Models for synthetic biology

Abstract

Synthetic biological engineering is emerging from biology as a distinct discipline based on quantification. The technologies propelling synthetic biology are not new, nor is the concept of designing novel biological molecules. What is new is the emphasis on system behavior. The objective is the design and construction of new biological devices and systems to deliver useful applications. Numerous synthetic gene circuits have been created in the past decade, including bistable switches, oscillators, and logic gates, and possible applications abound, including biofuels, detectors for biochemical and chemical weapons, disease diagnosis, and gene therapies. More than fifty years after the discovery of the molecular structure of DNA, molecular biology is mature enough for real quantification that is useful for biological engineering applications, similar to the revolution in modeling in chemistry in the 1950s. With the excitement that synthetic biology is generating, the engineering and biological science communities appear remarkably willing to cross disciplinary boundaries toward a common goal.

Figure 1

A major challenge in synthetic biology is to rationally select DNA sequences that result in targeted dynamic phenotypes. For example, with simulations using Hy3S [29] we are experimenting with multiple alternative promoter sequences to identify the optimal AND gate synthetic gene network, with tetracycline (atc) and IPTG as inputs and green fluorescence protein (GFP) as output.