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On-chip detection of a single nucleotide polymorphism without polymerase amplification

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Abstract

A nanoparticle-assembled photonic crystal (PC) array was used to detect single nucleotide polymorphism (SNP). The assay platform with PC nanostructure enhanced the fluorescent signal from nanoparticle-hybridized DNA complexes due to phase matching of excitation and emission. Nanoparticles coupled with probe DNA were trapped into nanowells in an array by using an electrophoretic particle entrapment system. The PC/DNA assay platform was able to identify a 1 base pair (bp) difference in synthesized nucleotide sequences that mimicked the mutation seen in a feline model of human autosomal dominant polycystic kidney disease (PKD) with a sensitivity of 0.9 fg/mL (50 aM)-sensitivity, which corresponds to 30 oligos/array. The reliability of the PC/DNA assay platform to detect SNP in a real sample was demonstrated by using genomic DNA (gDNA) extracted from the urine and blood of two PKD-wild type and three PKD positive cats. The standard curves for PKD positive (PKD+) and negative (PKD-) DNA were created using two feline-urine samples. An additional three urine samples were analyzed in a similar fashion and showed satisfactory agreement with the standard curve, confirming the presence of the mutation in affected urine. The limit of detection (LOD) was 0.005 ng/mL which corresponds to 6 fg per array for gDNA in urine and blood. The PC system demonstrated the ability to detect a number of genome equivalents for the PKD SNP that was very similar to the results reported with real time polymerase chain reaction (PCR). The favorable comparison with quantitative PCR suggests that the PC technology may find application well beyond the detection of the PKD SNP, into areas where a simple, cheap and portable nucleic acid analysis is desirable.

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References

  1. Ota, M.; Fukushima, H.; Kulski, J. K.; Inoko, H. Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism. Nat. Protoc. 2007, 2, 2857–2864.

    Article  Google Scholar 

  2. Baris, I.; Etlik, O.; Koksal, V.; Ocak, Z.; Baris, S. T. SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay. Anal. Biochem. 2013, 441, 225–231.

    Article  Google Scholar 

  3. Galvin, P. A nanobiotechnology roadmap for high-throughput single nucleotide polymorphism analysis. Psychiatr. Genet. 2002, 12, 75–82.

    Article  Google Scholar 

  4. Briones, C.; Moreno, M. Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal. Bioanal. Chem. 2012, 402, 3071–3089.

    Article  Google Scholar 

  5. Liu, G.; Lao, R. J.; Xu, L.; Xu, Q.; Li, L. Y.; Zhang, M.; Song, S. P.; Fan, C. H. Single-nucleotide polymorphism genotyping using a novel multiplexed electrochemical biosensor with nonfouling surface. Biosens. Bioelectron. 2013, 42, 516–521.

    Article  Google Scholar 

  6. Wang, D. Z.; Tang, W.; Wu, X. J.; Wang, X. Y.; Chen, G. J.; Chen, Q.; Li, N.; Liu, F. Highly selective detection of single-nucleotide polymorphisms using a quartz crystal microbalance biosensor based on the toehold-mediated strand displacement reaction. Anal. Chem. 2012, 84, 7008–7014.

    Article  Google Scholar 

  7. Altintas, Z.; Tothill, I. E. DNA-based biosensor platforms for the detection of TP53 mutation. Sensor. Actuat. B-Chem. 2012, 169, 188–194.

    Article  Google Scholar 

  8. Lee, J. K.; Cho, S. H.; Lee, J.; Lee, J. H.; Kim, A. Y.; Park, B. H.; Park, J. G.; Busnaina, A.; Lee, H. Y. Detection of single nucleotide polymorphisms using a biosensor-containing titanium-well array. J. Nanosci. Nanotechnol. 2013, 13, 139–143.

    Article  Google Scholar 

  9. Qavi, A. J.; Mysz, T. M.; Bailey, R. C. Isothermal discrimination of single-nucleotide polymorphisms via realtime kinetic desorption and label-free detection of DNA using silicon photonic microring resonator arrays. Anal. Chem. 2011, 83, 6827–6833.

    Article  Google Scholar 

  10. Oh, J. H.; Lee, J. S. Designed hybridization properties of DNA-gold nanoparticle conjugates for the ultraselective detection of a sngle-base mutation in the breast cancer gene BRCA1. Anal. Chem. 2011, 83, 7364–7370.

    Article  Google Scholar 

  11. Block, I. D.; Mathias, P. C.; Ganesh, N.; Jones, S. I.; Dorvel, B. R.; Vikram, C.; Vodkin, L. O.; Bashir, R.; Cunningham, B. T. A detection instrument for enhanced-fluorescence and label-free imaging on photonic crystal surfaces. Opt. Express 2009, 17, 13222–13235.

    Article  Google Scholar 

  12. Huang, C. S.; George, S.; Lu, M.; Chaudhery, V.; Tan, R. M.; Zangar, R. C.; Cunningham, B. T. Application of photonic crystal enhanced fluorescence to cancer biomarker microarrays. Anal. Chem. 2011, 83, 1425–1430.

