Programmable DNA receptors

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Today we are jumping into artificial cell receptors, using nothing but DNA! Fully programmable, modular and capable of self-assembly on cell membranes, what more do you want?

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Programmable DNA receptors

Last week we explored how lipid nanoparticles can be used to deliver different RNA drugs: today, we discover more exotic systems we could deliver! Let’s go.

Transmembrane receptors: how cells sense the world

Cells survive by sensing their environment: transmembrane receptors detect external signals and translate them into intracellular responses. This signal transduction affects pretty much everything, from immune activation, to apoptosis and gene expression. Natural transmembrane receptors are protein-based: they are extremely good at what they do, but also very complex and difficult to modify. And this gets in the way when scientists want to re-engineer them for other applications.

Synthetic biologists would love to design artificial receptors that can detect and respond to specific signals. One of the most notable successes is synNotch, a synthetic version of the Notch family of receptors, involved in development and cellular communication. Unfortunately, successes like this are limited. Designing synthetic protein receptors is an uphill battle, requiring intricate protein engineering with limited modularity and potential immunogenicity risks when used in living organisms. Could AI eventually help solve these challenges? Maybe.

A New Approach: DNA-Based Transmembrane Receptors

But in the meantime, what if moved away from proteins and we turned to a different material, far more programmable? This where the authors of today’s paper stepped in, using my favorite material: DNA. In short, they developed synthetic transmembrane DNA receptors, which are:

• Fully programmable 

• Modular

• Self-assembling on cell membranes!

Very cool, but how do they work?

How Do These DNA Receptors Work?

Each DNA receptors consist of 3 key components:

1. Extracellular sensing module: This part, external to the cell, contain DNA aptamers that recognize and bind target molecules. When activated, the receptor undergoes dimerization or conformational changes.

2. Transmembrane anchoring module: A hydrophobic anchor inserts the receptor into the membrane, ensuring stability and proper orientation.

3. Intracellular signal module: This converts the detected signal into a cellular response, such as RNA modulation or a catalytic DNAzyme (the DNA equivalent of an enzyme).

After successfully integrating the synthetic receptors into cell membranes using liposomes, the researchers showed that they could transduce signals: once activated, the intracellular catalytic DNAzymes produced a fluorescent signal, proving the system worked. This is already pretty cool, but the best is yet to come.

Built-In Logic: DNA Receptors as Boolean Gates

To ensure high specificity, the researchers designed Boolean logic gates using the DNA receptors. Boolean logic gates take one or more input and produce a single output: in this way, the receptors can compute on the cell, and activate only when necessary! They created 2 logic gates:

• AND gate receptor: It requires 2 inputs, for example tumor markers, to activate, minimizing the risk of off-target effects.

• OR gate receptor: It activates when either of the two signals is present, reducing specificity but increasing sensitivity.

This allow the researchers to fine-tune cellular responses, making it possible to design highly selective therapies, that only trigger when specific conditions are met.

Using DNA Receptors to Target Cancer

The team tested their receptor on tumor-specific antigens like MUC1 and Met, proteins overexpressed in HeLa cells (a widely used cervical cancer cell line). They first confirmed the system’s functionality using fluorescence imaging, ensuring that the receptors correctly detected tumor markers. Once validated, they moved on the real test. The researchers treated T cells and tumor cells with the DNA receptors. If the tumor markers were present, the receptors activated, triggering DNAzyme-mediated gene silencing. This suppresses the expression of PD-L1, a key protein involved in immune evasion in cancer. In this way, the tumor cells are more susceptible to attacks from T-cells. The new system was highly selective: not only could distinguish between healthy cells and cancer cells, but also between different types of cancer cells that did not express the correct markers. This proof-of-concept shows the sensitivity of these synthetic receptors, which is crucial to minimize damage to healthy cells!

Challenges and Next Steps

The synthetic receptors presented here are exciting: they have some clear advantages over artificial proteins, mainly around their simplicity and full programmability (you know, it’s DNA). And there are fascinating applications for them:

• Diagnostics: They could be used to detect disease biomarkers with incredible precision.

• Therapy: Like the researchers demonstrated, there is definitely a potential to create new therapies.

• Regenerative medicine: What if we could use them to program cells to self-repair? That would be cool!

Despite the potential, there are still hurdles, of course:

• Stability in biological environments: DNA is not very stable in physiological conditions, although chemical modifications are improving its durability.

• Efficient delivery methods: Current options, like lipid nanoparticles and DNA origami, are promising but need optimization.

• Scalability for therapeutics: Last but not least, DNA synthesis costs are dropping, but scaling up production remains a challenge.

So, if you want to know more, just go and read the paper here! I recommend it.

And as always, thank you for reading! What are your thoughts on this paper and synthetic DNA receptors? Reply and let me know.

More room:

• Cas9, nucleosomes and more: If you have ever wondered how nucleases like Cas9 can interact with the genome when nucleosomes are in the way, this is your paper. It finds that Cas9 targets the linker DNA and entry-exit regions of nucleosomes, but not the tightly wrapped DNA. Cryo-electron microscopy revealed multiple interaction sites between Cas9 and nucleosomes. Interesting!

• Nanoliters droplet in a micrometer world: The idea of being able to create a nanoliter of something is pretty crazy: but microfluidic allows it. This study introduces a method for controlling the size and quantity of 3D DNA crystals using microfluidic double-emulsion droplets. The droplets ensure only one crystal forms per droplet, achieving a 98.6% success rate. The crystals have controlled sizes (19.3 to 56.8 μm) and the method can be applied to various types of DNA crystals, advancing DNA crystal self-assembly and microengineering. Cool.

• Easier wireframe DNA origami: Wireframe DNA origami have a special space in my heart, since they were the focus of my PhD. So I think this paper is quite interesting: it introduces a generative design framework for creating wireframe DNA origami nanostructures without predefined meshes. It uses optimization problems to guide the design process, allowing users to explore various design options through a web-based interface. This approach helps designers discover novel nanostructures by considering design trade-offs. I am happy to see people expanding the field!

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