SBIR Phase II: An Intelligent Rapid Prototyping System for Synthetic Biology

这一小型企业创新研究(SBIR)第二阶段项目的更广泛影响/商业潜力将是加快微生物开发步伐，以生产有价值的蛋白质、工业用高级酶或治疗药物。DNA克隆是以工业和大学为基础的研究过程中的日常做法。在过去的20年里，克隆技术基本上没有变化。因此，研究人员花费了大量的时间和金钱来设计和构建DNA，而不是设计和进行实验。在过去的几年里，标准化的实验DNA构建方法已经被开发出来，这些方法很好地有助于DNA的自动化和快速组装。过程自动化正在从奢侈品发展到必需品，因为目标应用需要制造大型组合DNA文库，以寻找更好的抗体、更快的酶和更高产的微生物菌株。拟议的技术将使重组DNA的快速正向工程生物库成为可能。这项技术的商业应用将为目前的方法提供一个低成本的替代方案。这个SBIR第二阶段项目旨在开发一种BioCAD/CAM(计算机辅助设计和制造)技术，使合成生物学的DNA快速组装成为可能。结合DNA组装方法的最新进展，以及用于设计DNA组装的软件算法，拟议的研究将产生一种平台技术，促进直接合成和DNA组装的优化组合，以建立大型组合文库。在DNA文库构建后，筛选具有所需活性的构建体仍然是限制规模的主要瓶颈，无论是在成本还是时间方面。这项拟议的技术将允许对重组DNA、蛋白质或整个细胞的正向工程生物库进行快速原型设计和表征。其目标是将一种易于使用的平台商业化，用于将复杂的结构组装到载体骨架上，将它们导入宿主微生物，并对产品产量进行快速评估。在数据清理和分析之后，结果被捕获、保存并返回到设计数据库。

The broader impact/commercial potential of this Small Business Innovation Research (SBIR) Phase II project will be to accelerate the pace of microbe development for the biomanufacture of valuable proteins, advanced enzymes for industry, or therapeutic medicines. DNA cloning is an everyday practice in the course of both industrial- and university-based research. Cloning technology has remained largely unchanged for the last 20 years. As a consequence, researchers consume a significant amount of time and money designing and constructing DNA, rather than on designing and conducting experiments. Over the past few years, standardized experimental DNA construction methods have been developed that lend themselves well to automation and rapid assembly of DNA. Process automation is progressing from luxury to necessity, as target applications demand the fabrication of large combinatorial DNA libraries in the search for better antibodies, faster enzymes, and more productive microbial strains. The proposed technology will allow rapid forward engineered biological libraries of recombinant DNA. The commercial availability of this technology will provide a low cost alternative to current methods.This SBIR Phase II project aims to develop a bioCAD/CAM (Computer Aided Design and Manufacturing) technology that enables rapid DNA assembly for synthetic biology. Wedding recent advances in DNA assembly methods, and the software algorithms used to design those DNA assemblies, the proposed research will result in a platform technology for facilitating an optimized combination of direct synthesis and DNA assembly to make large combinatorial libraries. After the construction of the DNA libraries, screening for constructs with the desired activity remains a major scale-limiting bottleneck, both in terms of cost and time. The proposed technology will allow rapid prototyping and characterization of forward engineered biological libraries of recombinant DNA, proteins, or whole cells. The goal is to commercialize an easy-to-use platform for assembling complex constructs onto vector backbones, transfecting them into host microbes, and doing a rapid assessment of product yield. Results are captured, saved, and returned to a design database after data cleansing and analysis.