Fluorescence calibration and color equivalence for quantitative synthetic biology.

Abstract

Synthetic Biology, the engineering of biology, is an evolving discipline. The complexity of the gene circuits being designed is increasing. And we are reaching the point where mathematical models are necessary and essential tools for the design of these gene circuits. Models can predict circuit behavior and guide the selection of suitable circuit components and implementations. However, it is necessary to perform a parameter estimation in order to use these models correctly. Measurement calibration, and in particular, fluorescence and absorbance calibrations, is essential for the reproducibility of biological experiments. Moreover, the use of calibrated measurements increases dramatically the usability and interpretability of models and parameters estimated with them. Here, we report a set of protocols and calibration procedures allowing us to obtain measurements of fluorescent E. coli cells in Molecules of Equivalent Fluorescein (MEFL) per cell for GFP constructs and Molecules of Equivalent Fluorophore for other proteins such as YFP, sfGFP and RFP. These simple, low-cost unit calibration protocols can be used to produce units and comparable models, improving dramatically the usability of these models for modular construction of genetic circuits in synthetic biology.