Skip to main content
SpringerLink
Log in

DNA aptamer-linked sandwich structure enhanced SPRi sensor for rapid, sensitive, and quantitative detection of SARS-CoV-2 spike protein

  • Research Paper
  • Published:
Analytical and Bioanalytical Chemistry Aims and scope Submit manuscript

Abstract

The harm and impact of the COVID-19 pandemic have highlighted the importance of fast, sensitive, and cost-effective virus detection methods. In this study, we developed a DNA aptamer sensor using nanoparticle-enhanced surface plasmon resonance imaging (SPRi) technology to achieve efficient labeling-free detection of SARS-CoV-2 S protein. We used the same DNA aptamer to modify the surface of the SPRi sensor chip and gold nanoparticles (AuNPs), respectively, for capturing target analytes and amplifying signals, achieving ideal results while greatly reducing costs and simplifying the preparation process. The SPRi sensing method exhibits a good linear relationship (R2 = 0.9926) in the concentration range of 1–20 nM before adding AuNPs to amplify the signal, with a limit of detection (LOD) of 0.32 nM. After amplifying the signal, there is a good linear relationship (R2 = 0.9829) between the concentration range of 25–1000 pM, with a LOD of 5.99 pM. The simulation results also verified the effectiveness of AuNPs in improving SPRi signal response. The SPRi sensor has the advantage of short detection time and can complete the detection within 10 min. In addition, the specificity and repeatability of this method can achieve excellent results. This is the first study to simultaneously capture a viral marker protein and amplify the signal using polyadenylic acid (polyA)–modified DNA aptamers on the SPR platform. This scheme can be used as a fast and inexpensive detection method for diagnosis at the point of care (POC) to combat current and future epidemics caused by the virus.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7

Similar content being viewed by others

References

  1. Morales-Narvaez E, Dincer C. The impact of biosensing in a pandemic outbreak: COVID-19. Biosens Bioelectron. 2020;163:112274. https://doi.org/10.1016/j.bios.2020.112274.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Orooji Y, Sohrabi H, Hemmat N, Oroojalian F, Baradaran B, Mokhtarzadeh A, et al. An overview on SARS-CoV-2 (COVID-19) and other human coronaviruses and their detection capability via amplification assay, chemical sensing, biosensing, immunosensing, and clinical assays. Nanomicro Lett. 2021;13(1):18. https://doi.org/10.1007/s40820-020-00533-y.

    Article  ADS  CAS  PubMed  Google Scholar 

  3. Ou X, Liu Y, Lei X, Li P, Mi D, Ren L, et al. Characterization of spike glycoprotein of SARS-CoV-2 on virus entry and its immune cross-reactivity with SARS-CoV. Nat Commun. 2020;11(1):1620. https://doi.org/10.1038/s41467-020-15562-9.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  4. Walls AC, Park YJ, Tortorici MA, Wall A, McGuire AT, Veesler D. Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell. 2020;181(2):281-92 e6. https://doi.org/10.1016/j.cell.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Hoffmann M, Kleine-Weber H, Schroeder S, Kruger N, Herrler T, Erichsen S, et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell. 2020;181(2):271-80 e8. https://doi.org/10.1016/j.cell.2020.02.052.

    Article  PubMed  PubMed Central  Google Scholar 

  6. Ji T, Liu Z, Wang G, Guo X, Akbar Khan S, Lai C, et al. Detection of COVID-19: a review of the current literature and future perspectives. Biosens Bioelectron. 2020;166:112455. https://doi.org/10.1016/j.bios.2020.112455.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Kim H. Outbreak of novel coronavirus (COVID-19): what is the role of radiologists? Eur Radiol. 2020;30(6):3266–7. https://doi.org/10.1007/s00330-020-06748-2.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Suleman S, Shukla SK, Malhotra N, Bukkitgar SD, Shetti NP, Pilloton R, et al. Point of care detection of COVID-19: advancement in biosensing and diagnostic methods. Chem Eng J. 2021;414:128759. https://doi.org/10.1016/j.cej.2021.128759.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Conklin SE, Martin K, Manabe YC, Schmidt HA, Miller J, Keruly M, et al. Evaluation of serological SARS-CoV-2 lateral flow assays for rapid point-of-care testing. J Clin Microbiol. 2021;59(2). https://doi.org/10.1128/JCM.02020-20.

