Detection of Non-Amplified Genomic DNA pp 67-87

Part of the Soft and Biological Matter book series (SOBIMA)

Engineered Nanostructures for the Ultrasensitive DNA Detection

Chapter

Abstract

Coupled with nanotechnologies, a wide variety of DNA sensing methods have been developed to achieve ultrahigh sensitivity and selectivity without the aid of enzymatic amplification procedures or complicated assay procedures. Structurally engineered nanomaterials have several useful aspects including their unique optical properties depending on size, shape, composition and structural details and electrical properties, which have been translated into various signal transduction modes. However, the most important challenge in DNA detection assay to compete with or complement the polymerase chain reaction (PCR) is matching the sensitivity of PCR, which can detect 10–100 copies in whole sample via various non-enzymatic amplification strategies. Here, we introduce recent advances in engineered nanostructure-based DNA detection methods that show potential for PCR-like sensitivity and can address the existing issues of conventional DNA detection assays. The basic principles, advantages, and limitations of engineered nanostructure-amplified DNA detection methods will be introduced and discussed.

References

  1. 1.
    Shim, S.-Y., Lim, D.-K., Nam, J.-M.: Ultrasensitive optical biodiagnostic methods using metallic nanoparticles. Nanomedicine 3(2), 215–232 (2008)CrossRefGoogle Scholar
  2. 2.
    Peng, H.-I., Miller, B.L.: Recent advancements in optical DNA biosensors: exploiting the plasmonic effects of metal nanoparticles. Analyst 136(3), 436–447 (2011)CrossRefADSGoogle Scholar
  3. 3.
    Jeon, J., Lim, D.-K., Nam, J.-M.: Functional nanomaterial-based amplified bio-detection strategies. J. Mater. Chem. 19(15), 2107–2117 (2009)CrossRefGoogle Scholar
  4. 4.
    Wittenberg, N.J., Haynes, C.L.: Using nanoparticles to push the limits of detection. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. 1(2), 237–254 (2009)CrossRefGoogle Scholar
  5. 5.
    Selhuber-Unkel, C., et al.: Quantitative optical trapping of single gold nanorods. Nano Lett. 8(9), 2998–3003 (2008)CrossRefADSGoogle Scholar
  6. 6.
    Khoury, C.G., Vo-Dinh, T.: Gold nanostars for surface-enhanced Raman scattering: synthesis, characterization and optimization. J. Phys. Chem. C 112(48), 18849–18859 (2008)Google Scholar
  7. 7.
    Personick, M.L., et al.: Synthesis and isolation of {110}-faceted gold bipyramids and rhombic dodecahedra. J. Am. Chem. Soc. 133(16), 6170–6173 (2011)CrossRefGoogle Scholar
  8. 8.
    Kitaygorodskiy, A., et al.: Nmr detection of single-walled carbon nanotubes in solution. J. Am. Chem. Soc. 127(20), 7517–7520 (2005)CrossRefGoogle Scholar
  9. 9.
    Si, Y., Samulski, E.T.: Synthesis of water soluble graphene. Nano Lett. 8(6), 1679–1682 (2008)CrossRefADSGoogle Scholar
  10. 10.
    Rosi, N.L., Mirkin, C.A.: Nanostructures in biodiagnostics. Chem. Rev. 105(4), 1547–1562 (2005)CrossRefGoogle Scholar
  11. 11.
    Mirkin, C.A., et al.: A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382(6592), 607–609 (1996)CrossRefADSGoogle Scholar
  12. 12.
    Elghanian, R., et al.: Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277(5329), 1078–1081 (1997)CrossRefGoogle Scholar
  13. 13.
    Storhoff, J.J., et al.: What controls the optical properties of DNA-linked gold nanoparticle assemblies? J. Am. Chem. Soc. 122(19), 4640–4650 (2000)CrossRefGoogle Scholar
  14. 14.
    Storhoff, J.J., et al.: One-pot colorimetric differentiation of polynucleotides with single base imperfections using gold nanoparticle probes. J. Am. Chem. Soc. 120(9), 1959–1964 (1998)CrossRefGoogle Scholar
  15. 15.
