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Functional DNA-Integrated Nanomaterials for Biosensing

Abstract

This chapter reviews recent progress in the development of biosensors by integrating functional DNA molecules with nanoscale science and technology. Functional DNA, a new class of DNA with functions beyond genetic information storage, can either bind to a target molecule (known as aptamers) or perform catalytic reactions (called DNAzymes). The targets of functional DNA can range from metal ions and small organic molecules to proteins, and even cells, making them a general platform for recognizing a broad range of targets. On the other hand, recent progress in nanoscale science and technology has resulted in a number of nanomaterials with interesting optical, electrical, magnetic, and catalytic properties. Inspired by functional DNA biology and nanotechnology, various methods have been developed to integrate functional DNA with these nanomaterials, such as gold nanoparticles, fluorescent nanoparticles, superparamagnetic iron oxide nanoparticles, and graphene, for designing a variety of fluorescent, colorimetric, surface-enhanced Raman scattering, and magnetic resonance imaging sensors for the detection of a broad range of analytes.

Keywords

  • Biosensor
  • DNA
  • Aptamer
  • DNAzyme
  • Nanomaterials

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References

  1. Alivisatos AP (1996) Semiconductor clusters, nanocrystals, and quantum dots. Science 271:933–937

    CAS  CrossRef  Google Scholar 

  2. Qian X, Peng XH, Ansari DO, Yin-Goen Q, Chen GZ, Shin DM, Yang L, Young AN, Wang MD, Nie S (2007) In vivo tumor targeting and spectroscopic detection with surface-enhanced Raman nanoparticle tags. Nat Biotechnol 26:83–90

    CrossRef  CAS  Google Scholar 

  3. Cheon J, Lee JH (2008) Synergistically integrated nanoparticles as multimodal probes for nanobiotechnology. Acc Chem Res 41:1630–1640

    CAS  CrossRef  Google Scholar 

  4. Cao YWC, Jin R, Mirkin CA (2002) Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297:1536–1540

    CAS  CrossRef  Google Scholar 

  5. Lim SI, Zhong CJ (2009) Molecularly mediated processing and assembly of nanoparticles: exploring the interparticle interactions and structures. Acc Chem Res 42:798–808

    CAS  CrossRef  Google Scholar 

  6. Liu J, Cao Z, Lu Y (2009) Functional nucleic acid sensors. Chem Rev 109:1948–1998

    CAS  CrossRef  Google Scholar 

  7. Storhoff JJ, Mirkin CA (1999) Programmed materials synthesis with DNA. Chem Rev 99:1849–1862

    CAS  CrossRef  Google Scholar 

  8. Robertson DL, Joyce GF (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded DNA. Nature 344:467–468

    CAS  CrossRef  Google Scholar 

  9. Tuerk C, Gold L (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510

    CAS  CrossRef  Google Scholar 

  10. Ellington AD, Szostak JW (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346:818–822

    CAS  CrossRef  Google Scholar 

  11. Breaker RR, Joyce GF (1994) A DNA enzyme that cleaves RNA. Chem Biol 1:223–229

    CAS  CrossRef  Google Scholar 

  12. Breaker RR (1997) DNA enzymes. Nat Biotechnol 15:427–431

    CAS  CrossRef  Google Scholar 

  13. Silverman SK (2005) In vitro selection, characterization, and application of deoxyribozymes that cleave RNA. Nucleic Acids Res 33:6151–6163

    CAS  CrossRef  Google Scholar 

  14. Robertson MP, Ellington AD (1999) In vitro selection of an allosteric ribozyme that transduces analytes to amplicons. Nat Biotechnol 17:62–66

    CAS  CrossRef  Google Scholar 

  15. Bunka DHJ, Stockley PG (2006) Aptamers come of age – at last. Nat Rev Microbiol 4:588–596

    CAS  CrossRef  Google Scholar 

  16. O’Sullivan CK (2002) Aptasensors – the future of biosensing? Anal Bioanal Chem 372:44–48

    CrossRef  CAS  Google Scholar 

  17. Lu Y, Liu J (2007) Smart nanomaterials inspired by biology: dynamic assembly of error-free nanomaterials in response to multiple chemical and biological stimuli. Acc Chem Res 40:315–323

    CAS  CrossRef  Google Scholar 

  18. Lu Y (2002) New transition-metal-dependent DNAzymes as efficient endonucleases and as selective metal biosensors. Chem Eur J 8:4588–4596

    CAS  CrossRef  Google Scholar 

  19. Lu Y, Liu J (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr Opin Biotechnol 17:580–588

    CAS  CrossRef  Google Scholar 

  20. Navani NK, Li Y (2006) Nucleic acid aptamers and enzymes as sensors. Curr Opin Chem Biol 10:272–281

    CAS  CrossRef  Google Scholar 

  21. Li D, Song S, Fan C (2010) Target-responsive structural switching for nucleic acid-based sensors. Acc Chem Res 43:631–641

    CrossRef  CAS  Google Scholar 

  22. Guo S, Wang E (2011) Functional micro/nanostructures: simple synthesis and application in sensors, fuel cells, and gene delivery. Acc Chem Res 44:491–500

