Sandwich Assays Based on QCM, SPR, Microcantilever, and SERS Techniques for Nucleic Acid Detection

  • Xiaoxia Hu
  • Quan YuanEmail author


Signal transducers which can read the signal toward targets are widely used for nucleic acid assay. Typically, the signal transducers based on quartz crystal microbalance (QCM), surface plasmon resonance (SPR) sensor, microcantilever, and surface-enhanced Raman scattering (SERS) play a significant role in the development of techniques for the detection of nucleic acid. The combination of these techniques with sandwich assay has received extensive attention due to the advantages of sensitivity and specificity. In this chapter, we summarized the recent development of the nucleic acid sandwich assay based on QCM, SPR sensor, microcantilever, and SERS. Additionally, the advantages and disadvantages of these sandwich assays along with the challenges and prospects are also presented, devoting to guide researches to design more of robust sandwich assays for nucleic acid assay.


Sandwich assay Nucleic acid Detection Quartz crystal microbalance Surface plasmon resonance Microcantilever Surface-enhanced Raman scattering 


  1. 1.
    Henne WA, Doorneweerd DD, Lee J, Low PS, Savran C (2006) Detection of folate binding protein with enhanced sensitivity using a functionalized quartz crystal microbalance sensor. Anal Chem 78:4880–4884CrossRefGoogle Scholar
  2. 2.
    Uludag Y, Tothill IE (2012) Cancer biomarker detection in serum samples using surface plasmon resonance and quartz crystal microbalance sensors with nanoparticle signal amplification. Anal Chem 84:5898–5904CrossRefGoogle Scholar
  3. 3.
    Ebersole RC, Ward MD (1988) Amplified mass immunosorbent-assay with a quartz crystal microbalance. J Am Chem Soc 110:8623–8628CrossRefGoogle Scholar
  4. 4.
    Zhou XC, O’Shea SJ, Li SFY (2000) Amplified microgravimetric gene sensor using Au nanoparticle modified oligonucleotides. Chem Commun 953–954Google Scholar
  5. 5.
    Lao RJ, Song SP, Wu HP, Wang LH, Zhang ZZ, He L, Fan CH (2005) Electrochemical interrogation of DNA monolayers on gold surfaces. Anal Chem 77:6475–6480CrossRefGoogle Scholar
  6. 6.
    Mao XL, Yang LJ, Su XL, Li YB (2006) A nanoparticle amplification based quartz crystal microbalance DNA sensor for detection of Escherichia coli O157:H7. Biosens Bioelectron 21:1178–1185CrossRefGoogle Scholar
  7. 7.
    Rasheed PA, Sandhyarani N (2016) Quartz crystal microbalance genosensor for sequence specific detection of attomolar DNA targets. Anal Chim Acta 905:134–139CrossRefGoogle Scholar
  8. 8.
    Sanchez CG, Su Q, Schonherr H, Grininger M, Noll G (2015) Multi-ligand-binding flavoprotein dodecin as a key element for reversible surface modification in nano-biotechnology. ACS Nano 9:3491–3500CrossRefGoogle Scholar
  9. 9.
    Zeng SW, Baillargeat D, Ho HP, Yong KT (2014) Nanomaterials enhanced surface plasmon resonance for biological and chemical sensing applications. Chem Soc Rev 43:3426–3452CrossRefGoogle Scholar
  10. 10.
    Ermini ML, Mariani S, Scarano S, Minunni M (2014) Bioanalytical approaches for the detection of single nucleotide polymorphisms by Surface Plasmon Resonance biosensors. Biosens Bioelectron 61:28–37CrossRefGoogle Scholar
  11. 11.
    Sipova H, Homola J (2013) Surface plasmon resonance sensing of nucleic acids: a review. Anal Chim Acta 773:9–23CrossRefGoogle Scholar
  12. 12.
    He L, Musick MD, Nicewarner SR, Salinas FG, Benkovic SJ, Natan MJ, Keating CD (2000) Colloidal Au-enhanced surface plasmon resonance for ultrasensitive detection of DNA hybridization. J Am Chem Soc 122:9071–9077CrossRefGoogle Scholar
  13. 13.
    Hayashida M, Yamaguchi A, Misawa H (2005) High sensitivity and large dynamic range surface plasmon resonance sensing for DNA hybridization using Au-nanoparticle-attached probe DNA. Jpn J Appl Phys Part 2—Lett Express Lett 44:1544–1546CrossRefGoogle Scholar
  14. 14.
