Protein microarrays with carbon nanotubes as multicolor Raman labels

Abstract

The current sensitivity of standard fluorescence-based protein detection limits the use of protein arrays in research and clinical diagnosis. Here, we use functionalized, macromolecular single-walled carbon nanotubes (SWNTs) as multicolor Raman labels for highly sensitive, multiplexed protein detection in an arrayed format. Unlike fluorescence methods, Raman detection benefits from the sharp scattering peaks of SWNTs with minimal background interference, affording a high signal-to-noise ratio needed for ultra-sensitive detection. When combined with surface-enhanced Raman scattering substrates, the strong Raman intensity of SWNT tags affords protein detection sensitivity in sandwich assays down to 1 fM—a three-order-of-magnitude improvement over most reports of fluorescence-based detection. We use SWNT Raman tags to detect human autoantibodies against proteinase 3, a biomarker for the autoimmune disease Wegener's granulomatosis, diluted up to 107-fold in 1% human serum. SWNT Raman tags are not subject to photobleaching or quenching. By conjugating different antibodies to pure 12C and 13C SWNT isotopes, we demonstrate multiplexed two-color SWNT Raman-based protein detection.

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Figure 1: Carbon nanotubes as Raman labels for protein microarray detection.
Figure 2: Highly selective recognition of surface-bound proteins by SWNT-antibody conjugates.
Figure 3: Femtomolar protein detection using SWNT Raman labels, compared with fluorescence-based protein microarray detection.
Figure 4: Calibration curve of mouse anti-human serum albumin measured in microarray format from nine duplicate protein spots at each analyte concentration by SWNT Raman tags.
Figure 5: Raman versus fluorescence-based protein microarray detection of aPR3, a biomarker for Wegener's granulomatosis, in human serum.
Figure 6: Multi-color SWNT Raman labels for multiplexed protein detection.

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Acknowledgements

This work was supported by the National Institutes of Health/National Cancer Institute–funded Center for Cancer Nanotechnology Excellence Focused on Therapeutic Response U54 CA119367 at Stanford University, and NIH-NCI R01 CA135109-01. The authors would like to thank Nozomi Nakayama-Ratchford and Sarunya Bangsaruntip for their assistance in developing carbon nanotube–protein conjugates.

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Contributions

Z.C. and S.M.T. contributed equally to the work, developing the SWNT passivation and conjugation schemes presented, as well as the procedure for obtaining SERS-active surfaces and the related protein immobilization methodology. A.P.G. contributed synthesis of 6-arm branched carboxy-PEG. M.G.K. and P.J.U. contributed to fluorescence-based detection of anti-proteinase 3. D.D. and Z.L. contributed by assisting in preparing SWNT-antibody and SWNT-peptide conjugates. X.W. and G.Z. contributed by assisting in the preparation of SERS-active substrates. X.L., K.J. and S.F. contributed by providing isotopomer SWNTs. H.D. designed the research and contributed much direction and assistance to this project.

Corresponding author

Correspondence to Hongjie Dai.

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Supplementary Figures 1–15, Supplementary Table 1, Supplementary Methods (PDF 724 kb)

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Chen, Z., Tabakman, S., Goodwin, A. et al. Protein microarrays with carbon nanotubes as multicolor Raman labels. Nat Biotechnol 26, 1285–1292 (2008). https://doi.org/10.1038/nbt.1501

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