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Scientific Techniques Using Antibody-Oligonucleotide Conjugates
Antibody-Oligonucleotide Conjugate Technology Development
- Antibody-oligonucleotide conjugation has revolutionized molecular detection since the 1992 introduction of Immuno-PCR, achieving femtomolar sensitivity through DNA amplification.
- Proximity Ligation Assay (PLA) marked a crucial technological breakthrough in 2004, enabling detection of proteins in a "sandwich" format with 2 antibodies to improve specificity + being an early "no wash" assay.
- Technical evolution from streptavidin-biotin bridges to direct conjugation chemistry has dramatically improved signal-to-noise ratios while reducing sample requirements.
- Integration of next-generation sequencing as a readout methodology has supercharged these techniques, enabling massive multiplexing capabilities impossible with traditional PCR detection.
- This technological foundation continues to drive scientific progress, demonstrating how innovative tools enable new scientific possibilities. "Progress depends on the interplay of techniques, discoveries, and ideas, probably in that order." - Sydney Brenner.
Intro and purpose
- This summary table catalogs key scientific techniques employing antibody-oligonucleotide conjugates, spanning from early detection methods to advanced spatial and multi-omics technologies.
- We aim to continuously update this resource as new methods emerge and existing techniques evolve.
- Future versions will include expanded technical details of oligo design, comparative sensitivity/specificity metrics, and emerging commercial applications.
Comprehensive Classification Table
| Technique | Primary Purpose | Mechanism | Key Applications | Readout Method | Sample Type | First Published | Notable References |
|---|---|---|---|---|---|---|---|
| IN-DEPTH | Multiplexed spatial analysis of proteins and RNAs | Antibody-oligo conjugates for proteomic mapping + RNA probes for transcriptomic analysis | High-resolution spatial mapping of multiple proteins and the transcriptome | Fluorescence imaging + NGS sequencing | Tissue sections | 2024 | Yeo et al, bioRxiv 2024 |
| MERFISH-Protein | Spatially resolved, multiplexed protein detection | Adaptation of MERFISH for protein detection using antibody-oligo conjugates | High-resolution spatial mapping of multiple proteins | Fluorescence imaging | Tissue sections | 2023 | Wang et al, SFN 2023 |
| Digital Spatial Profiling (DSP) | Multiplexed spatial quantification of proteins and RNAs | UV-cleavable oligo tags on antibodies or RNA probes; oligos released and quantified | Spatial profiling of up to 44 proteins and 1,412 genes in FFPE tissues | NGS sequencing | FFPE tissue sections | 2019 | Merritt et al, Nature Biotechnology (2019) |
| Immuno-SABER | Signal amplification for spatial protein detection | DNA concatemers for signal amplification; DNA-barcoded antibodies imaged via iterative fluorescence cycles | High-resolution spatial mapping of proteins in tissues | Fluorescence imaging | Tissue sections | 2019 | Saka et al, Nature Biotechnology (2019) |
| Immuno-PCR (IPCR) | Increased sensitivity vs ELISA | Biotinylated DNA + streptavidin-Protein A + Antibody-PCR amplification | Protein detection at femtomolar/attomolar levels; pathogen detection | PCR-Based | Solution-Phase | 1992 | Sano et al., Science (1992) |
| Proximity Ligation Assay (PLA) | Protein detection | Antibody pairs with attached oligos brought into proximity allow DNA ligation and amplification | Protein-protein interactions; post-translational modifications; multiplexed detection using qPCR in 2007 | PCR-Based | Solution-Phase | 2006 | Gullberg et al (2004); Fredriksson et al (2007) |
| In situ PLA | Visualization of proteins and protein-protein interactions in tissue | Version of PLA. Rolling Circle Amplification then fluorescent oligos for visualization | Tissue-specific protein interactions; cancer biomarkers | Microscopy-Based | Fixed Cells/Tissues | 2006 | Söderberg et al., Nature Methods (2006); Klaesson et al., Scientific Reports (2018) |
| Proximity Extension Assay (PEA) | Multiplex protein detection | Paired antibodies with DNA tags but using polymerase not ligase | Biomarker discovery; proteomics; multiplexed assays | PCR-Based; NGS-Based | Solution-Phase | 2011 | Lundberg et al 2011; Assarsson et al., PLoS One (2014) |
| DNA-PAINT | Super-resolution imaging | Transient binding of fluorescent oligos to antibody-coupled DNA docking strands | Nanoscale imaging; subcellular structures; protein complexes | Microscopy-Based | Fixed Cells/Tissues | 2010 | Schnitzbauer et al., Nature Protocols (2017) |
| CODEX (CO-Detection by indEXing) | Highly multiplexed imaging | Sequential imaging using DNA-barcoded antibodies and cyclic nucleotide exchange | Spatial proteomics; tumor microenvironment; cell atlases | Microscopy-Based | Spatially-Resolved Tissue | 2018 | Goltsev et al., Cell (2018) |
| CITE-seq/REAP-seq | Simultaneous protein-RNA profiling | Antibody-oligos detected alongside transcriptome in single cells | Cell atlas building; immunology; cancer heterogeneity | NGS-Based | Single-Cell Suspensions | 2017 | Stoeckius et al., Nature Methods (2017); Peterson et al., Nature Biotechnology (2017) |
| Spatial-CITE-seq | Spatial protein-RNA co-mapping | Integration of spatial transcriptomics with CITE-seq | Spatial cell typing; tissue microenvironment; developmental biology | NGS-Based | Resolved Tissue | 2023 | Liu et al., Nature Biotechnology (2023) |