Protein detection using proximity-dependent DNA ligation assays

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Abstract

The advent of in vitro DNA amplification has enabled rapid acquisition of genomic information. We present here an analogous technique for protein detection, in which the coordinated and proximal binding of a target protein by two DNA aptamers promotes ligation of oligonucleotides linked to each aptamer affinity probe . The ligation of two such proximity probes gives rise to an amplifiable DNA sequence that reflects the identity and amount of the target protein. This proximity ligation assay detects zeptomole (40 × 10−21 mol) amounts of the cytokine platelet-derived growth factor (PDGF) without washes or separations, and the mechanism can be generalized to other forms of protein analysis.

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Figure 1: Schematic view of the homodimeric PDGF-BB (ref. 23) bound by two aptamer-based proximity probes, A1 and A2, for detection by proximity ligation.
Figure 2: Optimization of reaction conditions for the proximity ligation assay.
Figure 3: Detection of a dilution series of PDGF-BB by proximity ligation (solid line) and by sandwich ELISA (dashed line).
Figure 4: Homogeneous detection of PDGF-BB in the presence of complex biological fluids and cell culture media: FCS, EMEM, and human CSF.
Figure 5: Detection of human α-thrombin by homogeneous proximity ligation.
Figure 6: Dilution series of PDGF-BB analyzed in a solid-phase assay, either by proximity ligation (circles) or by aptamer-based immuno-PCR (squares).

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Acknowledgements

Mats Nilsson and Carl-Henrik Heldin offered valuable comments on the manuscript. Olli Leppänen and Nils-Erik Heldin kindly supplied the PDGF β-receptor fragment and the SW-1736 cell line, respectively. Frida Berg contributed to the connector oligonucleotide studies. S.M.G. was funded by a Norfa stipend. The work was supported by the Beijer and Wallenberg Foundations, the Technical and Medical Research Councils of Sweden, the Swedish Cancer Fund, and by Polysaccharide Research AB (Uppsala).

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Correspondence to Ulf Landegren.

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