RNA Organelles in DNA-Based Artificial Cells Provide Spatial Aptamer Functions and Enhanced Signal Processing

Naturally occurring biomolecular condensates orchestrate key cellular processes by creating spatially distinct reaction environments, yet engineering synthetic condensates that combine structural programmability with spatioselectively encoded function remains challenging. Here, we report multiphase DNA-RNA artificial cells (ACs) that embed functional RNA condensates as organelle-like compartments within programmable DNA core-shell ACs. A single thermal assembly protocol yields three-phase ACs comprising a glassy RNA core organelle embedded in a liquid-like DNA compartment, surrounded by a crosslinked DNA shell. The RNA organelles contain aptamer function, enabling selective protein recruitment and small-molecule activation, while the DNA scaffold provides independent addressability, modulates RNA-condensate size, and enhances resistance to serum-mediated degradation. We further show that RNA chemistry can be used to adjust environmental responsiveness: unmodified RNA organelles undergo rapid degradation in serum and release captured protein cargo, whereas 2'-fluoro-modified RNA organelles remain stable for at least 24 h. Finally, by coupling transcriptional modules localized in the DNA core to cell-free protein translation in the surrounding medium, we establish sender-receiver communication between AC populations and self-actuating signal processing within individual DNA-RNA ACs. These results establish hybrid nucleic-acid ACs as programmable, spatially organized systems that couple compartment architecture, RNA molecular recognition, and biochemical communication.