程。一个领先的分子图形程序，VMD（可视化分子动力学），将开发无缝可视化Cadnano设计，提供他们的结构解释，并使结构的进一步修改使用计算结构生物学和纳米技术工具的武库。这两项开发都将利用云计算技术的最新进展，使DNA结构设计软件以独立于平台的方式在任何地方和任何人都可以使用。该项目得到了计算机信息科学工程局高级网络基础设施办公室和工程局土木、机械和制造创新司的支持。

项目成果

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

• DOI: 10.1093/nar/gkaa200
• 发表时间: 2020-05-21
• 期刊: NUCLEIC ACIDS RESEARCH
• 影响因子: 14.9
• 作者: Maffeo, Christopher;Aksimentiev, Aleksei
• 通讯作者: Aksimentiev, Aleksei

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