Genetically Encoded DNA-RNA Segregation Stimulates Biomimetic Multiphase Compartments

DNA and RNA are compartmentalized into distinct, heterogeneous structures within cells. However, the separation between RNA and DNA, especially in the absence of modern transcription machinery, is inherently hindered by thermodynamic constraints such as complementary base pairing and entropic mixing. Here, we demonstrate that atomic-level molecular difference between single-stranded DNA and RNA bearing identical sequences can drive the separation of DNA and RNA when complexed with peptides. This molecular mechanism is exploited to develop a family of oligonucleotides that enables DNA-RNA segregation within coacervates, resulting in a library of genetically encoded multiphase droplets containing coexisting DNA- and RNA-rich phases. These droplets emulate the structures and functions of multiphase nuclear compartments found in cells. Our results underscore the significance of pentose sugar mutation in DNA and RNA, which affect the genetic material organization in contemporary cells and could provide an evolutionary advantage during the transition from RNA to DNA genomes.