    Article  Google Scholar 

  13. Li, H.; Wang, J. X.; Pan, Z. L.; Cui, L. Y.; Xu, L.; Wang, R. M.; Song, Y. L.; Jiang, L. Amplifying fluorescence sensing based on inverse opal photonic crystal toward trace TNT detection. J. Mater. Chem. 2011, 21, 1730–1735.

    Article  Google Scholar 

  14. Li, H.; Wang, J. X.; Liu, F.; Song, Y. L.; Wang, R. M. Fluorescence enhancement by heterostructure colloidal photonic crystals with dual stopbands. J. Colloid Interface Sci. 2011, 356, 63–68.

    Article  Google Scholar 

  15. Han, J. H.; Sudheendra, L.; Kim, H. J.; Gee, S. J.; Hammock, B. D.; Kennedy, I. M. Ultrasensitive on-chip immunoassays with a nanoparticle-assembled photonic crystal. ACS Nano 2012, 6, 8570–8582.

    Article  Google Scholar 

  16. Han, J. H.; Kim, H. J.; Sudheendra, L.; Gee, S. J.; Hammock, B. D.; Kennedy, I. M. Photonic crystal lab-on-a chip for detecting Staphylococcal enterotoxin B at low attomolar concentration. Anal. Chem. 2013, 85, 3104–3109.

    Article  Google Scholar 

  17. Rogozin, I. B.; Pavlov, Y. I. Theoretical analysis of mutation hotspots and their DNA sequence context specificity. Mutat. Res. 2003, 544, 65–85.

    Article  Google Scholar 

  18. The International Polycystic Kidney Disease Consortium. Polycystic kidney disease: The complete structure of the PKD1 gene and its protein. Cell 1995, 81, 289–298.

    Google Scholar 

  19. Rossetti, S.; Stmecki, L.; Gamble, V.; Burton, S.; Sneddon, V.; Peral, B.; Roy, S.; Bakkaloglu, A.; Komel, R.; Winearls, C. G. et al. Mutation analysis of the entire PKD1 gene: Genetic and diagnostic implications. Am. J. Hum. Genet. 2001, 68, 46–63.

    Article  Google Scholar 

  20. Migaki, G. Compendium of inherited metabolic diseases in animals. Prog. Clin. Biol. Res. 1982, 94, 473–501.

    Google Scholar 

  21. Son, A.; Dhirapong, A.; Dosev, D. K.; Kennedy, I. M.; Weiss, R. H.; Hristova, K. R. Rapid and quantitative DNA analysis of genetic mutations for polycystic kidney disease (PKD) using magnetic/luminescent nanoparticles. Anal. Bioanal. Chem. 2008, 390, 1829–1835.

    Article  Google Scholar 

  22. Lyons, L. A.; Biller, D. S.; Erdman, C. A.; Lipinski, M. J.; Young, A. E.; Roe, B. A.; Qin, B. F.; Grahn, R. A. Feline polycystic kidney disease mutation identified in PKD1. J. Am. Soc. Nephrol. 2004, 15, 2548–2555.

    Article  Google Scholar 

  23. Deelman, L. E.; Wouden, E. A. v. d.; Duin, M.; Henning, R. H. A Method for the ultra rapid isolation of PCR-ready DNA from urine and buccal swabs. Mol. Biol. Today 2002, 3, 51–54.

    Google Scholar 

  24. Spencer, D. H.; Sellenriek, P.; Burnham, C. A. D. Validation and implementation of the GeneXpert MRSA/SA blood culture assay in a pediatric setting. Am. J. Clin. Pathol. 2011, 136, 690–694.

    Article  Google Scholar 

  25. Helps, C. R.; Tasker, S.; Barr, F. J.; Wills, S. J.; Gruffydd-Jones, T. J. Detection of the single nucleotide polymorphism causing feline autosomal-dominant polycystic kidney disease in Persians from the UK using a novel real-time PCR assay. Mol. Cell. Probe. 2007, 21, 31–34.

    Article  Google Scholar 

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Authors and Affiliations

  1. Department of Mechanical and Aerospace Engineering, University of California, Davis, California, 95616, USA

    Jinhee Han, Lakshmana Sudheendra & Ian M. Kennedy

  2. Division of Nephrology, Department of Internal Medicine, University of California, Davis, California, 95616, USA

    Matthew Tan & Robert H. Weiss

  3. Medical Service, Sacramento VA Medical Center, Sacramento, California, 95655, USA

    Robert H. Weiss

Authors
  1. Jinhee Han
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  2. Matthew Tan
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  3. Lakshmana Sudheendra
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  4. Robert H. Weiss
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  5. Ian M. Kennedy
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Correspondence to Ian M. Kennedy.

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Han, J., Tan, M., Sudheendra, L. et al. On-chip detection of a single nucleotide polymorphism without polymerase amplification. Nano Res. 7, 1302–1310 (2014). https://doi.org/10.1007/s12274-014-0494-z

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  • DOI: https://doi.org/10.1007/s12274-014-0494-z

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