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

这个小企业创新研究（SBIR）二期项目的更广泛的影响/商业潜力将是加快微生物开发的步伐，用于生物制造有价值的蛋白质、工业用高级酶或治疗药物。DNA克隆是工业和大学基础研究过程中的日常实践。克隆技术在过去的20年里基本没有改变。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。在过去的几年中，标准化的实验DNA构建方法已经开发出来，这些方法可以很好地实现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，更快的酶和更多产的微生物菌株。提出的技术将允许重组DNA的快速向前工程生物文库。该技术的商业化将为现有方法提供一种低成本的替代方案。SBIR二期项目旨在开发一种生物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，以及用于设计这些DNA组装的软件算法，所提出的研究将产生一个平台技术，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仍然是限制规模的主要瓶颈，无论是在成本还是时间方面。所提出的技术将允许快速成型和表征重组DNA，蛋白质或整个细胞的正向工程生物文库。目标是将一个易于使用的平台商业化，将复杂的构建物组装到载体主干上，将它们转染到宿主微生物中，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.