Biomolecular condensates are involved in everything: protein expression, stress responses, and disease processes. And I didn’t even study them!
Can we create a synthetic version of these membraneless organelles, made only with RNA?
Today’s paper takes a shot at it!
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RNA Goes Condensing
Researchers created artificial RNA condensates that form programmable membraneless organelles inside cells.
Biomolecular Condensates: Membraneless Organelles
Cells are complicated.
Proteins moving around, nutrients getting in and out, and organelles working… all at once! It’s fascinating. And we keep discovering new pathways, new proteins, and even whole new organelles (the nitroplast!).
Take biomolecular condensates.
These are membraneless organelles that form via liquid-liquid phase separation. Instead of being wrapped in a lipid membrane, cells can form temporary, functional “droplets” that concentrate proteins and RNA to get work done.
For a long time, we didn’t even know about them!
Scientists were convinced that everything in a cell had to be separated by a lipid membrane. But around 2009, scientists realized that proteins and RNA can cluster through weak interactions and form distinct phases with different compositions.
From then on, everything opened up.
Researchers discovered biomolecular condensates everywhere: stress granules, P-bodies, glycogen granules, and more! They’re central to gene expression, stress responses, and many disease processes.
As you can imagine, scientists started asking: Can we build artificial condensates to control cellular behaviour? The dream? Being able to control their compositions, elastic properties, and localization… All at once!
Today, you have 2 options:
Protein-based condensates: Useful, but based on weak and promiscuous interactions → hard to control
RNA-based condensates: Can be designed much more rationally using RNA nanostars
We have a clear winner here! The problem? Most RNA condensate systems have only been tested outside of cells.
Bringing Nanostars into Cells
This is exactly what today’s paper sets out to solve!
The authors show that RNA nanostars can be used to build condensates inside living mammalian cells! And these condensates can be programmed to:
form in the nucleus or cytoplasm,
mix or stay separate,
recruit proteins, small molecules, and even other RNAs!
A whole new way to control matter inside cells, with sequence and geometry working together to determine where the condensates form and what they do!
But first: what are RNA nanostars?
RNA Nanostars: Single-Stranded Building Blocks
RNA nanostars are the core building block of the system.
Each is a short RNA strand that folds into a star-like structure with three or more arms. These arms interact through kissing loops (KLs), which are sequence-specific loop–loop interactions.
Because the KLs are programmable, you can make different nanostars:
interact with each other
ignore each other
or recruit other molecules
The researchers express the nanostars in mammalian cells using the Tornado circular RNA expression system. Once inside the cells, the nanostars self-assemble via KL interactions and form membraneless cellular compartments!
The arms can also have extra functions:
Fluorogenic aptamers for visualization: Broccoli → green fluorescence, Pepper → red fluorescence, Mango → yellow fluorescence.
Aptamers for binding to small molecules, proteins, or intracellular RNA
A completely modular system! You can change everything:
arm length
arm number
KL sequence → binding strength
linker presence or absence
The result? The authors can program condensate abundance, mixing, and localization!
What They Built: Basic RNA Condensates in Cells
The team started simple.
The first demonstration uses a 3-arm nanostar with 15-nt arms, a KL variant A, and a Broccoli aptamer. This system produced condensates in HEK293T, HeLa, and U-2 OS cells. So yes, they really can create condensates inside cells!
They compared with controls:
Only circularized Broccoli: much fewer granules than designed RNA
Removing KLs: no full droplets → only shells
This confirms that loop-loop interactions are driving condensation.
But the droplets are not just pretty.
The researchers also showed that nanostars can recruit guest proteins. It works like this:
One nanostar carries the MS2 aptamer → it binds to the MS2 coat protein (MCP)
Co-express MCP-mCherry (red fluorescence) and the RNA-aptamer nanostar
MCP-mCherry is pulled into the RNA condensate! You see some nice red-and-green fluorescence.
And without the MS2 aptamer? No co-localization. This is strong proof that these are not just passive RNA clumps: they work as programmable molecular compartments!
Programming RNA Condensates
The team modified the system to show how the RNA condensate can be programmed.
Programming Intracellular Localization
The coolest result is that you can control the intracellular localization of the condensates. This is important because cells are spatially organized systems. A condensate in the nucleus is not the same as one in the cytoplasm!
Condensate formation is a balance of:
transcription in the nucleus
export through nuclear pores
cytoplasmic degradation
and phase separation once concentration exceeds a threshold
All this can be tuned by design! 3 design principles:
Longer arms (10 to 25 nt) → nuclear enrichment
More arms (2 to 4) → nuclear enrichment
Stronger KLs → you know it, nuclear enrichment
The team systematically changed these parameters and explored the results. A few examples:
10-nt arm nanostars form condensates only in the cytoplasm.
15-nt and 20-nt arm nanostars form nuclear condensates first, and later accumulate more in the cytoplasm.
Switching from a weaker KL to a stronger KL increases nuclear enrichment.
Controlling miscibility, subpopulations, and subcompartments
The next big advance is mixing control.
The authors first show a two-nanostar system with complementary KLs and different fluorescent aptamers. The condensates only appear when both nanostars are present! Orthogonal and sequence-specific interactions.
Then, they built a 3-nanostar system using different palindromic KLs (A, B, C) and different aptamers (Broccoli, Pepper, Mango). These nanostars form separate, non-mixing condensates when co-expressed!
And the subcellular localization can still be tuned independently.
But why not connect them? The authors added RNA linkers carrying two KLs, allowing otherwise non-mixing condensates to connect. You get some amazing overlapping fluorescence! And the mixing is controlled by the number of arms in the linker (2 vs 4).
This gives the system a real “organelle-with-subcompartments” feel. You can build condensates that:
stay separate,
partially contact one another,
or fully mix,
depending on the linker.
Functional proof: recruiting RNA in trans
Finally, they showed some (early) functional proof: cellular RNA recruitment.
The simplest version uses a target RNA that contains a KL complementary to the condensate KL. The target RNA colocalized with the condensates only when both sides have matching KLs. If the KL is missing on either side → no co-localization.
The more general version has a 21-nt hybridization domain on the nanostar that binds a matching sequence on a target RNA. Here, standard base pairing recruits the target: the authors show that colocalization occurs only when the target RNA carries the matching sequence!
Artificial RNA Condensates: a Powerful New Tool?
I love papers with great figures! And this one has many.
And it also brings a super cool design framework for making RNA condensates that work inside cells. Oh, and programmable ones! You can control:
localization,
mixing behavior,
internal subcompartments,
and recruitment specificity.
This is a completely new way to manipulate intracellular RNA! It could help regulate processes like rRNA processing and mRNA translation. And who knows where this could be useful: drugs, bioprocesses, controlled materials!
The authors point out some limitations:
There is always some shell-like structure (empty structure). We still don’t understand RNA biophysics in cells!
High expression of circular RNA creates metabolic stress. There is no toxicity or immunogenicity (they checked), but still.
Target RNA recruitment by hybridization is powerful, but it might not work on every target.
All things considered, a cool paper! Go read it here.
If you made it this far, thank you! What do you think of RNA nanotech? Do you think it has a place in biomedicine? Reply and let me know!
P.S: Know someone interested in RNA nanotech and SynBio? Share it with them!
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