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Reagentless biomolecular analysis using a molecular pendulum

Nature Chemistry volume 13, pages 428–434 (2021)Cite this article

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Abstract

The development of reagentless sensors that can detect molecular analytes in biological fluids could enable a broad range of applications in personalized health monitoring. However, only a limited set of molecular inputs can currently be detected using reagentless sensors. Here, we report a sensing mechanism that is compatible with the analysis of proteins that are important physiological markers of stress, allergy, cardiovascular health, inflammation and cancer. The sensing method is based on the motion of an inverted molecular pendulum that exhibits field-induced transport modulated by the presence of a bound analyte. We measure the sensor’s electric field-mediated transport using the electron-transfer kinetics of an attached reporter molecule. Using time-resolved electrochemical measurements that enable unidirectional motion of our sensor, the presence of an analyte bound to our sensor complex can be tracked continuously in real time. We show that this sensing approach is compatible with making measurements in blood, saliva, urine, tears and sweat and that the sensors can collect data in situ in living animals.

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Fig. 1: Modelling the dynamics of the MP tethered to an electrode surface.
Fig. 2: Modulation of MP dynamics by protein binding.
Fig. 3: Panel of proteins and biofluids that can be monitored using MPs.
Fig. 4: MP-based monitoring of a cardiac marker in living animals.

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Data availability

The main data supporting the findings of the current study are available within the paper and its Supplementary Information. Data for figures in the Supplementary Information are included as additional Supplementary files. Data for chemical and physical protein parameters were derived from UniProt (https://www.uniprot.org/) and PhosphoSitePlus (https://www.phosphosite.org/). Source data are provided with this paper.

Code availability

The code corresponding to the theoretical model for the MP can be accessed at https://github.com/sgomis/MP-biosensor.

References

  1. Kim, J., Campbell, A. S., de Ávila, B. E. F. & Wang, J. Wearable biosensors for healthcare monitoring. Nat. Biotechnol. 37, 389–406 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Bandodkar, A. J., Jeang, W. J., Ghaffari, R. & Rogers, J. A. Wearable sensors for biochemical sweat analysis. Annu. Rev. Anal. Chem. 12, 1–22 (2019).

    Article  Google Scholar 

  3. Giljohann, D. A. & Mirkin, C. A. Drivers of biodiagnostic development. Nature 462, 461–464 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Gaster, R. S. et al. Matrix-insensitive protein assays push the limits of biosensors in medicine. Nat. Med. 15, 1327–1332 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Rong, G., Corrie, S. R. & Clark, H. A. In vivo biosensing: progress and perspectives. ACS Sens. 2, 327–338 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Gao, W. et al. Fully integrated wearable sensor arrays for multiplexed in situ perspiration analysis. Nature 529, 509–514 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Wassum, K. M. et al. Transient extracellular glutamate events in the basolateral amygdala track reward-seeking actions. J. Neurosci. 32, 2734–2746 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Sarter, M. & Kim, Y. Interpreting chemical neurotransmission in vivo: techniques, time scales and theories. ACS Chem. Neurosci. 6, 8–10 (2015).

    Article  CAS  PubMed  Google Scholar 

  9. Lipani, L. et al. Non-invasive, transdermal, path-selective and specific glucose monitoring via a graphene-based platform. Nat. Nanotechnol. 13, 504–511 (2018).

    Article  CAS  PubMed  Google Scholar 

  10. Lee, H. et al. A graphene-based electrochemical device with thermoresponsive microneedles for diabetes monitoring and therapy. Nat. Nanotechnol. 11, 566–572 (2016).

    Article  PubMed  Google Scholar 

  11. Bindra, D. S. et al. Design and in vitro studies of a needle-type glucose sensor for subcutaneous monitoring. Anal. Chem. 63, 1692–1696 (1991).

    Article  CAS  PubMed  Google Scholar 

  12. Koh, A. et al. A soft, wearable microfluidic device for the capture, storage and colorimetric sensing of sweat. Sci. Transl. Med. 8, 366ra165 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  13. Kang, D. et al. New architecture for reagentless, protein-based electrochemical biosensors. J. Am. Chem. Soc. 139, 12113–12116 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Arroyo-Currás, N. et al. Real-time measurement of small molecules directly in awake, ambulatory animals. Proc. Natl Acad. Sci. USA 114, 645–650 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  15. Ferguson, B. S. et al. Real-time, aptamer-based tracking of circulating therapeutic agents in living animals. Sci. Transl. Med. 5, 213ra165 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Mage, P. L. et al. Closed-loop control of circulating drug levels in live animals. Nat. Biomed. Eng. 1, 0070 (2017).

