A DNA deliverer-receiver mechanism for DNA recruitment in phase-separated transcriptional condensates

DNA transcription is a complex process involving numerous components that can assemble into phase-separated transcriptional condensates. However, whether condensates formed by multiple transcription factors behave through simple additive effects or instead exhibit non-additive, emergent properties remains unclear. Here, we use large-scale molecular dynamics simulations to investigate how three core transcription factors regulating pluripotency and early embryonic development--Nanog, Oct4, and Sox2--organize biomolecular condensates in the absence and presence of DNA. We find that condensate formation is primarily driven by intrinsically-disordered-region-mediated interactions of Nanog and Sox2, each of which individually promotes Oct4 phase separation; by contrast, when Nanog and Sox2 coexist in the absence of DNA, Oct4 is less efficiently incorporated into condensates. In the presence of DNA, condensates display a distinct spatial organization: Nanog and Sox2 form dense, well-mixed clusters, whereas Oct4 remains more dispersed in interstitial regions where DNA preferentially localizes, resulting in [~]20% higher DNA content in Oct4-containing condensates. Notably, phase separation reshapes DNA-protein interaction landscapes, altering the intramolecular regions that engage DNA. Together, these results support a synergistic DNA deliverer-receiver mechanism and suggest that non-additive, multi-component condensate organization constitutes an additional layer of gene expression regulation beyond canonical transcription factor-DNA binding.