Synthetic Biology (The Cell as a Nanosystem). COSMOS Nanotechnology UCSC Summer 2009. Synthetic Biology. Nanotechnology is emulating biology Molecular assemblers, molecular sensors ‘Bots’ that deliver medicine to specific cells Biotechnology is helping out
UCSC Summer 2009
Earth’s early nanostructures ~ 2 billion years ago
Figure1: 3D diagram of a lipid bilayer membrane - water molecules not represented for clarity
Concept by Robert Cormia
INVERSE LOGIC. A digital inverter that consists of a gene encoding the instructions for protein B and containing a region (P) to which protein A binds. When A is absent (left)—a situation representing the input bit 0—the gene is active. and B is formed—corresponding to an output bit 1. When A is produced (right)—making the input bit 1—it binds to P and blocks the action of the gene—preventing B from being formed and making the output bit 0. Weiss http://www.ee.princeton.edu/people/Weiss.php
In this biological AND gate, the input proteins X and Y bind to and deactivate different copies of the gene that encodes protein R. This protein, in turn, deactivates the gene for protein Z, the output protein. If X and Y are both present, making both input bits 1, then R is not built but Z is, making the output bit 1. In the absence of X or Y or both, at least one of the genes on the left actively builds R, which goes on to block the construction of Z, making the output bit 0. Weiss
Modeling life as an information system
Gross anatomy of a minimal gene regulatory network (GRN) embedded in a regulatory network. A regulatory network can be viewed as a cellular input-output device.http://doegenomestolife.org/
Just as in a computer, data bits and processing bits are made from the same material, 0 or 1, or A, T, C, G, or U in biology
Once you have an ‘altered genome’ ready to test beyond a simple one cell environment, you leverage the ability of stem cells to ‘mass produce’ your synthetic biology solution
Algal cell suspension / cells
These little critters are very happy just to be working!
Yellow arrow marks insertion of hydrogenase promoter.
Right side data cell optimized for continuous H2 production.
Gene expression tells you how the machine is working
Bioinformatics shows you where the control points are
All proteins are ‘synthetic’ – peptides => polymers