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

生物有机体利用DNA编码合成多种多样的物质，从光合植物到珍珠状物质，从软体动物到蜘蛛和蠕虫的丝。近年来，利用DNA本身作为一种建筑材料，并将其转化为各种不易从自然进化的生物体中产生的材料，已经成为可能。为此，本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基于dna的结构材料，这些材料具有不同寻常的化学、机械和光学特性。合成的DNA材料被设计成开放的孔结构，适合与蛋白质、酶、发色团、金属颗粒和其他有机和无机材料进一步修饰。这些组合为创建复杂的多尺度dna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源，以促进全球研究人员和从业者参与复杂dna材料的定制设计和合成。本研究项目旨在开发一种通用的计算框架，用于合理设计具有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整合的方式进行实验验证。与之前利用DNA合理组织的非结构化和无孔胶体颗粒类似，结构化DNA纳米颗粒和单链DNA瓦片正被用于在无限扩展的晶格或有限离散的纳米级团簇中实现复杂的结构化和多孔的三维材料。利用纯合成的单链瓷砖寡聚物，可以实现高达千兆道级的dna基材料，具有独特的纳米级寻址能力，使用的序列规范可以与金属纳米颗粒、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，使全世界都能获得这项研究项目的结果。在项目过程中开发的软件也将在开源许可下免费提供，供世界各地的研究人员进一步开发和集成到其他软件包中。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分层dna基材料。例如，计算模型可用于在硅屏幕上执行目标结构和功能特性，从而大大减少了为工业应用部署功能性dna材料所需的时间。

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.