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A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA

Abstract

A fluorescent method is described for simultaneous recognition of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). It is based on the quenching of the fluorescence of fluorophore labeled DNA probes by gold nanoparticles (AuNPs). To demonstrate feasibility, two DNA probes labeled with spectrally different fluorophores were designed. The first DNA probe (P1) was modified with 6-carboxyfluorescein (FAM; with green fluorescence, peaking at 518 nm), while the second (P2) was modified with carboxy-X-rhodamine (ROX; with yellow fluorescence, 610 nm). The fluorescence signals of the labels are quenched if P1 or P2 are adsorbed on AuNPs. Upon addition of ssDNA and dsDNA, hybridization occurs between P1 and ssDNA to form a dsDNA. In contrast, P2 hybridizes with dsDNA such that a triplex DNA is formed. As a result, the dsDNA and the triplex DNA, respectively, are desorbed from the surface of the AuNPs so that quenching no longer can occur and strong fluorescence can be observed. Under the optimal conditions, ssDNA and dsDNA can be detected simultaneously via the green and yellow fluorescence, respectively. The detection limits can be as low as 330 pM. In particular, the method has excellent selectivity for the target DNAs over control DNAs.

A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA is developed based on the fluorescence quenching of gold nanoparticles to different fluorophore labeled DNA probes.

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References

  1. Cao YC, Jin R, Mirkin CA (2002) Nanoparticles with raman spectroscopic fingerprints for DNA and RNA detection. Science 297(5586):1536–1540

    CAS  Article  Google Scholar 

  2. Heller MJ (2002) DNA microarray technology: devices, systems, and applications. Annu Rev Biomed Eng 4(1):129

    CAS  Article  Google Scholar 

  3. Fechter EJ, Olenyuk B, Dervan PB (2005) Sequence-specific fluorescence detection of DNA by polyamide-thiazole orange conjugates. J Am Chem Soc 127(47):16685–16691

    CAS  Article  Google Scholar 

  4. Pavlov V, Shlyahovsky B, Willner I (2005) Fluorescence detection of DNA by the catalytic- activation of an aptamer/thrombin complex. J Am Chem Soc 127(18):6522–6523

    CAS  Article  Google Scholar 

  5. Wang M, Zhang D, Zhang G, Tang Y, Wang S, Zhu D (2008) Fluorescence turn-on detection of DNA and label-free fluorescence nuclease assay based on the aggregation-induced emission of silole. Anal Chem 80(16):6443–6448

    CAS  Article  Google Scholar 

  6. Niu S, Jiang Y, Zhang S (2010) Fluorescence detection for DNA using hybridization chain reaction with enzyme-amplification. Chem Commun 46(18):3089–3091

    CAS  Article  Google Scholar 

  7. Qian ZS, Shan XY, Chai LJ, Ma JJ, Chen JR, Feng H (2014) A universal fluorescence sensing strategy based on biocompatible graphene quantum dots and graph- ene oxide for the detection of DNA. Nano 6(11):5671–5674

    CAS  Google Scholar 

  8. Lepoitevin M, Lemouel M, Bechelany M, Janot JM, Balme S (2015) Gold nanoparticles for the bare-eye based and spectrophotometric detection of proteins, po- lynucleotides and DNA. Microchim Acta 182(5–6):1223–1229

    CAS  Article  Google Scholar 

  9. Rucker VC, Foister S, Melander C, Dervan PB (2003) Sequence specific fluorescence detection of double strand DNA. J Am Chem Soc 125(5):1195–1202

    CAS  Article  Google Scholar 

  10. Zhao D, Chan WH, He Z, Qiu T (2009) Quantum dot-ruthenium complex dyads: recogni- tion of double-strand DNA through dual-color fluorescence detection. Anal Chem 81(9):3537–3543

    CAS  Article  Google Scholar 

  11. Xiao Z, Guo X, Ling L (2013) Sequence-specific recognition of double-stranded DNA with molecular beacon with the aid of ag (+) under neutral pH environment. Chem Commun 49(34):3573–3575

    CAS  Article  Google Scholar 

  12. Zhang Y, Zheng B, Zhu C, Zhang X, Tan C, Li H, Huang Y (2015) Single-layer transition metal dichalcogenide nanosheet-based nanosensors for rapid, sensitive, and multiplexed detection of DNA. Adv Mater 27(5):935–939

    CAS  Article  Google Scholar 

  13. Zhang Y, Zhu C, Zhang L, Tan C, Yang J, Chen B, Zhang H (2015) DNA-templated silver nanoclusters for multiplexed fluorescent DNA detection. Small 11(12):1384–1384

    Article  Google Scholar 

  14. Parvin N, Jin Q, Wei Y, Yu R, Zheng B, Huang L, Gao M (2017) Few-layer graphdiyne nanosheets applied for multiplexed real-time DNA detection. Adv Mater 29(18):1606–1755

    Article  Google Scholar 

  15. Enkin N, Wang F, Sharon E, Albada HB, Willner I (2014) Multiplexed analysi of genes using nucleic acid-stabilized silver-nanocluster quantum dots. ACS Nano 8(11):11666–11673

    CAS  Article  Google Scholar 

  16. Spellman PT, Gray JW (2014) Detecting cancer by monitoring circulating tumor DNA. Nat Med 20(5):474–475

    CAS  Article  Google Scholar 

  17. Elghanian R, Storhoff JJ, Mucic RC, Letsinger RL, Mirkin CA (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optic- al properties of gold nanoparticles. Science 277(5329):1078