    Storhoff, J.J., et al.: Homogeneous detection of unamplified genomic DNA sequences based on colorimetric scatter of gold nanoparticle probes. Nat. Biotechnol. 22(7), 883–887 (2004)CrossRefGoogle Scholar
  16. 16.
    Ling, J., et al.: Light-scattering signals from nanoparticles in biochemical assay, pharmaceutical analysis and biological imaging. TrAC Trends Anal. Chem. 28(4), 447–453 (2009)CrossRefGoogle Scholar
  17. 17.
    Taton, T.A., Mirkin, C.A., Letsinger, R.L.: Scanometric DNA array detection with nanoparticle probes. Science 289(5485), 1757–1760 (2000)CrossRefADSGoogle Scholar
  18. 18.
    Cao, Y.C., Jin, R., Mirkin, C.A.: Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297(5586), 1536–1540 (2002)CrossRefADSGoogle Scholar
  19. 19.
    Park, S.-J., Taton, T.A., Mirkin, C.A.: Array-based electrical detection of DNA with nanoparticle probes. Science 295(5559), 1503–1506 (2002)ADSGoogle Scholar
  20. 20.
    Thompson, D.G., et al.: Ultrasensitive DNA detection using oligonucleotide – silver nanoparticle conjugates. Anal. Chem. 80(8), 2805–2810 (2008)CrossRefGoogle Scholar
  21. 21.
    Lee, J.-S., et al.: Silver nanoparticle – oligonucleotide conjugates based on DNA with triple cyclic disulfide moieties. Nano Lett. 7(7), 2112–2115 (2007)CrossRefADSGoogle Scholar
  22. 22.
    Cao, Y., Jin, R., Mirkin, C.A.: DNA-modified core–shell Ag/Au nanoparticles. J. Am. Chem. Soc. 123(32), 7961–7962 (2001)CrossRefGoogle Scholar
  23. 23.
    Lim, D.-K., Kim, I.-J., Nam, J.-M.: DNA-embedded Au/Ag core-shell nanoparticles. Chem. Commun. 42, 5312–5314 (2008)CrossRefGoogle Scholar
  24. 24.
    Li, H., Rothberg, L.: Colorimetric detection of DNA sequences based on electrostatic interactions with unmodified gold nanoparticles. Proc. Natl. Acad. Sci. USA 101(39), 14036–14039 (2004)CrossRefADSGoogle Scholar
  25. 25.
    Xia, F., et al.: Colorimetric detection of DNA, small molecules, proteins, and ions using unmodified gold nanoparticles and conjugated polyelectrolytes. Proc. Natl. Acad. Sci. USA 107(24), 10837–10841 (2010)CrossRefADSGoogle Scholar
  26. 26.
    Xu, X., et al.: Homogeneous detection of nucleic acids based upon the light scattering properties of silver-coated nanoparticle probes. Anal. Chem. 79(17), 6650–6654 (2007)CrossRefGoogle Scholar
  27. 27.
    Nam, J.-M., Thaxton, C.S., Mirkin, C.A.: Nanoparticle-based bio-bar codes for the ultrasensitive detection of proteins. Science 301(5641), 1884–1886 (2003)CrossRefADSGoogle Scholar
  28. 28.
    Goluch, E.D., et al.: A bio-barcode assay for on-chip attomolar-sensitivity protein detection. Lab Chip 6(10), 1293–1299 (2006)CrossRefGoogle Scholar
  29. 29.
    Stoeva, S.I., et al.: Multiplexed DNA detection with biobarcoded nanoparticle probes. Angew. Chem. Int. Ed. 45(20), 3303–3306 (2006)CrossRefGoogle Scholar
  30. 30.
    Zhang, D., Carr, D.J., Alocilja, E.C.: Fluorescent bio-barcode DNA assay for the detection of Salmonella enterica serovar Enteritidis. Biosens. Bioelectron. 24(5), 1377–1381 (2009)CrossRefGoogle Scholar
  31. 31.
    Nam, J.-M., Jang, K.-J., Groves, J.T.: Detection of proteins using a colorimetric bio-barcode assay. Nat. Protoc. 2(6), 1438–1444 (2007)CrossRefGoogle Scholar
  32. 32.
    Graham, D., et al.: Control of enhanced Raman scattering using a DNA-based assembly process of dye-coded nanoparticles. Nat. Nanotechnol. 3(9), 548–551 (2008)CrossRefADSGoogle Scholar
  33. 33.
    Im, H., et al.: Vertically oriented sub-10-nm plasmonic nanogap arrays. Nano Lett. 10(6), 2231–2236 (2010)CrossRefADSGoogle Scholar
  34. 34.
    Kang, T., et al.: Patterned multiplex pathogen DNA detection by Au particle-on-wire SERS sensor. Nano Lett. 10(4), 1189–1193 (2010)CrossRefADSGoogle Scholar
  35. 35.
    Li, W., et al.: Dimers of silver nanospheres: facile synthesis and their use as hot spots for surface-enhanced Raman scattering. Nano Lett. 9(1), 485–490 (2008)CrossRefADSGoogle Scholar