    Yao X, Li X, Toledo F, Zurita-Lopez C, Gutova M, Momand J, Zhou FM (2006) Sub-attomole oligonucleotide and p53 cDNA determinations via a high-resolution surface plasmon resonance combined with oligonucleotide-capped gold nanoparticle signal amplification. Anal Biochem 354:220–228CrossRefGoogle Scholar
  15. 15.
    Yang XH, Wang Q, Wang KM, Tan WH, Li HM (2007) Enhanced surface plasmon resonance with the modified catalytic growth of Au nanoparticles. Biosens Bioelectron 22:1106–1110CrossRefGoogle Scholar
  16. 16.
    Wark AW, Lee HJ, Qavi AJ, Corn RM (2007) Nanoparticle-enhanced diffraction gratings for ultrasensitive surface plasmon biosensing. Anal Chem 79:6697–6701CrossRefGoogle Scholar
  17. 17.
    D’Agata R, Corradini R, Grasso G, Marchelli R, Spoto G (2008) Ultrasensitive detection of DNA by PNA and nanoparticle-enhanced surface plasmon resonance imaging. ChemBioChem 9:2067–2070CrossRefGoogle Scholar
  18. 18.
    Joung HA, Lee NR, Lee SK, Ahn J, Shin YB, Choi HS, Lee CS, Kim S, Kim MG (2008) High sensitivity detection of 16s rRNA using peptide nucleic acid probes and a surface plasmon resonance biosensor. Anal Chim Acta 630:168–173CrossRefGoogle Scholar
  19. 19.
    Moon S, Kim DJ, Kim K, Kim D, Lee H, Lee K, Haam S (2010) Surface-enhanced plasmon resonance detection of nanoparticle-conjugated DNA hybridization. Appl Optics 49:484–491CrossRefGoogle Scholar
  20. 20.
    D’Agata R, Breveglieri G, Zanoli LM, Borgatti M, Spoto G, Gambari R (2011) Direct detection of point mutations in nonamplified human genomic DNA. Anal Chem 83:8711–8717CrossRefGoogle Scholar
  21. 21.
    Hong X, Hall EAH (2012) Contribution of gold nanoparticles to the signal amplification in surface plasmon resonance. Analyst 137:4712–4719CrossRefGoogle Scholar
  22. 22.
    Gu Y, Tan YJ, Wang CY, Nie JL, Yu JR, Li YH (2012) A surface plasmon resonance sensor platform coupled with gold nanoparticle probes for unpurified nucleic acids detection. Anal Lett 45:2210–2220CrossRefGoogle Scholar
  23. 23.
    Mariani S, Scarano S, Spadavecchia J, Minunni M (2015) A reusable optical biosensor for the ultrasensitive and selective detection of unamplified human genomic DNA with gold nanostars. Biosens Bioelectron 74:981–988CrossRefGoogle Scholar
  24. 24.
    Okumura A, Sato Y, Kyo M, Kawaguchi H (2005) Point mutation detection with the sandwich method employing hydrogel nanospheres by the surface plasmon resonance imaging technique. Anal Biochem 339:328–337CrossRefGoogle Scholar
  25. 25.
    Mousavi MZ, Chen HY, Wu SH, Peng SW, Lee KL, Wei PK, Cheng JY (2013) Magnetic nanoparticle-enhanced SPR on gold nanoslits for ultra-sensitive, label-free detection of nucleic acid biomarkers. Analyst 138:2740–2748CrossRefGoogle Scholar
  26. 26.
    Mousavi MZ, Chen HY, Lee KL, Lin H, Chen HH, Lin YF, Wong CS, Li HF, Wei PK, Cheng JY (2015) Urinary micro-RNA biomarker detection using capped gold nanoslit SPR in a microfluidic chip. Analyst 140:4097–4104CrossRefGoogle Scholar
  27. 27.
    Zhou WJ, Halpern AR, Seefeld TH, Corn RM (2012) Near infrared surface plasmon resonance phase imaging and nanoparticle-enhanced surface plasmon resonance phase imaging for ultrasensitive protein and DNA biosensing with oligonucleotide and aptamer microarrays. Anal Chem 84:440–445CrossRefGoogle Scholar
  28. 28.
    Goodrich TT, Lee HJ, Corn RM (2004) Enzymatically amplified surface plasmon resonance imaging method using RNase H and RNA microarrays for the ultrasensitive detection of nucleic acids. Anal Chem 76:6173–6178CrossRefGoogle Scholar
  29. 29.
    Zeng DM, Wang JX, Yin LJ, Zhang YT, Zhang Y, Zhou FM (2007) Sequence-specific analysis of oligodeoxynucleotides by precipitate-amplified surface plasmon resonance measurements. Front Biosci 12:5117–5123CrossRefGoogle Scholar
  30. 30.
