Skip to main content
SpringerLink
Log in

Fluorescence Sandwich Assays for Nucleic Acid Detection

  • Chapter
  • First Online:
Biosensors Based on Sandwich Assays

  • 1192 Accesses

Abstract

Fluorescence sandwich assays have wide application in the detection of nucleic acids due to its well-developed synthesis process, simple detection procedures, and high sensitivity. Specifically, two oligonucleotide probes, named capture probe and signal probe respectively, are introduced and hybridize with different regions of a single-stranded target gene, forming a “capture probe-target-signal probe” sandwiched format. Distinctive fluorescent emission is therefore generated with the formation of sandwich-format and can be directly detected by conventional instruments without further procedures. In this chapter, we conclude the principle and recent developments of this assay based on the classification of fluorophore materials, including fluorescent organic dyes and fluorescent nanomaterials. For each section, the principle of design strategy is firstly introduced, which contains fluorescence resonance energy transfer (FRET) and DNA hybridization-induced fluorescence enhancement. Furthermore, we discuss the limitations and challenges in the development of fluorescent sandwich assays regarding sensitivity and multiple detection capacity, thus providing an overview of the developing situation and offering insight to further developments of nucleic acid assay.

The original version of this chapter was revised: Foreword has been included and authors’ affiliations have been updated. The erratum to this chapter is available at https://doi.org/10.1007/978-981-10-7835-4_13

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 54.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Zuo XB, Yang XH, Wang KM, Tan WH, Wen JH (2007) A novel sandwich assay with molecular beacon as report probe for nucleic acids detection on one-dimensional microfluidic beads array. Anal Chim Acta 587:9–13

    Article  CAS  Google Scholar 

  2. Shen JW, Li YB, Gu HS, Xia F, Zuo XL (2014) Recent development of sandwich assay based on the nanobiotechnologies for proteins, nucleic acids, small molecules, and ions. Chem Rev 114:7631–7677

    Article  CAS  Google Scholar 

  3. Epstein JR, Biran I, Walt DR (2002) Fluorescence-based nucleic acid detection and microarrays. Anal Chim Acta 469:3–36

    Article  CAS  Google Scholar 

  4. Sapsford KE, Berti L, Medintz IL (2006) Materials for fluorescence resonance energy transfer analysis: Beyond traditional donor-acceptor combinations. Angew Chem Int Ed 45:4562–4588

    Article  CAS  Google Scholar 

  5. Clapp AR, Medintz IL, Mauro JM, Fisher BR, Bawendi MG, Mattoussi H (2004) Fluorescence resonance energy transfer between quantum dot donors and dye-labeled protein acceptors. J Am Chem Soc 126:301–310

    Article  CAS  Google Scholar 

  6. Marti AA, Li XX, Jockusch S, Stevens N, Li ZM, Raveendra B, Kalachikov S, Morozova I, Russo JJ, Akins DL, Ju JY, Turro NJ (2007) Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection. Tetrahedron 63:3591–3600

    Article  CAS  Google Scholar 

  7. Heller M, Morrison L, Prevatt W, Akin C (1983) Light-emitting polynucleotide hybridization diagnostic method. European patent application 70:685

    Google Scholar 

  8. Lubin AA, Plaxco KW (2010) Folding-based electrochemical biosensors: the case for responsive nucleic acid architectures. Acc Chem Res 43:496–505

    Article  CAS  Google Scholar 

  9. Kolpashchikov DM (2010) Binary probes for nucleic acid analysis. Chem Rev 110:4709–4723

    Article  CAS  Google Scholar 

  10. Tsuji A, Koshimoto H, Sato Y, Hirano M, Sei-Iida Y, Kondo S, Ishibashi K (2000) Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope. Biophys J 78:3260–3274

    Article  CAS  Google Scholar 

  11. Mergny JL, Boutorine AS, Garestier T, Belloc F, Rougee M, Bulychev NV, Koshkin AA, Bourson J, Lebedev AV, Valeur B, Thuong NT, Helene C (1994) Fluorescence energy-transfer as a probe for nucleic-acid structures and sequences. Nucleic Acids Res 22:920–928

    Article  CAS  Google Scholar 

  12. Didenko VV (2001) DNA probes using fluorescence resonance energy transfer (FRET): designs and applications. Biotechniques 31:1106–1107

    CAS  Google Scholar 

  13. Cardullo RA, Agrawal S, Flores C, Zamecnik PC, Wolf DE (1988) Detection of nucleic-acid hybridization by nonradiative fluorescence resonance energy-transfer. Proc Natl Acad Sci USA 85:8790–8794