  36. 36.
    Theiss, J., et al.: Plasmonic nanoparticle arrays with nanometer separation for high-performance SERS substrates. Nano Lett. 10(8), 2749–2754 (2010)CrossRefADSGoogle Scholar
  37. 37.
    Qian, X., Zhou, X., Nie, S.: Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling. J. Am. Chem. Soc. 130(45), 14934–14935 (2008)CrossRefGoogle Scholar
  38. 38.
    Johnson, D.S., et al.: Genome-wide mapping of in vivo protein-DNA interactions. Science 316, 1497–1502 (2007)CrossRefADSGoogle Scholar
  39. 39.
    Wabuyele, M.B., Vo-Dinh, T.: Detection of human immunodeficiency virus type 1 DNA sequence using plasmonics nanoprobes. Anal. Chem. 77(23), 7810–7815 (2005)CrossRefGoogle Scholar
  40. 40.
    Huh, Y.S., et al.: Surface-enhanced Raman scattering based ligase detection reaction. J. Am. Chem. Soc. 131(6), 2208–2213 (2009)CrossRefGoogle Scholar
  41. 41.
    Xi, D., et al.: The detection of HBV DNA with gold-coated iron oxide nanoparticle gene probes. J. Nanopart. Res. 10(3), 393–400 (2008)CrossRefGoogle Scholar
  42. 42.
    Perez, J.M., et al.: Magnetic relaxation switches capable of sensing molecular interactions. Nat. Biotechnol. 20(8), 816–820 (2002)Google Scholar
  43. 43.
    Gerion, D., et al.: Room-temperature single-nucleotide polymorphism and multiallele DNA detection using fluorescent nanocrystals and microarrays. Anal. Chem. 75(18), 4766–4772 (2003)CrossRefGoogle Scholar
  44. 44.
    Wu, Z.-S., et al.: Optical detection of DNA hybridization based on fluorescence quenching of tagged oligonucleotide probes by gold nanoparticles. Anal. Biochem. 353(1), 22–29 (2006)CrossRefGoogle Scholar
  45. 45.
    Wang, H., et al.: Combination of DNA ligase reaction and gold nanoparticle-quenched fluorescent oligonucleotides: a simple and efficient approach for fluorescent assaying of single-nucleotide polymorphisms. Anal. Chem. 82(18), 7684–7690 (2010)CrossRefGoogle Scholar
  46. 46.
    Son, A., et al.: Rapid and quantitative DNA analysis of genetic mutations for polycystic kidney disease (PKD) using magnetic/luminescent nanoparticles. Anal. Bioanal. Chem. 390(7), 1829–1835 (2008)CrossRefGoogle Scholar
  47. 47.
    Malicka, J., Gryczynski, I., Lakowicz, J.R.: DNA hybridization assays using metal-enhanced fluorescence. Biochem. Biophys. Res. Commun. 306(1), 213–218 (2003)CrossRefGoogle Scholar
  48. 48.
    Gunnarsson, A., et al.: Single-molecule detection and mismatch discrimination of unlabeled DNA targets. Nano Lett. 8(1), 183–188 (2007)CrossRefADSGoogle Scholar
  49. 49.
    Shiddiky, M.J.A., Rahman, M.A., Shim, Y.-B.: Hydrazine-catalyzed ultrasensitive detection of DNA and proteins. Anal. Chem. 79(17), 6886–6890 (2007)CrossRefGoogle Scholar
  50. 50.
    Verigene System, Nanosphere, Inc., Northbrook, IL, USA. www.nanosphere.us
  51. 51.
    Zhang, J., et al.: Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes. J. Am. Chem. Soc. 128(26), 8575–8580 (2006)CrossRefGoogle Scholar
  52. 52.
    Bailey, R.C., et al.: Real-time multicolor DNA detection with chemoresponsive diffraction gratings and nanoparticle probes. J. Am. Chem. Soc. 125(44), 13541–13547 (2003)CrossRefGoogle Scholar
  53. 53.
    Zhao, X., Tapec-Dytioco, R., Tan, W.: Ultrasensitive DNA detection using highly fluorescent bioconjugated nanoparticles. J. Am. Chem. Soc. 125(38), 11474–11475 (2003)CrossRefGoogle Scholar
  54. 54.
    Qin, L., et al.: Nanodisk codes. Nano Lett. 7(12), 3849–3853 (2007)CrossRefADSGoogle Scholar
  55. 55.
    Lim, D.-K., et al.: Nanogap-engineerable Raman-active nanodumbbells for single-molecule detection. Nat. Mater. 9(1), 60–67 (2010)CrossRefADSGoogle Scholar
  56. 56.
    Lim, D.-K., et al.: Highly uniform and reproducible surface-enhanced Raman scattering from DNA-tailorable nanoparticles with 1-nm interior gap. Nat. Nanotechnol. 6(7), 452–460 (2011)CrossRefADSGoogle Scholar
