The DNA Matrix is a dynamic supramolecular adjuvant assembled from five short, unmodified DNA strands. Its right-handed colloidal architecture prolongs antigen retention and enhances lymphatic transport, thereby eliciting strong antibody responses through the TLR9–MyD88 pathway. This safe and multifunctional platform provides potent protection against both viral and bacterial infections, offering a promising strategy for next-generation vaccine design. We are currently optimizing DNA hydrogel sequences to understand how material properties influence immune activation, employing near-infrared (NIR) imaging to systematically evaluate the in vivo behavior of hydrogels with different sequence motifs (e.g., CpG vs. non-CpG) and physical characteristics (e.g., gel strength). These studies aim to elucidate the intrinsic link between antigen dynamics and carrier behavior, ultimately guiding the rational design of DNA hydrogel-based vaccines with enhanced immunogenicity and controlled antigen delivery.