Efficient Small-Scale Conjugation of DNA to Primary Antibodies for Multiplexed Cellular Targeting

The combination of the specificity of antibodies and the programmability of DNA nanotechnology has provided the scientific community with a powerful tool to label and unambiguously distinguish a large number of subcellular targets using fluorescence-based read-out methods. Whereas primary antibodies are commercially available for a large class of targets, a general stoichiometric site-selective DNA labeling strategy for this affinity reagent is lacking. Here we present a universal, site selective conjugation method using a small photo-cross-linkable protein G adaptor that allows labeling of antibodies of different host species with a controlled number of short oligonucleotides (ODNs). Importantly, we illustrate that this conjugation method can be directly performed on commercially available primary antibodies on a small scale and without cross-reactivity towards bovine serum albumin. In addition, we present a general benchtop-compatible strategy to purify DNA-labeled antibodies without a loss of function. The application of protein G-ODN-labeled primary antibodies is demonstrated by employing three well-known methods for detecting subcellular targets using fluorescence read-out, including flow cytometry, DNA-PAINT, and dSTORM. This work thus establishes a general and efficient platform for the synthesis of a library of unique ODN-antibody conjugates, facilitating the broader use of DNA-based programmable tags for multiplexed labeling to identify subcellular features with nanometer precision and improving our understanding of cellular structure and function.