    Article  Google Scholar 

  17. Somasundaram, S. & Easley, C. J. A nucleic acid nanostructure built through on-electrode ligation for electrochemical detection of a broad range of analytes. J. Am. Chem. Soc. 141, 11721–11726 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nakatsuka, N. et al. Aptamer–field-effect transistors overcome Debye length limitations for small-molecule sensing. Science 362, 319–324 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. White, R. J. & Plaxco, K. W. Exploiting binding-induced changes in probe flexibility for the optimization of electrochemical biosensors. Anal. Chem. 82, 73–76 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. White, R. J., Phares, N., Lubin, A. A., Xiao, Y. & Plaxco, K. W. Optimization of electrochemical aptamer-based sensors via optimization of probe packing density and surface chemistry. Langmuir 24, 10513–10518 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Ferapontova, E. E. & Gothelf, K. V. Optimization of the electrochemical RNA-aptamer based biosensor for theophylline by using a methylene blue redox label. Electroanalysis 21, 1261–1266 (2009).

    Article  CAS  Google Scholar 

  22. Xiao, Y., Uzawa, T., White, R. J., DeMartini, D. & Plaxco, K. W. On the signaling of electrochemical aptamer-based sensors: collision- and folding-based mechanisms. Electroanalysis 21, 1267–1271 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Pellitero, M. A., Shaver, A. & Arroyo-Currás, N. Critical review—approaches for the electrochemical interrogation of DNA-based sensors: a critical review. J. Electrochem. Soc. 167, 037529 (2020).

    Article  CAS  Google Scholar 

  24. White, R. J. et al. Wash-free, electrochemical platform for the quantitative, multiplexed detection of specific antibodies. Anal. Chem. 84, 1098–1103 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Plaxco, K. W., Cash, K. J. & Ricci, F. An electrochemical sensor for the detection of protein-small molecule interactions directly in serum and other complex matrices. J. Am. Chem. Soc. 131, 6955–6957 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  26. Parolo, C. et al. E-DNA scaffold sensors and the reagentless, single-step, measurement of HIV-diagnostic antibodies in human serum. Microsyst. Nanoeng. 6, 4–11 (2020).

    Article  Google Scholar 

  27. Ogden, N. E., Kurnik, M., Parolo, C. & Plaxco, K. W. An electrochemical scaffold sensor for rapid syphilis diagnosis. Analyst 144, 5277–5283 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Kang, D. et al. Expanding the scope of protein-detecting electrochemical DNA ‘scaffold’ sensors. ACS Sens. 3, 1271–1275 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Huang, K. C. & White, R. J. Random walk on a leash: a simple single-molecule diffusion model for surface-tethered redox molecules with flexible linkers. J. Am. Chem. Soc. 135, 12808–12817 (2013).

    Article  CAS  PubMed  Google Scholar 

  30. Kelley, S. O. et al. Orienting DNA helices on gold using applied electric fields. Langmuir 14, 6781–6784 (1998).

    Article  CAS  Google Scholar 

  31. Erdmann, M., David, R., Fornof, A. & Gaub, H. E. Electrically controlled DNA adhesion. Nat. Nanotechnol. 5, 154–159 (2010).

    Article  CAS  PubMed  Google Scholar 

  32. Langer, A., Kaiser, W., Svejda, M., Schwertler, P. & Rant, U. Molecular dynamics of DNA–protein conjugates on electrified surfaces: solutions to the drift-diffusion equation. J. Phys. Chem. B 118, 597–607 (2014).

    Article  CAS  PubMed  Google Scholar 

  33. Dauphin-Ducharme, P. et al. Simulation-based approach to determining electron transfer rates using square-wave voltammetry. Langmuir 33, 4407–4413 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Uzawa, T., Cheng, R. R., White, R. J., Makarov, D. E. & Plaxco, K. W. A mechanistic study of electron transfer from the distal termini of electrode-bound, single-stranded DNAs. J. Am. Chem. Soc. 132, 16120–16126 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Arroyo-Currás, N. et al. Subsecond-resolved molecular measurements in the living body using chronoamperometrically interrogated aptamer-based sensors. ACS Sens. 3, 360–366 (2018).

    Article  PubMed  Google Scholar 

  36. Dauphin-Ducharme, P. et al. Chain dynamics limit electron transfer from electrode-bound, single-stranded oligonucleotides. J. Phys. Chem. C 122, 21441–21448 (2018).

    Article  CAS  Google Scholar 

  37. Santos-Cancel, M., Lazenby, R. A. & White, R. J. Rapid two-millisecond interrogation of electrochemical, aptamer-based sensor response using intermittent pulse amperometry. ACS Sens. 3, 1203–1209 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Das, J. & Kelley, S. O. Tuning the bacterial detection sensitivity of nanostructured microelectrodes. Anal. Chem. 85, 7333–7338 (2013).

