Evaluation of FRET X for single-molecule protein fingerprinting
Carlos de Lannoy (Wageningen University & Research)
M. Filius (Kavli institute of nanoscience Delft, TU Delft - BN/Chirlmin Joo Lab)
Raman van Wee (Kavli institute of nanoscience Delft, TU Delft - BN/Chirlmin Joo Lab)
Chirlmin Joo (TU Delft - BN/Chirlmin Joo Lab, Kavli institute of nanoscience Delft)
Dick de Ridder (Wageningen University & Research)
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Abstract
Single-molecule protein identification is an unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands and accumulated FRET efficiencies constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines, and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics.
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