Protein recognition by a pattern-generating fluorescent molecular probe


Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical ‘noses/tongues’). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

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Figure 1: Distinct approaches for recognizing proteins with fluorescent molecular probes.
Figure 2: Chemical structure of the ID-probe.
Figure 3: Identifying MMPs, GSTs and PDGF in mixtures.
Figure 4: Recycling the ID-probe.
Figure 5: Tracking binding interactions and screening for new inhibitors.
Figure 6: Characterizing intracellular states of individual living cells.


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The authors thank I. Sagi for kindly donating MMP-12 and MMP-14. This research was supported by the European Research Council Starting Grant 338265. We thank G. Cohen (Grand Israel National Center for Personalized Medicine) for her help in performing the HTS experiments and O. Matalon (Department Structural Biology) for assisting in cell imaging.

Author information




Z.P., L.M. and D.M. conceived the research; Z.P. synthesized the probe, performed the experiments and analysed the data. Z.P., R.P.-N. and T.I. carried out the cell-culture work and IF assays. Z.P., J.M.G. and V.K. performed the confocal fluorescence microscopy experiments. T.U. cloned and expressed the GSTs. Z.P. and H.M.B. performed the HTS assays. Z.P., H.M.B. and B.M. analysed the HTS data. The manuscript was written by Z.P., L.M. and D.M.

Corresponding author

Correspondence to David Margulies.

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The authors declare no competing financial interests.

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Pode, Z., Peri-Naor, R., Georgeson, J. et al. Protein recognition by a pattern-generating fluorescent molecular probe. Nature Nanotech 12, 1161–1168 (2017).

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