    Article  CAS  PubMed  Google Scholar 

  39. Esteban Fernández De Ávila, B. et al. Determinants of the detection limit and specificity of surface-based biosensors. Anal. Chem. 85, 6593–6597 (2013).

    Article  PubMed  Google Scholar 

  40. Shaver, A., Curtis, S. D. & Arroyo-Currás, N. Alkanethiol monolayer end groups affect the long-term operational stability and signaling of electrochemical, aptamer-based sensors in biological fluids. ACS Appl. Mater. Interfaces 12, 11214–11223 (2020).

    Article  CAS  PubMed  Google Scholar 

  41. Herman, E. H. & Ferrans, V. J. Preclinical animal models of cardiac protection from anthracycline-induced cardiotoxicity. Semin. Oncol. 25, 15–21 (1998).

    CAS  PubMed  Google Scholar 

  42. Langer, A. et al. Protein analysis by time-resolved measurements with an electro-switchable DNA chip. Nat. Commun. 4, 2099 (2013).

    Article  PubMed  Google Scholar 

  43. Rant, U. et al. Detection and size analysis of proteins with switchable DNA layers. Nano Lett. 9, 1290–1295 (2009).

    Article  CAS  PubMed  Google Scholar 

  44. Knezevic, J. et al. Quantitation of affinity, avidity and binding kinetics of protein analytes with a dynamically switchable biosurface. J. Am. Chem. Soc. 134, 15225–15228 (2012).

    Article  CAS  PubMed  Google Scholar 

  45. Yang, Y. et al. A laser-engraved wearable sensor for sensitive detection of uric acid and tyrosine in sweat. Nat. Biotechnol. 38, 217–224 (2020).

    Article  CAS  PubMed  Google Scholar 

  46. Xu, S. et al. Soft microfluidic assemblies of sensors, circuits and radios for the skin. Science 344, 70–74 (2014).

    Article  CAS  PubMed  Google Scholar 

  47. Wang, S. et al. Skin electronics from scalable fabrication of an intrinsically stretchable transistor array. Nature 555, 83–88 (2018).

    Article  CAS  PubMed  Google Scholar 

  48. Bard, A. & Faulkner, L. Electrochemical Methods: Fundamentals and Applications 2nd edn (John Wiley & Sons, 1944).

  49. Maffeo, C. et al. Close encounters with DNA. J. Phys. Condens. Matter 26, 413101 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Lam, B. et al. Optimized templates for bottom-up growth of high-performance integrated biomolecular detectors. Lab Chip 13, 2569–2575 (2013).

    Article  CAS  PubMed  Google Scholar 

  51. Rand, D. A. J. & Woods, R. The nature of adsorbed oxygen on rhodium, palladium and gold electrodes. J. Electroanal. Chem. 31, 29–38 (1971).

    Article  CAS  Google Scholar 

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Acknowledgements

This research is supported by the Canadian Institutes of Health Research (FDN-148415, CHRPJ 523597-18) and the Natural Sciences and Engineering Research Council of Canada (2016-06090, CHRPJ 523597-18). Assets from BioRender.com were used in the main text figures. All correspondence and requests for materials should be made to S.O.K.

Author information

Author notes

  1. These authors contributed equally: Jagotamoy Das, Surath Gomis.

Authors and Affiliations

  1. Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada

    Jagotamoy Das, Hanie Yousefi, Sharif Ahmed & Shana O. Kelley

  2. The Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada

    Surath Gomis, Alam Mahmud, Wendi Zhou & Edward H. Sargent

  3. Department of Chemistry, University of Toronto, Toronto, Ontario, Canada

    Jenise B. Chen & Shana O. Kelley

  4. Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada

    Shana O. Kelley

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Contributions

J.D., S.G., E.H.S. and S.O.K. conceived the experiments. J.D. and S.G. designed and performed the experiments. S.G. conceived the theoretical model. J.B.C. fabricated the chips. J.D. and A.M. fabricated electrodes. H.Y. and W.Z. performed conjugation of ferrocence to oligo and antibody to oligo. S.A., J.D. and S.G. performed experiments with the animal model and J.D., S.G., E.H.S. and S.O.K. co-wrote the manuscript.

Corresponding authors

Correspondence to Edward H. Sargent or Shana O. Kelley.

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The authors declare no competing interests.

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Peer review information Nature Chemistry thanks Netz Arroyo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Tables 1 and 2 and Figs. 1–26.

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Supplementary Data 1

Statistical source data used to generate Supplementary figures.

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Source Data Fig. 1

Statistical source data used to generate Fig. 1.

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Statistical source data used to generate Fig. 2.

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Statistical source data used to generate Fig. 4.

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Das, J., Gomis, S., Chen, J.B. et al. Reagentless biomolecular analysis using a molecular pendulum. Nat. Chem. 13, 428–434 (2021). https://doi.org/10.1038/s41557-021-00644-y

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