    Su XD, Teh HF, Aung KMM, Zong Y, Gao ZQ (2008) Femtomol SPR detection of DNA-PNA hybridization with the assistance of DNA-guided polyaniline deposition. Biosens Bioelectron 23:1715–1720CrossRefGoogle Scholar
  31. 31.
    Seefeld TH, Zhou WJ, Corn RM (2011) Rapid microarray detection of DNA and proteins in microliter volumes with surface plasmon resonance imaging measurements. Langmuir 27:6534–6540CrossRefGoogle Scholar
  32. 32.
    Fasoli JB, Corn RM (2015) Surface enzyme chemistries for ultrasensitive microarray biosensing with SPR imaging. Langmuir 31:9527–9536CrossRefGoogle Scholar
  33. 33.
    Li YA, Wark AW, Lee HJ, Corn RM (2006) Single-nucleotide polymorphism genotyping by nanoparticle-enhanced surface plasmon resonance imaging measurements of surface ligation reactions. Anal Chem 78:3158–3164CrossRefGoogle Scholar
  34. 34.
    Fang SP, Lee HJ, Wark AW, Corn RM (2006) Attomole microarray detection of MicroRNAs by nanoparticle-amplified SPR imaging measurements of surface polyadenylation reactions. J Am Chem Soc 128:14044–14046CrossRefGoogle Scholar
  35. 35.
    Sendroiu IE, Gifford LK, Luptak A, Corn RM (2011) Ultrasensitive DNA microarray biosensing via in situ RNA transcription-based amplification and nanoparticle-enhanced SPR imaging. J Am Chem Soc 133:4271–4273CrossRefGoogle Scholar
  36. 36.
    Zagorodko O, Spadavecchia J, Serrano AY, Larroulet I, Pesquera A, Zurutuza A, Boukherroub R, Szunerits S (2014) Highly sensitive detection of DNA hybridization on commercialized graphene-coated surface plasmon resonance interfaces. Anal Chem 86:11211–11216Google Scholar
  37. 37.
    Liu RJ, Wang Q, Li Q, Yang XH, Wang KM, Nie WY (2017) Surface plasmon resonance biosensor for sensitive detection of microRNA and cancer cell using multiple signal amplification strategy. Biosens Bioelectron 87:433–438Google Scholar
  38. 38.
    Cao YWC, Jin RC, Mirkin CA (2002) Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297:1536–1540Google Scholar
  39. 39.
    Ghosh S, Mishra S, Mukhopadhyay R (2014) Enhancing sensitivity in a piezoresistive cantilever-based label-free DNA detection assay using ssPNA sensor probes. J Mat Chem B 2:960–970CrossRefGoogle Scholar
  40. 40.
    Huber F, Lang HP, Backmann N, Rimoldi D, Gerber C (2013) Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays. Nat Nanotechnol 8:125–129CrossRefGoogle Scholar
  41. 41.
    Mertens J, Rogero C, Calleja M, Ramos D, Martin-Gago JA, Briones C, Tamayo J (2008) Label-free detection of DNA hybridization based on hydration-induced tension in nucleic acid films. Nat Nanotechnol 3:301–307CrossRefGoogle Scholar
  42. 42.
    Zhu R, Howorka S, Proll J, Kienberger F, Preiner J, Hesse J, Ebner A, Pastushenko VP, Gruber HJ, Hinterdorfer P (2010) Nanomechanical recognition measurements of individual DNA molecules reveal epigenetic methylation patterns. Nat Nanotechnol 5:788–791CrossRefGoogle Scholar
  43. 43.
    Zheng S, Choi JH, Lee SM, Hwang KS, Kim SK, Kim TS (2011) Analysis of DNA hybridization regarding the conformation of molecular layer with piezoelectric microcantilevers. Lab Chip 11:63–69CrossRefGoogle Scholar
  44. 44.
    McKendry R, Zhang JY, Arntz Y, Strunz T, Hegner M, Lang HP, Baller MK, Certa U, Meyer E, Guntherodt HJ, Gerber C (2002) Multiple label-free biodetection and quantitative DNA-binding assays on a nanomechanical cantilever array. Proc Natl Acad Sci U S A 99:9783–9788CrossRefGoogle Scholar
  45. 45.
    Su M, Li SU, Dravid VP (2003) Microcantilever resonance-based DNA detection with nanoparticle probes. Appl Phys Lett 82:3562–3564CrossRefGoogle Scholar
  46. 46.
    Wu GH, Ji HF, Hansen K, Thundat T, Datar R, Cote R, Hagan MF, Chakraborty AK, Majumdar A (2001) Origin of nanomechanical cantilever motion generated from biomolecular interactions. Proc Natl Acad Sci U S A 98:1560–1564CrossRefGoogle Scholar
  47. 47.
