EAGER: Collaborative Research: Algorithmic design principles for programmed DNA nanocages

3D打印革命性地改变了使用简单的计算机辅助设计(CAD)文件作为输入在宏观尺度上制造复杂实体对象的能力。在此过程中，用户使用简单的几何基元或基于曲面的网格指定实体对象。这项革命性技术的最新应用包括打印假肢、植入物和组织工程支架，以及从服装和眼镜到汽车、航空航天和艺术等行业产品的快速原型制作。20世纪70年代，自动化制造领域也开始了类似的变革，使用CAD设计复杂的电子产品，使用超大规模集成电路(VLSI)设计由数千个晶体管组成的电路。这场CAD革命也极大地增加和扩大了设计师的参与，他们没有设计和合成定制电路所需的详细技术诀窍，适用于从移动设备到生物医学植入物等行业的各种应用。在纳米尺度上，合成DNA的程序化自组装提供了类似的能力，可以用精确定义的3D结构特征“打印”复杂的3D纳米级物体。虽然结构DNA纳米技术领域比前面的例子要年轻得多，但最近的技术和科学进步使各种结构DNA纳米对象的低成本和可重复合成成为可能，使许多技术创新成为可能，包括为光子学和光捕获设备铸造金属纳米颗粒，制造用于药物和基因输送的模仿病毒的治疗载体，以及开发用于疾病诊断中生物标志物检测的纳米级传感器。结构DNA纳米技术目前在设计师的广泛参与方面面临着类似的瓶颈，因为需要为这些纳米物体提供基于CAD的自动化设计软件。在这里，建议开发下一代CAD框架，以实现纳米级结构DNA组件的全自动化设计。作为一个起点，这里提出了一个CAD程序的开发，用于合成一类独特的基于DNA的对象，称为DNA纳米笼。DNA纳米笼可以被编程为在这种规模上采用几乎任意的对称性和大小。此外，这些基于DNA的颗粒可以与蛋白质、RNA、生色团和其他小分子进行化学功能化，以用于生物分子科学和技术的不同应用。此外，这些纳米材料可以转化为包括金属和二氧化硅在内的结构无机材料。为了实现转变设计和制造基于DNA的纳米材料的能力的目标，将开发一个开源软件包，使用一种简单的高级语言和通过万维网分布在世界各地的CAD环境，从自上而下的纳米笼尺寸和对称性进行几何规定。自组装形成这些CAD指定结构的合成DNA序列将自动生成用于纳米笼制造。纳米笼合成的验证将使用高分辨率结构和折叠分析进行实验。这项工作构成了一种新的高级编程语言的起点，该语言使用合成DNA在纳米级打印3D对象，这将使这些组件在不同的研究和工业应用中广泛使用和应用。未来的工作可能会将这一框架扩展到任意的基于2D和3D DNA的组装，以及模仿并远远超出自然进化设计的分子功能化DNA组装。

3D printing has revolutionized the ability to fabricate complex solid objects at the macroscopic scale using simple Computer-Aided Design (CAD) files as input. In this process, the user specifies the solid object using simple geometric primitives or surface-based meshes. Recent applications of this revolutionary technology include printing limb prosthetics and implants and tissue engineering scaffolds, as well as rapid prototyping of products in industries ranging from apparel and eyeware to automotive, aerospace, and art. A similar transformation in automated fabrication began in the 1970s using CAD for the design of complex electronics using very large scale integration (VLSI) to design circuits consisting of thousands of transistors. This CAD revolution also dramatically increased and broadened the participation of designers without detailed technical know-how needed to design and synthesize custom electrical circuits for diverse applications in industries ranging from mobile devices to biomedical implants. At the nanometer-scale, programmed self-assembly of synthetic DNA offers a similar ability to "print" complex 3D nanometer-scale objects with precisely defined 3D structural features. While the field of structural DNA nanotechnology is considerably younger than the preceding examples, recent technological and scientific advances have enabled the low-cost and reproducible synthesis of diverse structured DNA nano-objects, enabling numerous technological innovations including casting metallic nanoparticles for photonics and light-harvesting devices, fabricating therapeutic vectors that mimic viruses for drug and gene delivery, and developing nanoscale sensors for biomarker detection in disease diagnosis. Structural DNA nanotechnology currently faces a similar bottleneck in the broad participation of designers due to the need for automated CAD-based design software for these nano-objects. Here, development of a next-generation CAD framework is proposed to enable the fully automated design of structured DNA assemblies at the nanometer scale. As a starting point, the development of a CAD program is proposed here for the synthesis of a unique class of DNA-based objects called DNA nanocages. DNA nanocages can be programmed to adopt nearly arbitrary symmetries and sizes on this scale. Further, these DNA-based particles may be functionalized chemically with proteins, RNAs, chromophores, and other small molecules for diverse applications in biomolecular science and technology. In addition, these nanoscale materials can be transformed into structured inorganic materials including metals and silicon dioxide. To realize the aim of transforming the ability to design and fabricate DNA-based nanomaterials, an open-source software package will be developed to prescribe geometrically from the top-down nanocage size and symmetry using a simple high-level language and CAD environment that is distributed worldwide through the world-wide web. Synthetic DNA sequences that self-assemble to form these CAD-specified structures will be automatically generated for nanocage fabrication. Validation of nanocage synthesis will be performed experimentally using high-resolution structural and folding assays. This work forms the starting point for a new high-level programming language to print 3D objects at the nanometer-scale using synthetic DNA that will broadly enable the use and application of these assemblies across diverse research and industrial applications. Future work may extend this framework to arbitrary 2D and 3D DNA-based assemblies, as well as molecularly functionalized DNA-assemblies that mimic, as well as extend far beyond, nature's evolutionary designs.