Team:EPF Lausanne
Logic Orthogonal GRNA Implemented Circuit
The aim of our project is to enable the simple and reproducible design of modular digital circuits within living cells. Cells possess the ability to accept biological data as input and process it according to predefined instructions. We plan to harness this potential by designing bio-elements that behave as transistors. Our goal is to assemble these transistors to create a programmable logic gate array.
Thinking Binary
Boolean Logic is the bedrock of the digital revolution. Developed by George Boole in the mid-19th century, it is based on a simple set of values: 0 (“FALSE”) or 1 (“TRUE”). In computers, all information is represented by strings of 0s and 1s - multiple representations of binary digits or “Bits”. Bits are physically implemented by two-state devices named transistors. The assembling of transistors forms logic gates - which enables digital circuits to exhibit incredibly complex behaviours in the everyday objects that surround us.
A Biological Computer
Creating customizable logic gates in living cells holds the promise of revolutionizing our ability to dictate the behaviour of organism and the way they react to distinct molecular cues. This involves designing logic circuits capable of linking the many genetic regulatory networks responsible for biologic operations. An ideal genetic logic device should therefore be modular and reusable, enabling scientists to implement any complex logic functions in multiple biological systems. Our goal this summer is to achieve this by using gRNA-dCas9 combinations as the biological equivalent of the wires that connect the different components of electric circuits.
Cas9 (CRISPR associated protein 9) is an RNA-guided DNA endonuclease enzyme that can target and cleave any DNA sequence complementary to its guide RNA (gRNA). Our logic gates will be based upon a derivative of this technology, the catalytically “dead” Cas9 (dCas9) that lacks the ability to cleave DNA. dCas9’s has the very interesting property of acting as programmable transcription regulator. It it can act either as repressor by preventing the binding of the RNA polymerase (RNAP) to the targeted DNA or as an activator when fused to a polymerase recruiting element (the omega subunit of RNAP in E. Coli and VP64 in Yeast).
To create a modular system based on these elements, we will design two different plasmids: a gate array and a linker. The gate array will contain a predefined set of logic gates. The code linking the different gates will be written on the customizeable linker plasmid.
With this project, we hope to help create robust biologically based digital devices by successfully implementing modular orthogonal logic gates in living organisms. The applications of logic circuits implemented in a biological context are vast and range from the creation of smart cells able to monitor their environment for external stimuli to new forms of cellular therapeutics with improved in vivo targeting and curing.