Sequence-encoded interactions program internal condensate architecture

Many cellular condensates, such as the nucleolus and stress granules, contain multiple coexisting phases with distinct compositions and material properties. This internal organization is crucial for function, yet how it is established remains unclear. Here, using a programmable DNA system, we reveal how molecular interactions can precisely encode multiphase architecture. We find that phase separation drives macromolecules into a semi-dilute regime where subtle differences in homotypic interaction energies are amplified into dominant organizational forces. A critical interaction energy threshold must be overcome to trigger internal demixing, after which molecular partitioning scales near-linearly with interaction strength. This universal relationship is captured by an associative polymer model, and enables engineering of condensates with up to four coexisting phases exhibiting 100-fold differences in viscosity within the same droplet. These design principles extend to RNA-peptide systems, establishing a general framework for how sequence can program hierarchical self-assembly and organize biological matter.