    Article  CAS  Google Scholar 

  14. Masuko M, Ohuchi S, Sode K, Ohtani H, Shimadzu A (2000) Fluorescence resonance energy transfer from pyrene to perylene labels for nucleic acid hybridization assays under homogeneous solution conditions. Nucleic Acids Res 28:E34

    Article  CAS  Google Scholar 

  15. Juskowiak B (2011) Nucleic acid-based fluorescent probes and their analytical potential. Anal Bioanal Chem 399:3157–3176

    Article  CAS  Google Scholar 

  16. Okamura Y, Kondo S, Sase I, Suga T, Mise K, Furusawa I, Kawakami S, Watanabe Y (2000) Double-labeled donor probe can enhance the signal of fluorescence resonance energy transfer (FRET) in detection of nucleic acid hybridization. Nucleic Acids Res 28:E107

    Article  CAS  Google Scholar 

  17. Root DD, Vaccaro C, Zhang ZL, Castro M (2004) Detection of single nucleotide variations by a hybridization proximity assay based on molecular beacons and luminescence resonance energy transfer. Biopolymers 75:60–70

    Article  CAS  Google Scholar 

  18. Santangelo PJ, Nix B, Tsourkas A, Bao G (2004) Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res 32:E57

    Article  Google Scholar 

  19. Birks J (1975) Excimers. Rep Prog Phys 38:903–974

    Article  CAS  Google Scholar 

  20. Ebata K, Masuko M, Ohtani H, Kashiwasakejibu M (1995) Nucleic-acid hybridization accompanied with excimer formation from 2 pyrene-labeled probes. Photochem Photobiol 62:836–839

    Article  CAS  Google Scholar 

  21. Masuko M, Ohtani H, Ebata K, Shimadzu A (1998) Optimization of excimer-forming two-probe nucleic acid hybridization method with pyrene as a fluorophore. Nucleic Acids Res 26:5409–5416

    Article  CAS  Google Scholar 

  22. Marti AA, Li XX, Jockusch S, Li ZM, Raveendra B, Kalachikov S, Russo JJ, Morozova I, Puthanveettil SV, Ju JY, Turro NJ (2006) Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy. Nucleic Acids Res 34:3161–3168

    Article  CAS  Google Scholar 

  23. Grate D, Wilson C (1999) Laser-mediated, site-specific inactivation of RNA transcripts. Proc Natl Acad Sci USA 96:6131–6136

    Article  CAS  Google Scholar 

  24. Babendure JR, Adams SR, Tsien RY (2003) Aptamers switch on fluorescence of triphenylmethane dyes. J Am Chem Soc 125:14716–14717

    Article  CAS  Google Scholar 

  25. Kolpashchikov DM (2005) Binary malachite green aptamer for fluorescent detection of nucleic acids. J Am Chem Soc 127:12442–12443

    Article  CAS  Google Scholar 

  26. Sando S, Narita A, Aoyama Y (2007) Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye. ChemBioChem 8:1795–1803

    Article  CAS  Google Scholar 

  27. Endo K, Nakamura Y (2010) A binary Cy3 aptamer probe composed of folded modules. Anal Biochem 400:103–109

    Article  CAS  Google Scholar 

  28. Paige JS, Wu KY, Jaffrey SR (2011) RNA mimics of green fluorescent protein. Science 333:642–646

    Article  CAS  Google Scholar 

  29. Kikuchi N, Kolpashchikov DM (2016) Split spinach aptamer for highly selective recognition of DNA and RNA at ambient temperatures. ChemBioChem 17:1589–1592

    Article  CAS  Google Scholar 

  30. AlSalhi MS, Alam J, Dass LA, Raja M (2011) Recent advances in conjugated polymers for light emitting devices. Int J Mol Sci 12:2036–2054

    Article  CAS  Google Scholar 

  31. Thomas SW, Joly GD, Swager TM (2007) Chemical sensors based on amplifying fluorescent conjugated polymers. Chem Rev 107:1339–1386

    Article  CAS  Google Scholar 

  32. Gaylord BS, Heeger AJ, Bazan GC (2002) DNA detection using water-soluble conjugated polymers and peptide nucleic acid probes. Proc Natl Acad Sci USA 99:10954–10957

    Article  CAS  Google Scholar 

  33. Pu F, Hu D, Ren JS, Wang S, Qu XG (2010) Universal platform for sensitive and label-free nuclease assay based on conjugated polymer and DNA/intercalating dye complex. Langmuir 26:4540–4545

    Article  CAS  Google Scholar 

  34. Xu C, Zhou RY, Zhang RC, Yang LY, Wang GJ (2014) Label-free DNA sequence detection through FRET from a fluorescent polymer with pyrene excimer to SG. ACS Macro Lett 3:845–848