  10. Kilic T, Weissleder R, Lee H. Molecular and immunological diagnostic tests of COVID-19: current status and challenges. iScience. 2020;23(8):101406. https://doi.org/10.1016/j.isci.2020.101406.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  11. Wang C, Liu M, Wang Z, Li S, Deng Y, He N. Point-of-care diagnostics for infectious diseases: from methods to devices. Nano Today. 2021;37:101092. https://doi.org/10.1016/j.nantod.2021.101092.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Seo G, Lee G, Kim MJ, Baek SH, Choi M, Ku KB, et al. Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor. ACS Nano. 2020;14(4):5135–42. https://doi.org/10.1021/acsnano.0c02823.

    Article  CAS  PubMed  Google Scholar 

  13. Yang Y, Peng Y, Lin C, Long L, Hu J, He J, et al. Human ACE2-functionalized gold “virus-trap” nanostructures for accurate capture of SARS-CoV-2 and single-virus SERS detection. Nanomicro Lett. 2021;13:109. https://doi.org/10.1007/s40820-021-00620-8.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  14. Cennamo N, Pasquardini L, Arcadio F, Lunelli L, Vanzetti L, Carafa V, et al. SARS-CoV-2 spike protein detection through a plasmonic D-shaped plastic optical fiber aptasensor. Talanta. 2021;233:122532. https://doi.org/10.1016/j.talanta.2021.122532.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Yano TA, Kajisa T, Ono M, Miyasaka Y, Hasegawa Y, Saito A, et al. Ultrasensitive detection of SARS-CoV-2 nucleocapsid protein using large gold nanoparticle-enhanced surface plasmon resonance. Sci Rep. 2022;12(1):1060. https://doi.org/10.1038/s41598-022-05036-x.

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  16. Maria MSM. Surface plasmon resonance applications in clinical analysis. Anal Bioanal Chem. 2014;406(9–10):2303–23. https://doi.org/10.1007/s00216-014-7647-5.

    Article  ADS  CAS  Google Scholar 

  17. Takemura K. Surface plasmon resonance (SPR)- and localized SPR (LSPR)-based virus sensing systems: optical vibration of nano- and micro-metallic materials for the development of next-generation virus detection technology. Biosensors (Basel). 2021;11(8). https://doi.org/10.3390/bios11080250.

  18. Qu JH, Leirs K, Maes W, Imbrechts M, Callewaert N, Lagrou K, et al. Innovative FO-SPR label-free strategy for detecting anti-RBD antibodies in COVID-19 patient serum and whole blood. ACS Sens. 2022;7(2):477–87. https://doi.org/10.1021/acssensors.1c02215.

    Article  CAS  PubMed  Google Scholar 

  19. Huang L, Ding L, Zhou J, Chen S, Chen F, Zhao C, et al. One-step rapid quantification of SARS-CoV-2 virus particles via low-cost nanoplasmonic sensors in generic microplate reader and point-of-care device. Biosens Bioelectron. 2021;171:112685. https://doi.org/10.1016/j.bios.2020.112685.

    Article  CAS  PubMed  Google Scholar 

  20. Dehghani S, Nosrati R, Yousefi M, Nezami A, Soltani F, Taghdisi SM, et al. Aptamer-based biosensors and nanosensors for the detection of vascular endothelial growth factor (VEGF): a review. Biosens Bioelectron. 2018;110:23–37. https://doi.org/10.1016/j.bios.2018.03.037.

    Article  CAS  PubMed  Google Scholar 

  21. Ulrich H. RNA aptamers: from basic science towards therapy. Handb Exp Pharmacol. 2006;173:305–26. https://doi.org/10.1007/3-540-27262-3_15.

    Article  CAS  Google Scholar 

  22. Bouchard PR, Hutabarat RM, Thompson KM. Discovery and development of therapeutic aptamers. Annu Rev Pharmacol Toxicol. 2010;50:237–57. https://doi.org/10.1146/annurev.pharmtox.010909.105547.