    CAS  Article  Google Scholar 

  18. Taton TA, Lu G, Mirkin CA (2001) Two-color labeling of oligonucleotide arrays via size-selective scattering of nanoparticle probes. J Am Chem Soc 123(21):5164–5165

    CAS  Article  Google Scholar 

  19. Li H, Rothberg L (2004) Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. P Natl Acad Sci USA 101(39):14036–14039

    CAS  Article  Google Scholar 

  20. Wang L, Liu X, Hu X, Song S, Fan C (2006) Unmodified gold nanoparticles as a colorimetric probe for potassium DNA aptamers. Chem Commun 36(36):3780–3782

    Article  Google Scholar 

  21. Novotny L, Bharadwaj P, Anger P (2006) Enhancement and quenching of single molecule fluorescence near a gold nanoparticle. Phys Rev Lett 96(11):113002

    Article  Google Scholar 

  22. Shi J, Chan C, Pang Y, Ye W, Tian F, Lyu J, Yang M (2015) A fluorescence resonance energy transfer (FRET) biosensor based on graphene quantum dots (GQDs) and gold nanoparticles (AuNPs) for the detection of mecA gene sequence of Staphylococcus Aureus. Biosens Bioelectron 67(5):595–600

    CAS  Article  Google Scholar 

  23. Li H, Rothberg LJ (2004) DNA sequence detection using selective fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles. Anal Chem 76(18):5414–5417

    CAS  Article  Google Scholar 

  24. Wu ZS, Jiang JH, Fu L, Shen GL, Yu RQ (2006) Optical detection of DNA hybridization based on fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles. Anal Biochem 353(1):22–29

    CAS  Article  Google Scholar 

  25. Spink CH, Chaires JB (1997) Thermodynamics of the binding of a cationic lipid to DNA. J Am Chem Soc 119(45):10920–10928

    CAS  Article  Google Scholar 

  26. Xodo LE, Manzini G, Quadrifoglio F (1990) Spectroscopic and calorimetric investigation on the DNA triplex formed by d(CTCTTCTTTCTTTTCTTTCTTCTC) and d(GAGAAGAAAGA) at acidic pH. Nucleic Acids Res 18(12):3557–3564

    CAS  Article  Google Scholar 

  27. Chen P, Peng W, Chen J, Peng Y, Zhang X, Zheng C, Hou X (2016) Label-free and separation-free atomic fluorescence spectrometry-based bioassay: sensitive determination of single-strand DNA, protein, and double-strand DNA. Anal Chem 88(4):2065–2071

    CAS  Article  Google Scholar 

  28. Qu F, Liu Y, Kong R, You J (2017) A versatile DNA detection scheme based on the quench ing of fluorescent silver nanoclusters by MoS2 nanosheets: application to aptamer-based determination of hepatitis B virus and of dopamine. Microchim Acta 184(11):4417–4424

    CAS  Article  Google Scholar 

  29. Liu Y, Ye M, Ge Q, Qu X, Guo Q, Hu X, Sun Q (2016) Ratiometric quantum dot-ligand system made by phase transfer for visual detection of double stranded DNA and single- nucleotide polymorphism. Anal Chem 88(3):1768–1774

    CAS  Article  Google Scholar 

  30. Thangaraj V, Lepoitevin M, Smietana M, Balanzat E, Bechelany M, Janot JM, Balme S (2016) Detection of short ssDNA and dsDNA by current-voltage me- asurements using conical nanopores coated with Al2O3 by atomic layer deposi- tion. Microchim Acta 183(3):1011–1017

    CAS  Article  Google Scholar 

  31. Deng H, Zhang X, Kumar A, Zou G, Zhang X, Liang XJ (2013) Long genomic DNA amplicons adsorption onto unmodified gold nanoparticles for colorimetric detection of bacillus anthracis. Chem Commun 49(1):51–53

    CAS  Article  Google Scholar 

  32. Singh I, Wendeln C, Clark AW, Cooper JM, Ravoo BJ, Burley GA (2013) Sequence-selective detection of double-stranded DNA sequences using pyrrole-imidazole polyamide microarrays. J Am Chem Soc 135(9):3449

    CAS  Article  Google Scholar 

  33. Zhang Y, Sun XY, Liu B (2009) Fluorescent recognition for single- and double-stranded oligonucleotides based on rhodamine B-modified self-assembled bilayers. Chinese. J Anal Chem 37(5):665–670

    CAS  Google Scholar 

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Acknowledgements

This work was supported by the National Natural Science Foundations of China (21305053), Postgraduate Research & Practice Innovation Program of Jiangsu Province (KYZZ16_0468), and the Research Innovation Program for College Graduates of Jiangsu Normal University (2017YXJ125).

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Correspondence to Xiangmin Miao.

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Ma, H., Li, Z., Xue, N. et al. A gold nanoparticle based fluorescent probe for simultaneous recognition of single-stranded DNA and double-stranded DNA. Microchim Acta 185, 93 (2018). https://doi.org/10.1007/s00604-017-2633-1

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  • DOI: https://doi.org/10.1007/s00604-017-2633-1

Keywords

  • Single-stranded DNA
  • Double-stranded DNA
  • Simultaneous detection
  • Fluorescence
  • Gold nanoparticles
  • DNA probe