Oligolysine Promotes and Inhibits DNA Condensate Formation

The formation of biomolecular condensates via phase separation relates to various cellular functions. Reconstituting these condensates with designed molecules allows for exploring their mechanisms and potential applications. Sequence-designed DNA nanostructures enable the investigation of the effects of structural design on condensate formation and construction of functional artificial condensates. Despite the high designability of DNA-based condensates, the presence of free nanostructures that do not assemble into condensates remains a challenge. Herein, we report the effects of cationic oligolysines on DNA condensate formation assembled from Y-shaped DNA nanostructures. Experimental results showed that DNA condensate formation was enhanced by adding oligolysines at an appropriate N/P ratio, the ratio of positively-charged amine groups (N) to negatively-charged nucleic acid phosphate groups (P), maintaining the sequence specificity of DNA. On the other hand, surprisingly, oligolysines significantly inhibited condensate formation depending on the N/P ratio and residue number, which was likely attributed to the deformation of the nanostructures induced by oligolysines. These results suggested that the amount and length of cationic peptides significantly affected the self-assembly of branched DNA nanostructures. We believe that this study will deepen our understanding of biomolecular condensates and provide insights for further development of DNA/peptide hybrid condensates to enhance the functions of artificial condensates for use in artificial cells and molecular robots.