Biological cells display complex internal architectures, with distinct micro environments that establish the chemical heterogeneity needed to sustain cellular functions. The continued efforts to create advanced cell mimics - artificial cells - demands strategies to robustly engineer micro-compartmentalised architectures, where the molecular makeup of distinct regions is coupled with localised functionalities. Here, we introduce a platform for constructing membrane-less artificial cells from the self-assembly of synthetic DNA nanostructures, in which internal domains can be established thanks to a rationally designed reaction-diffusion process. The method, rationalised through numerical modelling, enables the formation of up to five distinct and addressable environments, in which functional moieties can be localised. As a proof-of-concept, we apply this platform to build artificial cells in which a prototypical nucleus synthesises fluorescent RNA aptamers, which then accumulate in a surrounding storage shell, thus demonstrating spatial segregation of functionalities reminiscent of that observed in biological cells.