Designer RNA Tiles: Programmable Nanostructures Inside Cell Nuclei!

DNA nanotech is a few steps ahead of RNA nanotech. Can the underdog overcome this gap, playing to its strengths?

Well, today’s paper tries! Turning cells into nanofactories that make programmable RNA materials, directly in the nucleus… Exciting!

RNA Goes Nuclear

RNA: Function and Information

RNA plays many roles in cells.

It regulates genes, catalyzes reactions, translates genetic info into proteins, and more. I love DNA, but RNA is an incredibly versatile molecule! You don’t have to convince me.

And the diversity is crazy. Messenger RNAs carry protein instructions. Ribosomal RNAs form the core of ribosomes. Small and long non-coding RNAs regulate gene expression. The list is endless!

The cell keeps track of all this. And the best regulation mechanism? Subcellular localization.

Messenger RNA is transcribed in the nucleus, processed, and then sent out to the cytoplasm. Meanwhile, non-coding RNAs never leave the nucleus. They stay behind to interact with the genome and regulate gene expression.

So, how does the cell decide who stays and who goes? Good question.

We know some RNAs have export sequences that let them escape the nucleus. But we only know a handful of these! So there must be more here. Most RNAs don’t follow rules we understand.

And RNA localization is not just an academic curiosity. With the advent of RNA therapeutics, these seemingly “small” details could make or break future technologies.

RNA Nanotech Inside Cells

You know me. I’m a DNA guy.

DNA is a powerful nanoscale building material, but it has one problem. You need to create your structures outside the cells. This leaves you with a big, delivery-shaped problem. And scientists are solving it, step by step!

But what if you didn’t have to deliver the structures at all?

RNA nanotechnology makes that possible. RNA can be produced directly inside cells, so you transform them, and voilà, you get designed nanostructures exactly where you need them!

Similar to proteins, RNA folds as it is made. The structures self-assemble inside cells, so you don’t have to worry about delivery-related headaches. This is called co-transcriptional folding.

Researchers have made huge progress, producing RNA structures in vitro, in E. coli, and even inside human cells! But one problem remains: many designs tend to escape to the cytoplasm.

Can we assemble large RNA structures that stay in the nucleus?

Building RNA Tiles

Well, today’s paper answers that question!

The team designed single-stranded RNA “tiles” that fold and assemble into larger structures. These molecular LEGO bricks can be functionalized with aptamers and form directly inside the cells’ nuclei.

Each tile binds to neighbours to make larger assemblies: rings, 2D lattices, and arrays!

The design is centered around 2 structural motifs:

• Paranemic cohesions (PC): A base-pairing interaction that holds 2 helices together without intertwining.

• Kissing loop interactions (KL): Complementary hairpin loops match to “glue” different tiles together.

Each tile is a continuous single-stranded RNA (ssRNA). The internal PC domains stabilize the structure, and the terminal KLs mediate inter-tile assembly, encoding the programmable binding rules.

Add a couple of parallel crossovers, choose the 5’, and you have a circular strand that folds while emerging from the RNA polymerase!

RNA Tiles: In Vitro Characterization

This is the basic idea. What did the team build?

Well, they designed many tile variants.

1. Basic tiles (D1-D5)
   They varied tile length, number/placement of crossovers, and KL angle to program the formation of hexameric rings (D1 tiles), zigzag and linear arrays (D2/D3), and 2D lattices (D4/D5). They examined the results with AFM: great folding!

2. Curved tiles (D6-D8)
   Small insertions/deletions of nucleotides between crossovers create curved tiles that assemble into rings with different diameters

Add Function: Broccoli & Biosensors

RNA combines the easy programmability of DNA with functionality.

In the tiles D9-D12, the team embedded the green fluorescent aptamer Broccoli at different locations (3’ termini, internal, branched extension, split forms). The designs assembled without needing purification. D9 and D12 produced the strongest fluorescence!

So, what do you do when you have a fluorescent nanostructure?

Of course, you turn it into a biosensor! Tile D13 is a split-Broccoli sensor that lights up when a KRAS-derived RNA sequence is present. KRAS is a biomarker for many cancers, including pancreatic and colorectal.

In a one-pot reaction assay, the KRAS target activated the D13 fluorescence with low-nanomolar sensitivity! D13 can also discriminate between mutated targets, even if not with amazing specificity.

In Cells: Trapped in the Nucleus

The headline of the paper! Producing and visualizing designed nanostructures inside human cell nuclei.

They picked tiles D4 and D10, which form large nanonet-like configurations. And D10 has the fluorescent Broccoli! The team transfected HEK293FT cells and turned to imaging (3 different kinds!):

1. dsRNA immunostaining: J2 antibodies bind to double-stranded RNA (dsRNA), present in the folded tiles. After 24 hours, >60% of cells showed signal from J2 assemblies! The localization varied for the two tiles, but the designs showed predominant nuclear retention, even with many structures still in the cytosol.

2. Live-cell Broccoli imaging: D10’s fluorescence can be turned on by adding a small molecule. So, they did just that! And the Broccoli imaging confirmed nuclear localization of the nanonets and aptamer functionality.

3. TEM imaging: The most amazing one! They directly observed the structures inside the nucleus. TEM revealed dense, organized 2D arrays matching the AFM patterns. It’s hard work, I’m telling you.

Moving on With RNA Nanotech

A cool work!

RNA nanotech will have a big impact. It combines the programmability of DNA nanotech with the ease of production of proteins. It can scale much better! Plus, there is more functionality than in DNA.

Big fan here!

This paper is interesting. It shows a rational, modular design for RNA tiles that can self-assemble into larger assemblies directly into cells nucleus! And they even remain fluorescent.

Now, why do they stay in the nucleus? It could be because of the large structures or because they lack export signals. We don’t know yet. But this makes these tiles great platforms to study what really matters!

Plus, there are possible applications: regulate genetic pathways, drugs, nuclear biosensing…

So, cool work: go here and read all the details!

If you made it this far, thank you! What do you think of RNA nanostructures? Do you think they have a place in biomedicine? Reply and let me know!

More Room:

• Reinforced (Nano)Oats: Oats go nano to solve a real problem! Iron deficiency is widespread, but many iron supplements have poor absorption or taste issues. This study introduces oat protein nanofibrils carrying iron nanoparticles, which show higher absorption than ferrous sulfate in iron-deficient women and maintain good sensory properties. The platform offers a plant-based approach for more effective iron fortification.

• Nano-Bio Interfaces: Their Time to Shine? Nano–bio interfaces connect nanomaterials with biological systems, enabling communication and signal exchange at the cellular level. This review discusses how material choice, surface chemistry, and nanoscale topography shape their function, with applications in detecting bioelectrical signals in heart and brain tissue and probing biochemical signaling across cell membranes. It also highlights future challenges in fabrication and accessibility needed to advance nano–bio interface technologies. Must-read!

• Listening with Artificial Cilia: Have you wondered if you could create artificial ears? You don’t have to worry anymore! Inspired by cochlear hair cells, the authors of this paper developed 3D-printed artificial cilia arrays that mechanically decode sound frequencies (100–6,000 Hz) without electronics or algorithms. The micrometer-scale cilia respond to specific acoustic resonances, enabling direct recognition of sounds. In water, sound-triggered vibrations can also control drug release, successfully regulating blood glucose in diabetic mice.