Development and validation of experimental workflows for a DNA foundry

Abstract

Synthetic biology aims to exploit the development of foundational technologies in the current expansion of biotechnology applications that makes the design and manufacturing of engineered biological systems easier and more reliable. Instrumental to fulfil this vision is the decoupling between design and fabrication. Decoupling is defined as breaking down a complex task into simpler and independent ones such that the resulting work can eventually be recombined to produce a functioning whole. This is in stark contrast with the traditional setting where individual researchers needed to carry out different tasks ranging from DNA design to assembly and quality controls. Thus, decoupling enables a team of complementary experts to leverage individual specializations to achieve better outcomes. By decoupling design from fabrication, we empower researchers to design complex constructs irrespective of and independently from the manufacturing technique thus unlocking the full potential of synthetic biology. A typical example is plasmid assembly where the large number of standard plasmid architectures (e.g., SEVA, MoClo, GoldenGate, RFC10) and related assembly techniques actually hinders researchers’ design capabilities rather than enabling it. In this PhD project I focused on the development and validation of DNA fabrication workflows capable of handling multiple assembly techniques completely independent from the design input. The set of workflows developed allows researchers to submit their DNA design without any constraints related to fabrication techniques. The work presented here represents the foundational technology to enable a truly automated DNA foundry for synthetic biology.