Immune-induced antibody-DNA hybrid condensates

We report here the combined use of Watson-Crick and antibody-antigen interactions to induce phase separation of DNA-antibody hybrid condensates. To achieve this, we have used an antigen-conjugated star-shaped DNA motif (nanostar) in which three arms terminate with single-stranded DNA sticky ends while the fourth arm is end-conjugated with a moiety (i.e. an antigen) that can be recognized by a specific bivalent antibody. Through the concerted action of selective Watson-Crick base pairing between the sticky ends and bivalent antibody-antigen binding, such antigen-conjugated nanostars phase-separate to form micron-scale hybrid condensates whose structural stability is provided by both nucleic acids and antibodies. We have demonstrated the specific and orthogonal antibody-induced phase separation of four different antigen-conjugated nanostars (biotin, DIG, DNP and MUC1) each with their corresponding antibody. By adding increasing concentrations of the specific antibody to a fixed concentration of antigen-conjugated nanostars (300 nM) we observe concentration-dependent formation of antibody-DNA condensates, starting at low nanomolar levels of the antibody. The DNA-antibody hybrid condensates are also reversible and can be cyclically formed/dissolved by the cyclic degradation/addition of the specific antibody. We qualitatively (and in some cases quantitatively) reproduce these results with an approach that conjugates theory and simulations of a phase-field model. The introduction of antibody-antigen interactions into the phase separation process of DNA brings these systems closer to natural cellular systems that rely on intricate networks of protein-protein or protein-nucleic acid interactions and allows for greater programmability and versatility that could have applications in sensing and drug delivery.