MAE Seminar

Analysis, design and in vitro implementation of robust biochemical circuits

June 8, 2012

Elisa Franco, Assistant Professor

Mechanical Engineering

University of California, Riverside

The functions of every living organism are embedded in the biochemical interactions among proteins, nucleic acids and all the other molecules that constitute life's building blocks. Understanding the general design principles of this "hardware of life" is an exciting and challenging task for modern bioengineers. In this seminar, I will focus
on the topic of robustness in molecular networks, highlighting both theoretical and experimental work carried out in our lab. Our analysis relies on control-theoretic tools, while experiments are pursued using in vitro transcription systems, minimal analogues to cellular genetic networks.

The first problem I will consider is flux control. I will describe a simple model problem where two reagents bind stoichiometrically to form an output product. In the absence of any regulation, imbalances in the reagents production rates can cause accumulation of unused molecules, and limit the output flow. To match the reagents flux, robustly with respect to the open loop rates, I will propose the use of negative or positive feedback schemes that rely on competitive binding.

The second topic I will examine is robustness of interconnected networks: molecular devices characterized in isolation may lose their properties once interconnected. This challenge will be illustrated with a case study: a synthetic transcriptional clock will be used to drive conformational changes in a molecular nanomachine called DNA tweezers. Mass conservation introduces parasitic interactions that perturb the oscillator trajectories proportionally to the total amount of tweezers "load". To overcome this problem, we can use a genetic switch acting as a buffer amplifier, achieving signal propagation and at the same time reducing the perturbations on the source of signal. We plan on using this simple principle in the context of programming periodic reconfiguration of self assembled DNA structures.

Finally, I will briefly describe our recent advances in understanding robust design of molecular clocks, using parameter-independent models. These models only capture sign, trend and boundedness of the system dynamic interactions: therefore, we consider them a structural representation. We propose a simple but rigorous classification of candidate oscillators and multi-stationary networks based on positive and negative loops.