Super-multiplexed optical imaging and barcoding with engineered polyynes

Optical multiplexing has a large impact in photonics, the life sciences and biomedicine. However, current technology is limited by a 'multiplexing ceiling' from existing optical materials. Here we engineered a class of polyyne-based materials for optical supermultiplexing. We achieved 20 distinct Raman frequencies, as 'Carbon rainbow', through rational engineering of conjugation length, bond-selective isotope doping and end-capping substitution of polyynes. With further probe functionalization, we demonstrated ten-color organelle imaging in individual living cells with high specificity, sensitivity and photostability. Moreover, we realized optical data storage and identification by combinatorial barcoding, yielding to our knowledge the largest number of distinct spectral barcodes to date. Therefore, these polyynes hold great promise in live-cell imaging and sorting as well as in high-throughput diagnostics and screening.

[1]  Dan Luo,et al.  Multiplexed detection of pathogen DNA with DNA-based fluorescence nanobarcodes , 2005, Nature Biotechnology.

[2]  Lu Wei,et al.  Live-cell imaging of alkyne-tagged small biomolecules by stimulated Raman scattering , 2014, Nature Methods.

[3]  Min Gu,et al.  Five-dimensional optical recording mediated by surface plasmons in gold nanorods , 2009, Nature.

[4]  Satoshi Kawata,et al.  Alkyne-tag Raman imaging for visualization of mobile small molecules in live cells. , 2012, Journal of the American Chemical Society.

[5]  Hongjie Dai,et al.  Multiplexed multicolor Raman imaging of live cells with isotopically modified single walled carbon nanotubes. , 2008, Journal of the American Chemical Society.

[6]  Robert McDonald,et al.  Synthesis, structure, and nonlinear optical properties of diarylpolyynes. , 2005, Organic letters.

[7]  Kang Sun,et al.  Suspension arrays based on nanoparticle-encoded microspheres for high-throughput multiplexed detection. , 2015, Chemical Society reviews.

[8]  Michael J. Ferguson,et al.  Evidence for solution-state nonlinearity of sp-carbon chains based on IR and Raman spectroscopy: violation of mutual exclusion. , 2009, Journal of the American Chemical Society.

[9]  Garry P Nolan,et al.  Fluorescent cell barcoding in flow cytometry allows high-throughput drug screening and signaling profiling , 2006, Nature Methods.

[10]  David G Spiller,et al.  Encoded microcarriers for high-throughput multiplexed detection. , 2006, Angewandte Chemie.

[11]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[12]  J. Paul Robinson,et al.  Stimulated Raman scattering flow cytometry for label-free single-particle analysis. , 2017, Optica.

[13]  C. Mirkin,et al.  Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. , 2002, Science.

[14]  Alex Rhee,et al.  Facile and rapid one-step mass preparation of quantum-dot barcodes. , 2008, Angewandte Chemie.

[15]  C. Castiglioni,et al.  Structure and chain polarization of long polyynes investigated with infrared and Raman spectroscopy , 2013 .

[16]  J. Paul Robinson,et al.  Tunable lifetime multiplexing using luminescent nanocrystals , 2013, Nature Photonics.

[17]  J. Derisi,et al.  Programmable Microfluidic Synthesis of Over One Thousand Uniquely Identifiable Spectral Codes , 2017, Advanced optical materials.

[18]  Seok Hyun Yun,et al.  Intracellular microlasers , 2015, Nature Photonics.

[19]  Kazuyoshi Itoh,et al.  High-speed molecular spectral imaging of tissue with stimulated Raman scattering , 2012, Nature Photonics.

[20]  Michael W. Davidson,et al.  Applying systems-level spectral imaging and analysis to reveal the organelle interactome , 2017, Nature.

[21]  Rafael Yuste,et al.  Super-multiplex vibrational imaging , 2017, Nature.

[22]  Wesley A. Chalifoux,et al.  Synthesis of polyynes to model the sp-carbon allotrope carbyne , 2010, Nature Chemistry.

[23]  B. Yakobson,et al.  Correction to Carbyne from First-Principles: Chain of C Atoms, a Nanorod or a Nanorope. , 2017, ACS nano.

[24]  A. Hirsch The era of carbon allotropes. , 2010, Nature materials.

[25]  S. Nie,et al.  Quantum-dot-tagged microbeads for multiplexed optical coding of biomolecules , 2001, Nature Biotechnology.

[26]  Satoshi Kawata,et al.  A sensitive and specific Raman probe based on bisarylbutadiyne for live cell imaging of mitochondria. , 2015, Bioorganic & medicinal chemistry letters.

[27]  G. Zerbi,et al.  Absolute Raman intensity measurements and determination of the vibrational second hyperpolarizability of adamantyl endcapped polyynes , 2012 .

[28]  Kevin M. Dean,et al.  Advances in fluorescence labeling strategies for dynamic cellular imaging. , 2014, Nature chemical biology.

[29]  Valerie B. Sitterle,et al.  Dye-labeled polystyrene latex microspheres prepared via a combined swelling-diffusion technique. , 2011, Journal of colloid and interface science.

[30]  Ping Wang,et al.  Microsecond scale vibrational spectroscopic imaging by multiplex stimulated Raman scattering microscopy , 2015, Light: Science & Applications.

[31]  Lu Wei,et al.  Multicolor Live-Cell Chemical Imaging by Isotopically Edited Alkyne Vibrational Palette , 2014, Journal of the American Chemical Society.

[32]  Chad A Mirkin,et al.  Glass-bead-based parallel detection of DNA using composite Raman labels. , 2006, Small.

[33]  M. Tommasini,et al.  Carbon-atom wires: 1-D systems with tunable properties. , 2016, Nanoscale.

[34]  Mortazavi,et al.  Supporting Online Material Materials and Methods Figs. S1 to S13 Tables S1 to S3 References Label-free Biomedical Imaging with High Sensitivity by Stimulated Raman Scattering Microscopy , 2022 .

[35]  M. Sauer,et al.  Multi-target spectrally resolved fluorescence lifetime imaging microscopy , 2016, Nature Methods.

[36]  Hoonkyung Lee,et al.  Carbyne from first principles: chain of C atoms, a nanorod or a nanorope. , 2013, ACS nano.