Light-activated, transcription-guided reconfiguration, aggregation, and intercommunication of structurally compartmentalized DNA condensates

A versatile concept for assembling photoresponsive microcompartmentalized phase-separated condensates as protocell models is introduced. The systems demonstrate the phototriggered activation of transcription machineries inducing dynamic switchable or transient spatiotemporal reconfiguration, aggregation/deaggregation, and intercommunication of microcompartmentalized condensates. The microcompartments are generated by competitive invasion of barcode-tethered cyanuric acid/polyadenine coacervates with o-nitrobenzyl phosphate ester caged DNA hairpin structures conjugated to strands exhibiting variable hybridization lengths to the barcode tethers. Photochemical uncaging of the hairpin structures results in the formation of constitutional compartments consisting of transcription templates or compartments composed of rearrangeable transcription template constituents. In the presence of T7 RNAp/NTPs, the transcription machineries in the respective compartments are activated, leading to RNA strands signaling dynamic reconfiguration of the microcompartments. By coupling RNase H to the T7 RNAp/NTP machineries, switchable or transient reconfiguration of the microcompartments is demonstrated. Moreover, by engineering a palindromic, self-complementary domain in one of the microcompartment constituents, cyclic switching or transient reconfiguration of the microcompartments, accompanied by reversible switchable/transient aggregation/deaggregation of the condensates, is demonstrated. Also, by employing two different microcompartmentalized condensates modified with complementary barcode tethers, aggregation of the condensates accompanied by the auxiliary transcription machinery-induced RNA-signaled intercommunication and reconfiguration of the two microcompartmentalized aggregated condensates is realized.