Test Render: Wiring A CRISPR Logic Gate

3D | Cinema 4D | Molecular Visualization
crispr circuit final layout

A 11×17” magazine spread on CRISPR-Cas9, depicting how these molecular scissors could be used to perform logical operations.

Client

Dr. Derek Ng

Tools

UCSF Chimera
Adobe Photoshop
Adobe Illustrator
Cinema 4D

 

Creative Process

CRISPR is one of the biggest science stories of the decade. However, most visualizations on CRISPR focuses on its structure and mechanism; the system’s application beyond gene editing however, is rarely depicted. Engineering living digital circuits is one of these emerging application of CRISPR that hasn’t been showcased visually. The challenge of explaining how a CRISPR circuit lies not just in creating a engaging yet accurate picture of each individual elements of the circuit, but also in helping the reader to understand how a logical operation is computed –– in the context of both electronics, and dynamic genetic control. By showing the logic of this system using a truth table, and constructing a cancer therapy scenario where CRISPR does more than just editing out a cancer gene, we hope to introduce a new perspective to CRISPR: It’s not just a pair of molecular scissors, it’s a synthetic decision-making system.

Part of coursework for MSC2020H (Visual Representation of Biomolecular Structure & Function): a 2-page Scientific American style spread depicting a molecular event for an educated lay audience.

Molecular Visualizaion

Protein and nucleotide structures are retrived from Protein Data Bank, processed with UCSF Chimera and ePMV, composed and rendered in Cinema 4D.

Scene Composition

I separated the proteins, DNA, and the background into different render passes; this way the scene renders more efficiently while offering maximum editing flexibility for compositing.

Storytelling

Content review and layout revision focused on the actor’s structure-function relationship, context, and level of detail. The key take-aways are organized using a truth table.

Scale with Style

X-ray style visualization is used to clarify hidden structures. We also used 8-bit visualization, atmospheric perspective, and bokeh to highlight distinct temporal events.

In 2017, I met a group of very cool people from the Toronto iGem team, whose iGem entry project aimed to fine-tune the CRISPR-Cas9 system via a light-sensitive switch. This is where I first learned about how you can turn a molecular network into logical functional units. In my research, I read about how researchers have constructed the largest living circuits in yeast cells. The coolest part of this yeast  circuit is that you only need a single type of logic gate, i.e., a single transcription cascade, to compute multiple logic functions and produce multiple genetic products to control how a cell functions. I made a few quick doodles to helpmyself understand a) the components of CRISPR-Cas9 system, and b) the reletive positions of the ciruit input/output:

The early draft focused more on the individual elements of the circuit. For example, to complete the circuit, you must keep the output of the circuit, a strand of guide RNA, inside the nucleus. By nature, RNA wants to exit the nucleus. How do we keep that RNA inside the nucleus? You flank the RNA export signal with two self-cleaving ribozymes. As the ribozymes cut themselves free from the guide RNA, they take the export signals with them leaving the guide RNA to roam inside the nucleus until it’s picked up by its Cas9 counterpart.

 

 

––– Spoilers, the ribozyme part did not make it into the final draft, neither did the ominous looking polymerase. After a few rounds of peer review, everyone points out that I need to include the application of the molecular gates to complete the narrative. The focus of this piece is not the molecular construct, but the possibility it inspires.

Making a molecule inside a cell has become pretty standard. But with advanced synthetic tools like CRISPR, we could add some logic to this production process. Say, let’s only make that molecule during special circumstances. I decided to describe the gene circuit in the context of cancer. The gene circuit detects cancer using some logic; such as, am I in a cancer cell, or am I in a normal cell? If the cell is in a cancer cell, we don’t make the molecule. If we are in a normal cell, we will make that molecule that kills the cell.

Coming up with a scenario got me very excited. Inspired the initial 8-bit font choice, I changed all the schematic elements into 8-bit representations after looking up tutorials on creating pixel art (WARNING, this is addictive)The graphic itself is a composite of several renders. The models are retrieved from the protein data bank by the epmv plugin, and rendered using Maxon Cinema 4D. The long DNA strand is taken from DNA strands associated with the protein themselves, and short segments I built using epmv.

If you have a molecular biology or biochemistry background, this is your assignment to shine. Dereck’s MSC2020 is one of my favourite BMC courses. The amount of practical tools you learn within 5 weeks is INSANE –– and these tools are useful beyond the scope of a molecular visualization course.

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Toronto, ON M6K 1X2

tracy.xiang@mail.utoronto.ca

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