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Optical sequencing of single synthetic polymers

Nature Chemistry volume 16, pages 210–217 (2024)Cite this article

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Abstract

Microscopic sequences of synthetic polymers play crucial roles in the polymer properties, but are generally unknown and inaccessible to traditional measurements. Here we report real-time optical sequencing of single synthetic copolymer chains under living polymerization conditions. We achieve this by carrying out multi-colour imaging of polymer growth by single catalysts at single-monomer resolution using CREATS (coupled reaction approach toward super-resolution imaging). CREATS makes a reaction effectively fluorogenic, enabling single-molecule localization microscopy of chemical reactions at higher reactant concentrations. Our data demonstrate that the chain propagation kinetics of surface-grafted polymerization contains temporal fluctuations with a defined memory time (which can be attributed to neighbouring monomer interactions) and chain-length dependence (due to surface electrostatic effects). Furthermore, the microscopic sequences of individual copolymers reveal their tendency to form block copolymers, and, more importantly, quantify the size distribution of individual blocks for comparison with theoretically random copolymers. Such sequencing capability paves the way for single-chain-level structure–function correlation studies of synthetic polymers.

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Fig. 1: CREATS for single-molecule super-resolution imaging of ROMP at high monomer concentrations.
Fig. 2: Super-resolution imaging of single-polymer growth at single-monomer resolution.
Fig. 3: Single-catalyst polymerization kinetics and dynamics at single-monomer resolution.
Fig. 4: Single copolymer sequencing.

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Data availability

All data are available in the main text or the Supplementary Information. Raw data supporting the findings of this study are available upon reasonable request. Source data are provided with this paper.

Code availability

MATLAB codes are included in Supplementary Software 1.

References

  1. Odian, G. In Principles of Polymerization 1–38 (Wiley, 2004).

  2. Korley, L. T. J., Epps, T. H., Helms, B. A. & Ryan, A. J. Toward polymer upcycling-adding value and tackling circularity. Science 373, 66–69 (2021).

    Article  ADS  CAS  PubMed  Google Scholar 

  3. Urban, M. W. et al. Key-and-lock commodity self-healing copolymers. Science 362, 220–225 (2018).

    Article  ADS  CAS  PubMed  Google Scholar 

  4. Lutz, J.-F., Ouchi, M., Liu, D. R. & Sawamoto, M. Sequence-controlled polymers. Science 341, 1238149 (2013).

    Article  PubMed  Google Scholar 

  5. Harris, T. D. et al. Single-molecule DNA sequencing of a viral genome. Science 320, 106–109 (2008).

    Article  ADS  CAS  PubMed  Google Scholar 

  6. Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009).

    Article  ADS  CAS  PubMed  Google Scholar 

  7. Alfaro, J. A. et al. The emerging landscape of single-molecule protein sequencing technologies. Nat. Methods 18, 604–617 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).

    Article  ADS  PubMed  Google Scholar 

  9. Sims, P. A., Greenleaf, W. J., Duan, H. & Xie, X. S. Fluorogenic DNA sequencing in PDMS microreactors. Nat. Methods 8, 575–580 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Reed, B. D. et al. Real-time dynamic single-molecule protein sequencing on an integrated semiconductor device. Science 378, 186–192 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  11. Dahlhauser, S. D. et al. Molecular encryption and steganography using mixtures of simultaneously sequenced, sequence-defined oligourethanes. ACS Cent. Sci. 8, 1125–1133 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Bazzi, H. S., Bouffard, J. & Sleiman, H. F. Self-complementary ABC triblock copolymers via ring-opening metathesis polymerization. Macromolecules 36, 7899–7902 (2003).

    Article  ADS  CAS  Google Scholar 

  13. Shin, S.-H. & Bayley, H. Stepwise growth of a single polymer chain. J. Am. Chem. Soc. 127, 10462–10463 (2005).

    Article  CAS  PubMed  Google Scholar 

  14. Pulcu, G. S. et al. Single-molecule kinetics of growth and degradation of cell-penetrating poly(disulfide)s. J. Am. Chem. Soc. 141, 12444–12447 (2019).

    Article  CAS  PubMed  Google Scholar 

  15. Guo, W. et al. Visualization of on-surface ethylene polymerization through ethylene insertion. Science 375, 1188–1191 (2022).

    Article  ADS  CAS  PubMed  Google Scholar 

  16. Liu, C. et al. Single polymer growth dynamics. Science 358, 352–355 (2017).

    Article  ADS  CAS  PubMed  Google Scholar 

  17. Liu, C. et al. Real-time single-polymer growth towards single-monomer resolution. Trends Chem. 3, 318–331 (2021).

    Article  CAS  Google Scholar 

  18. Edman, L., Földes-Papp, Z., Wennmalm, S. & Rigler, R. The fluctuating enzyme: a single molecule approach. Chem. Phys. 247, 11–22 (1999).

    Article  CAS  Google Scholar 

  19. Flomenbom, O. et al. Stretched exponential decay and correlations in the catalytic activity of fluctuating single lipase molecules. Proc. Natl Acad. Sci. USA 102, 2368–2372 (2005).