  57. 57.
    Weizmann, Y., Chenoweth, D.M., Swager, T.M.: DNA – CNT nanowire networks for DNA detection. J. Am. Chem. Soc. 133(10), 3238–3241 (2011)CrossRefGoogle Scholar
  58. 58.
    Roy, S., et al.: Mass-produced nanogap sensor arrays for ultrasensitive detection of DNA. J. Am. Chem. Soc. 131(34), 12211–12217 (2009)CrossRefGoogle Scholar
  59. 59.
    Xiao, Y., et al.: An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. J. Am. Chem. Soc. 131(42), 15311–15316 (2009)CrossRefGoogle Scholar
  60. 60.
    Lubin, A.A., et al.: Sequence-specific, electronic detection of oligonucleotides in blood, soil, and foodstuffs with the reagentless, reusable e-DNA sensor. Anal. Chem. 78(16), 5671–5677 (2006)CrossRefGoogle Scholar
  61. 61.
    Lubin, A.A., et al.: Effects of probe length, probe geometry, and redox-tag placement on the performance of the electrochemical e-DNA sensor. Anal. Chem. 81(6), 2150–2158 (2009)CrossRefGoogle Scholar
  62. 62.
    Gao, A., et al.: Silicon-nanowire-based CMOS-compatible field-effect transistor nanosensors for ultrasensitive electrical detection of nucleic acids. Nano Lett. 11(9), 3974–3978 (2011)CrossRefADSGoogle Scholar
  63. 63.
    Chen, C.-P., et al.: Ultrasensitive in situ label-free DNA detection using a GaN nanowire-based extended-gate field-effect-transistor sensor. Anal. Chem. 83(6), 1938–1943 (2011)CrossRefGoogle Scholar
  64. 64.
    Shendure, J., Ji, H.: Next-generation DNA sequencing. Nat. Biotechnol. 26(10), 1135–1145 (2008)CrossRefGoogle Scholar
  65. 65.
    Hutchison, C.A.: DNA sequencing: bench to bedside and beyond. Nucleic Acids Res. 35, 6227–6237 (2007)CrossRefGoogle Scholar
  66. 66.
    Shendure, J., et al.: Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 5, 335–344 (2004)CrossRefGoogle Scholar
  67. 67.
    Agrawal, A., et al.: Counting single native biomolecules and intact viruses with color-coded nanoparticles. Anal. Chem. 78(4), 1061–1070 (2006)CrossRefGoogle Scholar
  68. 68.
    Liu, K.J., et al.: Decoding circulating nucleic acids in human serum using microfluidic single molecule spectroscopy. J. Am. Chem. Soc. 132(16), 5793–5798 (2010)CrossRefGoogle Scholar
  69. 69.
    Levene, M.J.: Zero-mode waveguides for single-molecule analysis at high concentrations. Science 299, 682–686 (2003)CrossRefADSGoogle Scholar
  70. 70.
    Li, S.-J., et al.: A nanochannel array-based electrochemical device for quantitative label-free DNA analysis. ACS Nano 4(11), 6417–6424 (2010)CrossRefGoogle Scholar
  71. 71.
    Menard, L.D., Ramsey, J.M.: Fabrication of sub-5 nm nanochannels in insulating substrates using focused ion beam milling. Nano Lett. 11(2), 512–517 (2010)CrossRefADSGoogle Scholar
  72. 72.
    Yang, S.Y., et al.: DNA-functionalized nanochannels for SNP detection. Nano Lett. 11(3), 1032–1035 (2011)CrossRefADSGoogle Scholar
  73. 73.
    Ivanov, A.P., et al.: DNA tunneling detector embedded in a nanopore. Nano Lett. 11(1), 279–285 (2010)CrossRefADSGoogle Scholar
  74. 74.
    Liang, X., et al.: Single sub-20 nm wide, centimeter-long nanofluidic channel fabricated by novel nanoimprint mold fabrication and direct imprinting. Nano Lett. 7(12), 3774–3780 (2007)CrossRefADSGoogle Scholar
  75. 75.
    Spiering, A., et al.: Nanopore translocation dynamics of a single DNA-bound protein. Nano Lett. 11(7), 2978–2982 (2011)CrossRefGoogle Scholar
  76. 76.
    McNally, B., et al.: Optical recognition of converted DNA nucleotides for single-molecule DNA sequencing using nanopore arrays. Nano Lett. 10(6), 2237–2244 (2010)CrossRefADSGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  1. 1.Department of ChemistrySeoul National UniversitySeoulSouth Korea

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