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

Abstract

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, regulates 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. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=125 SRC="FIGDIR/small/733869v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@23ee9org.highwire.dtl.DTLVardef@1706336org.highwire.dtl.DTLVardef@181a241org.highwire.dtl.DTLVardef@1c374d8_HPS_FORMAT_FIGEXP M_FIG C_FIG Multiphase DNA-RNA artificial cells integrate a protective DNA shell, a transcriptionally active DNA core, and a functional RNA organelle. Spatial compartmentalization enables signal generation, external protein expression, and selective recapture via RNA aptamers.