Artificial biochemical circuits on a chip

We’re back from the break (under the firm direction of chair Bill Goddard, who is a great emcee) for the first of the final three lectures: “Engineering Artificial Biochemical Circuits” by Roy Bar-Ziv of Weizmann Institute of Science in Israel. These are cell-free gene expressions carried out on a chip. To get proteins to assemble properly it’s very important to make them in the correct order. These synthetic networks can also be done inside the cell, in vivo. Now describing work by a colleague to do this, making a “repressor oscillator” circuit inside the cell. His question is, why can’t we do this outside the cell? Need a materials platform: 2D surface or 3D soft closed compartments (artificial cell).

He does cell-free protein synthesis: DNA to mRNA to protein in a test tube. He is giving a simple example: a two-stage cascade with experimental data. Next, a three-stage cascade, with an input functioning as an AND gate. Next a synthetic switch, with inducer, activator, and repressor, again with experimental data. Very simple biochemical switch. Next, putting this on a chip.

Genes can be localized at the micro-scale, don’t need to put them down with nanoscale precision for this purpose. Why go 2D in artificial systems? To make protein factories, protein assembly lines.

He uses a photolithography approach (like Affymetrix) to do light-directed localization of the genes. First Avidin attached, then the DNA in patterns on the chip. No clean room needed, can do with microscope. The density of the genes on the surface is important. Example of nano-assemblies made: 3 micron long nanotube made from a viral protein (20 nm wide).

Q from Bruce Smith about computation using these systems. A: Not planning to do computation. Want degrees of freedom to do self-organization. Q: Addressable bacteria from synthetic biology. A: that’s a parallel approach.

As always, apologies to Roy for any errors introduced by me in the above. —Christine

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