Spatially confined multivalent aptamers in the cavity of a DNA nanocage against bacterial superantigens infection

Aptamers as single-strand oligonucleotides obtained through in vitro screening techniques exhibit significant application potential due to their high target specificity, strong binding affinity, and inherent inhibitory capabilities. However, the easy entanglement among single-strand aptamers and excessive flexibility remains a huge challenge for keep high binding capabilities and dispersed spatial positioning in practical applications. Herein, we rationally designed a DNA nanocage structure loaded with multiple neutralizing aptamers (DNC-Apt). The programmability and the spatial confinement effect of DNC enable multiple single-strand aptamers to be reasonably fixed in the ideal spatial positions and achieve enhanced structural stability. Taking the enterotoxin A and B (SEs) secreted by Staphylococcus aureus as model target, both molecular docking and the ELONA experiment confirmed that the neutralizing aptamers integrated by this strategy achieved binding to different antigenic epitopes on SEs rely on spatially dispersed positioning, and exhibited enhanced binding ability (∼ 6 fold). The PBMC cell proliferation experiment demonstrated that this strategy could mediate the binding of SEs to receptors, thereby reducing the proliferation of T cells and the release of pro-inflammatory factors. Furthermore, the application of DNC-Apt in mice significantly reduced the inflammatory response and tissue damage caused by SEs. In conclusion, our research provided a reference for enhancing the application ability of aptamers and offered new strategies for alleviating the toxicity of bacterial toxins.