    Article  CAS  PubMed  Google Scholar 

  23. Liu B, Liu J. Freezing directed construction of bio/nano interfaces: reagentless conjugation, denser spherical nucleic acids, and better nanoflares. J Am Chem Soc. 2017;139(28):9471–4. https://doi.org/10.1021/jacs.7b04885.

    Article  MathSciNet  CAS  PubMed  Google Scholar 

  24. Pei H, Li F, Wan Y, Wei M, Liu H, Su Y, et al. Designed diblock oligonucleotide for the synthesis of spatially isolated and highly hybridizable functionalization of DNA-gold nanoparticle nanoconjugates. J Am Chem Soc. 2012;134(29):11876–9. https://doi.org/10.1021/ja304118z.

    Article  CAS  PubMed  Google Scholar 

  25. Huertas CS, Soler M, Estevez MC, Lechuga LM. One-step immobilization of antibodies and DNA on gold sensor surfaces via a poly-adenine oligonucleotide approach. Anal Chem. 2020;92(18):12596–604. https://doi.org/10.1021/acs.analchem.0c02619.

    Article  CAS  PubMed  Google Scholar 

  26. Schreiner SM, Shudy DF, Hatch AL, Opdahl A, Whitman LJ, Petrovykh DY. Controlled and efficient hybridization achieved with DNA probes immobilized solely through preferential DNA-substrate interactions. Anal Chem. 2010;82(7):2803–10. https://doi.org/10.1021/ac902765g.

    Article  CAS  PubMed  Google Scholar 

  27. Zhang Z, Li J, Gu J, Amini R, Stacey HD, Ang JC, et al. A universal DNA aptamer that recognizes spike proteins of diverse SARS-CoV-2 variants of concern. Chemistry. 2022;28(15):e202200078. https://doi.org/10.1002/chem.202200078.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Hu M, Yuan C, Tian T, Wang X, Sun J, Xiong E, et al. Single-step, salt-aging-free, and thiol-free freezing construction of AuNP-based bioprobes for advancing CRISPR-based diagnostics. J Am Chem Soc. 2020;142(16):7506–13. https://doi.org/10.1021/jacs.0c00217.

    Article  CAS  PubMed  Google Scholar 

  29. Zhu D, Yan Y, Lei P, Shen B, Cheng W, Ju H, et al. A novel electrochemical sensing strategy for rapid and ultrasensitive detection of Salmonella by rolling circle amplification and DNA-AuNPs probe. Anal Chim Acta. 2014;846:44–50. https://doi.org/10.1016/j.aca.2014.07.024.

    Article  ADS  CAS  PubMed  Google Scholar 

  30. Fang Y, Jiang L, Jin S, Li Y, Jiang C, Zhang X, et al. AuNPs beacons-enhanced surface plasmon resonance imaging sensor for rapid, high-throughput and ultra-sensitive detection of three fusion genes related to acute promyelocytic leukemia. Sens Actuators B Chem. 2022;361. https://doi.org/10.1016/j.snb.2022.131728.

  31. Li Y, Zou Y, Tan H, Jiang L, Fang Y, Jin S. Simultaneous and sensitive detection of two pathogenic genes of thrombotic diseases using SPRi sensor with one-step fixation probe by a poly-adenine oligonucleotide approach. Colloids Surf B Biointerfaces. 2022;209(Pt 1):112184. https://doi.org/10.1016/j.colsurfb.2021.112184.

    Article  CAS  PubMed  Google Scholar 

  32. Qian H, Huang Y, Duan X, Wei X, Fan Y, Gan D, et al. Fiber optic surface plasmon resonance biosensor for detection of PDGF-BB in serum based on self-assembled aptamer and antifouling peptide monolayer. Biosens Bioelectron. 2019;140:111350. https://doi.org/10.1016/j.bios.2019.111350.

    Article  CAS  PubMed  Google Scholar 

  33. Sperling RA, Parak WJ. Surface modification, functionalization and bioconjugation of colloidal inorganic nanoparticles. Philos Trans A Math Phys Eng Sci. 1915;2010(368):1333–83. https://doi.org/10.1098/rsta.2009.0273.

    Article  CAS  Google Scholar 

  34. Hong X, Hall EA. Contribution of gold nanoparticles to the signal amplification in surface plasmon resonance. Analyst. 2012;137(20):4712–9. https://doi.org/10.1039/c2an35742a.

