Modular DNA Barcoding of Nanobodies Enables Multiplexed in situ Protein Imaging and High-throughput Biomolecule Detection (PRJCA018693)

The antibody-antigen interaction-based immunodetection methods are routinely used in biological and clinical laboratories. DNA-labeled antibodies have the advantage of detecting multiple target molecules simultaneously via orthogonal DNA barcode sequences. However, current antibody-DNA conjugation commonly uses non-site-specific modifications tailor-made for each specific application, which is laborious and often compromises antibody affinity and specificity. To overcome these limitations, here we introduce a simple, precise, and cost-efficient DNA barcoding strategy - multiplexed and modular barcoding of antibodies (MaMBA). Via nanobodies as the modular adaptor, MaMBA enables direct site-specific labeling to off-the-shelf IgG antibodies with one-component design. We first used MaMBA to develop the misHCR method for highly multiplexed in situ protein imaging via orthogonal hybridization chain reaction (HCR). A cleavable version of MaMBA allows iterative employment of the same HCR probes sets and thus further enhances the multiplexity of misHCR (misHCRn). misHCRn achieves simultaneous labeling of 12 different target molecules within the same mouse brain sections. We next extended the cleavable MaMBA to develop the barcode-linked immunosorbent assay (BLISA) for multiplexed and high-throughput biomolecule detections. By combining BLISA and the next-generation sequencing, we successfully measured SARS-CoV-2 IgG and HBV-associated antigens in a large number of human serum samples. Thus, MaMBA offers a highly modular and easily adaptable approach for antibody DNA-barcoding, which can be broadly applied in basic research and clinical diagnostics.