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  20. English, B. P. et al. Ever-fluctuating single enzyme molecules: Michaelis–Menten equation revisited. Nat. Chem. Biol. 2, 87–94 (2006).

    Article  CAS  PubMed  Google Scholar 

  21. Roeffaers, M. B. J. et al. Spatially resolved observation of crystal-face-dependent catalysis by single turnover counting. Nature 439, 572–575 (2006).

    Article  ADS  CAS  PubMed  Google Scholar 

  22. Xu, W., Kong, J. S., Yeh, Y.-T. E. & Chen, P. Single-molecule nanocatalysis reveals heterogeneous reaction pathways and catalytic dynamics. Nat. Mater. 7, 992–996 (2008).

    Article  ADS  CAS  PubMed  Google Scholar 

  23. Naito, K., Tachikawa, T., Fujitsuka, M. & Majima, T. Real-time single-molecule imaging of the spatial and temporal distribution of reactive oxygen species with fluorescent probes: applications to TiO2 photocatalysts. J. Phys. Chem. C 112, 1048–1059 (2008).

    Article  CAS  Google Scholar 

  24. Easter, Q. T. & Blum, S. A. Single turnover at molecular polymerization catalysts reveals spatiotemporally resolved reactions. Angew. Chem. Int. Ed. 56, 13772–13775 (2017).

    Article  CAS  Google Scholar 

  25. Yu, D., Garcia, A. I. V., Blum, S. A. & Welsher, K. D. Growth kinetics of single polymer particles in solution via active-feedback 3D tracking. J. Am. Chem. Soc. 144, 14698–14705 (2022).

    Article  CAS  PubMed  Google Scholar 

  26. Eivgi, O. & Blum, S. A. Exploring chemistry with single-molecule and -particle fluorescence microscopy. Trends Chem. 4, 5–14 (2022).

    Article  CAS  Google Scholar 

  27. Wang, S. et al. Surface-grafting polymers: from chemistry to organic electronics. Mater. Chem. Front. 4, 692–714 (2020).

    Article  CAS  Google Scholar 

  28. Barbey, R. et al. Polymer brushes via surface-initiated controlled radical polymerization: synthesis, characterization, properties and applications. Chem. Rev. 109, 5437–5527 (2009).

    Article  CAS  PubMed  Google Scholar 

  29. Bielawski, C. W. & Grubbs, R. H. Living ring-opening metathesis polymerization. Prog. Polym. Sci. 32, 1–29 (2007).

    Article  CAS  Google Scholar 

  30. Kobayashi, T. et al. Highly activatable and environment-insensitive optical highlighters for selective spatiotemporal imaging of target proteins. J. Am. Chem. Soc. 134, 11153–11160 (2012).

    Article  CAS  PubMed  Google Scholar 

  31. Yildiz, A. & Selvin, P. R. Fluorescence imaging with one nanometer accuracy: application to molecular motors. Acc. Chem. Res. 38, 574–582 (2005).

    Article  CAS  PubMed  Google Scholar 

  32. Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).

    Article  ADS  CAS  PubMed  Google Scholar 

  33. Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–796 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Su, L. et al. Super-resolution localization and defocused fluorescence microscopy on resonantly coupled single-molecule, single-nanorod hybrids. ACS Nano 10, 2455–2466 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Vougioukalakis, G. C. & Grubbs, R. H. Ruthenium-based heterocyclic carbene-coordinated olefin metathesis catalysts. Chem. Rev. 110, 1746–1787 (2010).

    Article  CAS  PubMed  Google Scholar 

  36. Lu, H. P., Xun, L. & Xie, X. S. Single-molecule enzymatic dynamics. Science 282, 1877–1882 (1998).

    Article  ADS  CAS  PubMed  Google Scholar 

  37. Sanford, M. S., Love, J. A. & Grubbs, R. H. Mechanism and activity of ruthenium olefin metathesis catalysts. J. Am. Chem. Soc. 123, 6543–6554 (2001).

    Article  CAS  PubMed  Google Scholar 

  38. Moritz, R. et al. Ion size approaching the bjerrum length in solvents of low polarity by dendritic encapsulation. Macromolecules 47, 191–196 (2014).

    Article  ADS  CAS  Google Scholar 

  39. Mutlu, H. & Lutz, J.-F. Reading polymers: sequencing of natural and synthetic macromolecules. Angew. Chem. Int. Ed. 53, 13010–13019 (2014).

    Article  CAS  Google Scholar 

  40. Grimm, J. B. et al. Bright photoactivatable fluorophores for single-molecule imaging. Nat. Methods 13, 985–988 (2016).

    Article  CAS  PubMed  Google Scholar 

  41. Lin, T.-P. et al. Control of grafting density and distribution in graft polymers by living ring-opening metathesis copolymerization. J. Am. Chem. Soc. 139, 3896–3903 (2017).

    Article  CAS  PubMed  Google Scholar 

  42. Chang, A. B. et al. Design, synthesis and self-assembly of polymers with tailored graft distributions. J. Am. Chem. Soc. 139, 17683–17693 (2017).

