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DMREF: Computational Design of Next-generation Nanoscale DNA-based Materials

DMREF：下一代纳米级 DNA 材料的计算设计

基本信息

批准号：
1729397
负责人：
Mark Bathe
金额：
$ 160万
依托单位：
Massachusetts Institute of Technology
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：
2018-01-01 至 2021-12-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1729397&HistoricalAwards=false
关键词：
DMREF Computational Design Next generation

项目摘要

Biological organisms utilize DNA to encode the synthesis of a remarkably diverse variety of materials ranging from photosynthetic plants to pearly substances from mollusks to silk from spiders and worms. In recent years, it has become possible to utilize DNA itself as a construction material and to turn it into a wide range of materials not readily produced from naturally evolved organisms. To this end, this research project focuses on identifying computational design rules that will accelerate the discovery of DNA-based, structured materials possessing unusual chemical, mechanical, and optical properties. The synthetic DNA materials are being designed with open pore configurations suitable for further modification with proteins, enzymes, chromophores, metallic particles, and other organic and inorganic materials. These combinations offer a next-generation platform for the creation of complex multi-scale DNA-based materials for diverse chemical, biological, mechanical, optical, and sensing applications. The predictive software tools developed in the course of the project are being made broadly accessible and open-sourced to facilitate engagement worldwide of researchers and practitioners in the custom design and synthesis of complex DNA-based materials. This research project aims to develop a generalized computational framework for the rational design of structured DNA-based materials of nearly arbitrary nanoscale geometric composition. Computational models of DNA-based self-assembly and structure are being validated experimentally in a highly iterative and integrative manner. Similar to unstructured and non-porous colloidal particles that have previously been organized rationally using DNA, structured DNA nanoparticles and single-stranded DNA tiles are being used to realize complex structured and porous 3-dimenional materials in infinite, extended lattices or finite, discrete nanoscale clusters. Utilization of purely synthetic, single-stranded tile oligos facilitates the realization of up to gigadalton-scale DNA-based materials with unique nanoscale addressability using sequence specification amenable to downstream functionalization with metallic nanoparticles, enzymes, or other functional moieties. Web-based dissemination of computational models is being done to make the results of this research project available worldwide. Software developed during the course of the project also is being made freely available, under an open source license, for further development and integration into other software packages by researchers worldwide. This broad dissemination of computational results facilitates the broader materials and nanotechnology communities to study this novel class of hierarchical DNA-based materials. For example, computational models could be used to perform in silico screens for target structural and functional properties, reducing significantly the time needed to deploy functional DNA-based materials for industrial applications.

生物有机体利用DNA编码合成各种各样的材料，从光合植物到软体动物的珍珠状物质，再到蜘蛛和蠕虫的丝。近年来，利用DNA本身作为建筑材料并将其转化为自然进化生物体不易产生的各种材料已经成为可能。为此，该研究项目的重点是确定计算设计规则，这些规则将加速发现具有不寻常化学，机械和光学特性的基于DNA的结构材料。合成DNA材料被设计成具有开孔结构，适合于用蛋白质、酶、发色团、金属颗粒和其他有机和无机材料进行进一步修饰。这些组合为创建复杂的多尺度基于DNA的材料提供了下一代平台，用于各种化学，生物，机械，光学和传感应用。在项目过程中开发的预测软件工具正在广泛使用和开放源码，以促进世界各地的研究人员和从业人员参与复杂的DNA材料的定制设计和合成。该研究项目旨在开发一个通用的计算框架，用于合理设计几乎任意纳米级几何组成的结构化DNA基材料。基于DNA的自组装和结构的计算模型正在以高度迭代和综合的方式进行实验验证。类似于先前已经使用DNA合理组织的非结构化和无孔胶体颗粒，结构化DNA纳米颗粒和单链DNA瓦片正在用于实现无限扩展晶格或有限离散纳米级簇中的复杂结构化和多孔3维材料。利用纯合成的单链寡核苷酸有助于实现高达千兆道尔顿规模的基于DNA的材料，其具有独特的纳米级可寻址性，使用序列规范，其适于用金属纳米颗粒、酶或其他功能部分进行下游功能化。目前正在通过网络传播计算模型，以便向全世界提供这一研究项目的成果。在该项目过程中开发的软件也在开放源码许可证下免费提供，供世界各地的研究人员进一步开发和纳入其他软件包。计算结果的广泛传播促进了更广泛的材料和纳米技术社区研究这种新型的基于DNA的分层材料。例如，计算模型可用于对目标结构和功能特性进行计算机筛选，从而显著减少为工业应用部署功能性DNA基材料所需的时间。