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发现和消除对我们国防的威胁。一种有希望的原子精确构建方法是采用来自生物体的分子构件，例如 DNA、RNA 和蛋白质，并重新利用它们以自组装成规定的形状、设备和材料。进步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集成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仿生纳米结构的开发。这项工作的产品将增强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，与实验室的实验验证相结合，将使生物纳米技术未来的需求满足应用成为可能。纳米级精度，该项目将开发两类分子设计程序之间的软件接口，迄今为止，这两类分子设计程序一直在相互独立地发展。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的结果，从而实现迭代结构设计过程。将开发领先的分子图形程序 VMD（视觉分子动力学），以无缝可视化 Cadnano 设计，提供其结构解释，并使用计算结构生物学和纳米技术工具库进一步修改结构。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、任何人都可用。该项目得到了计算机与信息科学与工程理事会高级网络基础设施办公室的支持，工程局土木、机械和制造创新司。

项目成果

Single molecule analysis of structural fluctuations in DNA nanostructures

DNA 纳米结构结构波动的单分子分析

• DOI: 10.1039/c9nr03826d
• 发表时间: 2019-10
• 期刊: Nanoscale
• 影响因子: 6.7
• 作者: Jepsen, Mette D.;Sørensen, Rasmus Schøler;Maffeo, Christopher;Aksimentiev, Aleksei;Kjems, Jørgen;Birkedal, Victoria
• 通讯作者: Birkedal, Victoria

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

MrDNA：用于预测 DNA 系统结构和动态的多分辨率模型

• DOI: 10.1093/nar/gkaa200
• 发表时间: 2020-03-31
• 期刊: Nucleic Acids Research
• 影响因子: 14.9
• 作者: C. Maffeo;A. Aksimentiev
• 通讯作者: A. Aksimentiev