    Article  ADS  CAS  PubMed  Google Scholar 

  35. Sun M, Liu S, Song T, Chen F, Zhang J, Huang JA, et al. Spherical neutralizing aptamer inhibits SARS-CoV-2 infection and suppresses mutational escape. J Am Chem Soc. 2021;143(51):21541–8. https://doi.org/10.1021/jacs.1c08226.

    Article  CAS  PubMed  Google Scholar 

  36. Zeng S, Baillargeat D, Ho HP, Yong KT. Nanomaterials enhanced surface plasmon resonance for biological and chemical sensing applications. Chem Soc Rev. 2014;43(10):3426–52. https://doi.org/10.1039/c3cs60479a.

    Article  CAS  PubMed  Google Scholar 

  37. Ghosh SN. Electromagnetic theory and wave propagation. CRC Press. 2002.

  38. Koledintseva MY, Dubroff RE, Schwartz RW. A Maxwell Garnett model for dielectric mixtures containing conducting particles at optical frequencies. Prog Electromagn Res. 2006;63:223–42. https://doi.org/10.2528/PIER06052601.

    Article  Google Scholar 

  39. Ishimaru A. Electromagnetic wave propagation, radiation, and scattering: from fundamentals to applications. John Wiley & Sons. 2017.

  40. Uchiho Y, Shimojo M, Furuya K, Kajikawa K. Optical response of gold-nanoparticle-amplified surface plasmon resonance spectroscopy. J Phys Chem C. 2010;114(11):4816–24. https://doi.org/10.1021/jp910438q.

    Article  CAS  Google Scholar 

  41. Golden MS, Bjonnes AC, Georgiadis RM. Distance- and wavelength-dependent dielectric function of Au nanoparticles by angle-resolved surface plasmon resonance imaging. J Phys Chem C. 2010;114(19):8837–43. https://doi.org/10.1021/jp101850d.

    Article  CAS  Google Scholar 

  42. Amouzadeh Tabrizi M, Nazari L, Acedo P. A photo-electrochemical aptasensor for the determination of severe acute respiratory syndrome coronavirus 2 receptor-binding domain by using graphitic carbon nitride-cadmium sulfide quantum dots nanocomposite. Sens Actuators B Chem. 2021;345:130377. https://doi.org/10.1016/j.snb.2021.130377.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Wang X, Zeng Y, Zhou J, Chen J, Miyan R, Zhang H, et al. Ultrafast surface plasmon resonance imaging sensor via the high-precision four-parameter-based spectral curve readjusting method. Anal Chem. 2021;93(2):828–33. https://doi.org/10.1021/acs.analchem.0c03347.

    Article  CAS  PubMed  Google Scholar 

  44. Subramanian P, Lesniewski A, Kaminska I, Vlandas A, Vasilescu A, Niedziolka-Jonsson J, et al. Lysozyme detection on aptamer functionalized graphene-coated SPR interfaces. Biosens Bioelectron. 2013;50:239–43. https://doi.org/10.1016/j.bios.2013.06.026.

    Article  CAS  PubMed  Google Scholar 

Download references

Funding

This work was supported by the Natural Science Foundation of Zhejiang Province under Grant No. LZ22F050004 and the National Natural Science Foundation of China under Grant Nos. 52271139, 51972292, and 22204154.

Author information

Authors and Affiliations

  1. College of Optical and Electronic Technology, China Jiliang University, Hangzhou, 310018, China

    Rengang Sun, Yadong Zhou, Yunzhu Fang, Yirui Qin, Yekai Zheng & Li Jiang

Authors
  1. Rengang Sun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yadong Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yunzhu Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yirui Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Yekai Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Li Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Yadong Zhou or Li Jiang.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary Information

Below is the link to the electronic supplementary material.

Supplementary file1 (DOC 59 KB)

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Sun, R., Zhou, Y., Fang, Y. et al. DNA aptamer-linked sandwich structure enhanced SPRi sensor for rapid, sensitive, and quantitative detection of SARS-CoV-2 spike protein. Anal Bioanal Chem 416, 1667–1677 (2024). https://doi.org/10.1007/s00216-024-05172-5

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00216-024-05172-5

Keywords

Search

Navigation