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

这个小企业创新研究（SBIR）第二阶段项目的更广泛的影响/商业潜力将加快微生物开发的步伐，用于有价值的蛋白质，工业用先进酶或治疗药物的生物制造。DNA克隆是工业和大学研究过程中的日常实践。克隆技术在过去的20年里基本上没有变化。 因此，研究人员花费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构建方法已经发展，这些方法很好地适应了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。所提出的技术将允许重组DNA的快速正向工程化生物文库。该技术的商业可用性将为当前方法提供低成本的替代方案。SBIR第二阶段项目旨在开发bioCAD/CAM（计算机辅助设计和制造）技术，使合成生物学的快速DNA组装成为可能。结合DNA组装方法的最新进展以及用于设计这些DNA组装的软件算法，拟议的研究将产生一种平台技术，用于促进直接合成和DNA组装的优化组合，以制作大型组合文库。 在构建DNA文库之后，筛选具有所需活性的构建体在成本和时间方面仍然是主要的规模限制瓶颈。 所提出的技术将允许重组DNA、蛋白质或全细胞的正向工程生物文库的快速原型制作和表征。 其目标是将一个易于使用的平台商业化，用于将复杂的构建体组装到载体骨架上，将它们转移到宿主微生物中，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.