    Article  CAS  PubMed  Google Scholar 

  43. Hilburg, S. L., Ruan, Z., Xu, T. & Alexander-Katz, A. Behavior of protein-inspired synthetic random heteropolymers. Macromolecules 53, 9187–9199 (2020).

    Article  ADS  CAS  Google Scholar 

  44. Herman, T. K., Mackowiak, S. A. & Kaufman, L. J. High power light emitting diode based setup for photobleaching fluorescent impurities. Rev. Sci. Instrum. 80, 016107 (2009).

    Article  ADS  PubMed  Google Scholar 

  45. Ng, J. D. et al. Single-molecule investigation of initiation dynamics of an organometallic catalyst. J. Am. Chem. Soc. 138, 3876–3883 (2016).

    Article  CAS  PubMed  Google Scholar 

  46. Kozma, I. Z., Krok, P. & Riedle, E. Direct measurement of the group-velocity mismatch and derivation of the refractive-index dispersion for a variety of solvents in the ultraviolet. J. Opt. Soc. Am. B 22, 1479–1485 (2005).

    Article  ADS  CAS  Google Scholar 

  47. Chen, T.-Y. et al. Concentration- and chromosome-organization-dependent regulator unbinding from DNA for transcription regulation in living cells. Nat. Commun. 6, 7445 (2015).

    Article  ADS  PubMed  Google Scholar 

  48. Chen, P. & Chen, T.-Y. MATLAB code package: iQPALM (image-based quantitative photo-activated localization microscopy) https://doi.org/10.6084/m9.figshare.12642617.v1 (2020).

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Acknowledgements

This research was supported by the Army Research Office (grant no. W911NF-18-1-0217). R.Y. acknowledges support from a Cornell Presidential Postdoctoral Fellowship. This work made use of the NMR and Chemistry Mass Spectrometry Facilities at Cornell University, which is supported, in part, by the National Science Foundation (NSF) under award CHE-1531632. The research was carried out using Cornell Center for Materials Research Shared Facilities supported by the NSF (grant no. DMR-1719875).

Author information

Author notes

  1. Rong Ye

    Present address: Department of Chemical Engineering and Catalysis Science and Technology Institute, University of Michigan, Ann Arbor, MI, USA

  2. Xiangcheng Sun

    Present address: Department of Chemical Engineering, Rochester Institute of Technology, Rochester, NY, USA

  3. Xianwen Mao

    Present address: Department of Materials Science and Engineering, Institute of Functional Intelligent Materials, and Centre for Advanced 2D Materials, National University of Singapore, Singapore, Singapore

  4. Susil Baral

    Present address: Department of Chemistry, Illinois State University, Normal, IL, USA

  5. Chunming Liu

    Present address: School of Polymer Science and Polymer Engineering and Department of Chemistry, University of Akron, Akron, OH, USA

  6. These authors contributed equally: Rong Ye, Xiangcheng Sun, Xianwen Mao.

Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA

    Rong Ye, Xiangcheng Sun, Xianwen Mao, Felix S. Alfonso, Susil Baral, Chunming Liu, Geoffrey W. Coates & Peng Chen

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Contributions

R.Y. improved the experimental design, performed imaging experiments and bulk polymerization, coded software, analysed data and performed simulations. X.S. designed, synthesized and characterized the caged monomers, characterized the monomer uncaging and polymerization reactivity, and performed early imaging experiments. X.M. developed the data analysis pipeline, coded software and analysed data. F.S.A. synthesized and characterized the catalyst labelling reagent. S.B. contributed to the bulk polymerization experiment and NMR characterization. C.L. contributed to early-stage data analysis. G.W.C. contributed to discussions. R.Y. and P.C. wrote the main text. R.Y., X.S., X.M., F.S.A. and P.C. wrote the Supplementary Information. P.C. conceived and directed the research.

Corresponding author

Correspondence to Peng Chen.

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Competing interests

Cornell University has filed a US patent application (no. 18/144,022) with P.C., R.Y., X.S. and X.M. as inventors, based on this research, including the methodology and potential applications. The remaining authors declare no competing interests.

Peer review

Peer review information

Nature Chemistry thanks Johan Hofkens and the other, anonymous, reviewer for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–43, Discussion, Tables 1–3 and Schemes 1–6.

Supplementary Software 1

Software for data analysis and simulation.

Source data

Source Data Fig. 1

Normalized spectra (1g-h) and time-intensity raw data (1i).

Source Data Fig. 2

Positions of marker particles/catalysts (2a,e,i,j); background-subtracted fluorescence trajectory (2b-c,f,g); raw data of histograms (2d,h).

Source Data Fig. 3

Statistical source data and averaged data for kinetics (3a-b,e-f), raw data for histograms (3c-d).

Source Data Fig. 4

Positions of marker particles/catalysts (4a); background-subtracted fluorescence trajectory (4b); raw data for histograms (4d); statistical source data or averaged data (4e-j).

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Ye, R., Sun, X., Mao, X. et al. Optical sequencing of single synthetic polymers. Nat. Chem. 16, 210–217 (2024). https://doi.org/10.1038/s41557-023-01363-2

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