    Article  CAS  Google Scholar 

  35. Chan WCW, Maxwell DJ, Gao XH, Bailey RE, Han MY, Nie SM (2002) Luminescent quantum dots for multiplexed biological detection and imaging. Curr Opin Biotechnol 13:40–46

    Article  CAS  Google Scholar 

  36. Eigen M, Rigler R (1994) Sorting single molecules-application to diagnostics and evolutionary biotechnology. Proc Natl Acad Sci USA 91:5740–5747

    Article  CAS  Google Scholar 

  37. Lee J, Kim IS, Yu HW (2010) Flow cytometric detection of bacillus spoOA gene in biofilm using quantum dot labeling. Anal Chem 82:2836–2843

    Article  CAS  Google Scholar 

  38. Yeh HC, Ho YP, Wang TH (2005) Quantum dot-mediated biosensing assays for specific nucleic acid detection. Nanomed-Nanotechnol Biol Med 1:115–121

    Article  CAS  Google Scholar 

  39. Ho YP, Kung MC, Yang S, Wang TH (2005) Multiplexed hybridization detection with multicolor colocalization of quantum dot nanoprobes. Nano Lett 5:1693–1697

    Article  CAS  Google Scholar 

  40. Zhang CY, Yeh HC, Kuroki MT, Wang TH (2005) Single-quantum-dot-based DNA nanosensor. Nat Mater 4:826–831

    Article  CAS  Google Scholar 

  41. Algar WR, Krull UJ (2010) Multiplexed interfacial transduction of nucleic acid hybridization using a single color of immobilized quantum dot donor and two acceptors in fluorescence resonance energy transfer. Anal Chem 82:400–405

    Article  CAS  Google Scholar 

  42. Algar WR, Krull UJ (2009) Interfacial transduction of nucleic acid hybridization using immobilized quantum dots as donors in fluorescence resonance energy transfer. Langmuir 25:633–638

    Article  CAS  Google Scholar 

  43. Noor MO, Tavares AJ, Krull UJ (2013) On-chip multiplexed solid-phase nucleic acid hybridization assay using spatial profiles of immobilized quantum dots and fluorescence resonance energy transfer. Anal Chim Acta 788:148–157

    Article  CAS  Google Scholar 

  44. Noor MO, Krull UJ (2014) Camera-based ratiometric fluorescence transduction of nucleic acid hybridization with reagentless signal amplification on a paper-based platform using immobilized quantum dots as donors. Anal Chem 86:10331–10339

    Article  CAS  Google Scholar 

  45. Li M, Cushing SK, Wang QY, Shi XD, Hornak LA, Hong ZL, Wu NQ (2011) Size-dependent energy transfer between CdSe/ZnS quantum dots and gold nanoparticles. J Phys Chem Lett 2:2125–2129

    Article  CAS  Google Scholar 

  46. Kang T, Kim HC, Joo SW, Lee SY, Ahn IS, Yoon KA, Lee K (2013) Optimization of energy transfer between quantum dots and gold nanoparticles in head-to-head configuration for detection of fusion gene. Sens Actuator B-Chem 188:729–734

    Article  CAS  Google Scholar 

  47. Jenkins R, Burdette MK, Foulger SH (2016) Mini-review: fluorescence imaging in cancer cells using dye-doped nanoparticles. RSC Adv 6:65459–65474

    Google Scholar 

  48. Zhao XJ, Tapec-Dytioco R, Tan WH (2003) Ultrasensitive DNA detection using highly fluorescent bioconjugated nanoparticles. J Am Chem Soc 125:11474–11475

    Article  CAS  Google Scholar 

  49. Montalti M, Prodi L, Rampazzo E, Zaccheroni N (2014) Dye-doped silica nanoparticles as luminescent organized systems for nanomedicine. Chem Soc Rev 43:4243–4268

    Article  CAS  Google Scholar 

  50. Zhou XC, Zhou JZ (2004) Improving the signal sensitivity and photostability of DNA hybridizations on microarrays by using dye-doped core-shell silica nanoparticles. Anal Chem 76:5302–5312

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People’s Republic of China

    Xinwen Liu & Quan Yuan

Authors
  1. Xinwen Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Quan Yuan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Quan Yuan .

Editor information

Editors and Affiliations

  1. Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, China

    Fan Xia

  2. Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, China

    Xiaojin Zhang

  3. Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan, Hubei, China

    Xiaoding Lou

  4. College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, China

    Quan Yuan

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Liu, X., Yuan, Q. (2018). Fluorescence Sandwich Assays for Nucleic Acid Detection. In: Xia, F., Zhang, X., Lou, X., Yuan, Q. (eds) Biosensors Based on Sandwich Assays. Springer, Singapore. https://doi.org/10.1007/978-981-10-7835-4_7

Download citation

Publish with us

Policies and ethics

Search

Navigation