    Lee SM, Hwang KS, Yoon HJ, Yoon DS, Kim SK, Lee YS, Kim TS (2009) Sensitivity enhancement of a dynamic mode microcantilever by stress inducer and mass inducer to detect PSA at low picogram levels. Lab Chip 9:2683–2690CrossRefGoogle Scholar
  48. 48.
    Shu WM, Liu DS, Watari M, Riener CK, Strunz T, Welland ME, Balasubramanian S, McKendry RA (2005) DNA molecular motor driven micromechanical cantilever arrays. J Am Chem Soc 127:17054–17060CrossRefGoogle Scholar
  49. 49.
    Cha BH, Lee SM, Park JC, Hwang KS, Kim SK, Lee YS, Ju BK, Kim TS (2009) Detection of Hepatitis B Virus (HBV) DNA at femtomolar concentrations using a silica nanoparticle-enhanced microcantilever sensor. Biosens Bioelectron 25:130–135CrossRefGoogle Scholar
  50. 50.
    Xu XB, Li HF, Hasan D, Ruoff RS, Wang AX, Fan DL (2013) Near-field enhanced plasmonic-magnetic bifunctional nanotubes for single cell bioanalysis. Adv Funct Mater 23:4332–4338CrossRefGoogle Scholar
  51. 51.
    Banholzer MJ, Millstone JE, Qin LD, Mirkin CA (2008) Rationally designed nanostructures for surface-enhanced Raman spectroscopy. Chem Soc Rev 37:885–897CrossRefGoogle Scholar
  52. 52.
    Larmour IA, Graham D (2011) Surface enhanced optical spectroscopies for bioanalysis. Analyst 136:3831–3853CrossRefGoogle Scholar
  53. 53.
    Prado E, Daugey N, Plumet S, Servant L, Lecomte S (2011) Quantitative label-free RNA detection using surface-enhanced Raman spectroscopy. Chem Commun 47:7425–7427CrossRefGoogle Scholar
  54. 54.
    Liu YC, Zhong MY, Shan GY, Li YJ, Huang BQ, Yang GL (2008) Biocompatible ZnO/Au nanocomposites for ultrasensitive DNA detection using resonance Raman scattering. J Phys Chem B 112:6484–6489CrossRefGoogle Scholar
  55. 55.
    Hu J, Zheng PC, Jiang JH, Shen GL, Yu RQ, Liu GK (2010) Sub-attomolar HIV-1 DNA detection using surface-enhanced Raman spectroscopy. Analyst 135:1084–1089CrossRefGoogle Scholar
  56. 56.
    Graham D, Thompson DG, Smith WE, Faulds K (2008) Control of enhanced Raman scattering using a DNA-based assembly process of dye-coded nanoparticles. Nat Nanotechnol 3:548–551CrossRefGoogle Scholar
  57. 57.
    Zhang ZL, Wen YQ, Ma Y, Luo J, Jiang L, Song YL (2011) Mixed DNA-functionalized nanoparticle probes for surface-enhanced Raman scattering-based multiplex DNA detection. Chem Commun 47:7407–7409CrossRefGoogle Scholar
  58. 58.
    Li JM, Ma WF, You LJ, Guo J, Hu J, Wang CC (2013) Highly sensitive detection of target ssDNA based on SERS liquid chip using suspended magnetic nanospheres as capturing substrates. Langmuir 29:6147–6155CrossRefGoogle Scholar
  59. 59.
    Sipova H, Zhang SL, Dudley AM, Galas D, Wang K, Homola J (2010) Surface plasmon resonance biosensor for rapid label-free detection of microribonucleic acid at subfemtomole level. Anal Chem 82:10110–10115CrossRefGoogle Scholar
  60. 60.
    Liu JY, Tian SJ, Tiefenauer L, Nielsen PE, Knoll W (2005) Simultaneously amplified electrochemical and surface plasmon optical detection of DNA hybridization based on ferrocene-streptavidin conjugates. Anal Chem 77:2756–2761CrossRefGoogle Scholar
  61. 61.
    Ding XJ, Yan YR, Li SQ, Zhang Y, Cheng W, Cheng Q, Ding SJ (2015) Surface plasmon resonance biosensor for highly sensitive detection of microRNA based on DNA super-sandwich assemblies and streptavidin signal amplification. Anal Chim Acta 874:59–65CrossRefGoogle Scholar

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© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  1. 1.College of Chemistry and Molecular SciencesWuhan UniversityWuhanPeople’s Republic of China

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