    CAS  CrossRef  Google Scholar 

  23. Daniel MC, Astruc D (2004) Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology. Chem Rev 104:293–346

    CAS  CrossRef  Google Scholar 

  24. Rosi NL, Mirkin CA (2005) Nanostructures in biodiagnostics. Chem Rev 105:1547–1562

    CAS  CrossRef  Google Scholar 

  25. Murphy CJ, Gole AM, Stone JW, Sisco PN, Alkilany AM, Goldsmith EC, Baxter SC (2008) Gold nanoparticles in biology: beyond toxicity to cellular imaging. Acc Chem Res 41:1721–1730

    CAS  CrossRef  Google Scholar 

  26. Storhoff JJ, Lazarides AA, Mucic RC, Mirkin CA, Letsinger RL, Schatz GC (2000) What controls the optical properties of DNA-linked gold nanoparticle assemblies? J Am Chem Soc 122:4640–4650

    CAS  CrossRef  Google Scholar 

  27. Mirkin CA, Letsinger RL, Mucic RC, Storhoff JJ (1996) A DNA-based method for rationally assembling nanoparticles into macroscopic materials. Nature 382:607–609

    CAS  CrossRef  Google Scholar 

  28. Alivisatos AP, Johnsson KP, Peng X, Wilson TE, Loweth CJ, Bruchez MP Jr, Schultz PG (1996) Organization of ‘nanocrystal molecules’ using DNA. Nature 382:609–611

    CAS  CrossRef  Google Scholar 

  29. Elghanian R, Storhoff JJ, Mucic RC, Letsinger RL, Mirkin CA (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277:1078–1081

    CAS  CrossRef  Google Scholar 

  30. Reynolds RA, Mirkin CA, Letsinger RL (2000) Homogeneous, nanoparticle-based quantitative colorimetric detection of oligonucleotides. J Am Chem Soc 122:3795–3796

    CAS  CrossRef  Google Scholar 

  31. Jin R, Wu G, Li Z, Mirkin CA, Schatz GC (2003) What controls the melting properties of DNA-linked gold nanoparticle assemblies. J Am Chem Soc 125:1643–1654

    CAS  CrossRef  Google Scholar 

  32. Liu J, Lu Y (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J Am Chem Soc 125:6642–6643

    CAS  CrossRef  Google Scholar 

  33. Liu J, Lu Y (2004) Accelerated color change of gold nanoparticles assembled by DNAzymes for simple and fast colorimetric Pb2+ detection. J Am Chem Soc 126:12298–12305

    CAS  CrossRef  Google Scholar 

  34. Liu J, Lu Y (2005) Stimuli-responsive disassembly of nanoparticle aggregates for light-up colorimetric sensing. J Am Chem Soc 127:12677–12683

    CAS  CrossRef  Google Scholar 

  35. Liu J, Lu Y (2006) Design of asymmetric DNAzymes for dynamic control of nanoparticle aggregation states in response to chemical stimuli. Org Biomol Chem 4:3435–3441

    CAS  CrossRef  Google Scholar 

  36. Liu J, Lu Y (2007) Colorimetric Cu2+ detection with a ligation DNAzyme and nanoparticles. Chem Commun 46:4872–4874

    CrossRef  CAS  Google Scholar 

  37. Li H, Rothberg LJ (2004) Label-free colorimetric detection of specific sequences in genomic DNA amplified by the polymerase chain reaction. J Am Chem Soc 126:10958–10961

    CAS  CrossRef  Google Scholar 

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

    CAS  CrossRef  Google Scholar 

  39. Li H, Rothberg LJ (2005) Detection of specific sequences in RNA using differential adsorption of single-stranded oligonucleotides on gold nanoparticles. Anal Chem 77:6229–6233

    CAS  CrossRef  Google Scholar 

  40. Lee JH, Wang Z, Liu J, Lu Y (2008) Highly sensitive and selective colorimetric sensors for uranyl (UO2 2+): development and comparison of labeled and label-free DNAzyme-gold nanoparticle systems. J Am Chem Soc 130:14217–14226

    CAS  CrossRef  Google Scholar 

  41. Wang Z, Lee JH, Lu Y (2008) Label-free colorimetric detection of lead ions with a nanomolar detection limit and tunable dynamic range by using gold nanoparticles and DNAzyme. Adv Mater 17:3263–3267

    CrossRef  CAS  Google Scholar 

  42. Wei H, Li B, Li J, Dong S, Wang E (2008) DNAzyme-based colorimetric sensing of lead (Pb2+) using unmodified gold nanoparticle probes. Nanotechnology 19:095501

    CrossRef  CAS  Google Scholar 

  43. Lee JS, Han MS, Mirkin CA (2007) Colorimetric detection of mercuric ion (Hg2+) in aqueous media using DNA-functionalized gold nanoparticles. Angew Chem Int Ed 46:4093–4096

    CAS  CrossRef  Google Scholar 

  44. Xue X, Wang F, Liu X (2008) One-step, room temperature, colorimetric detection of mercury (Hg2+) using DNA/nanoparticle conjugates. J Am Chem Soc 130:3244–3245

    CAS  CrossRef  Google Scholar 

  45. Torabi SF, Lu Y (2011) Small-molecule diagnostics based on functional DNA nanotechnology: a dipstick test for mercury. Faraday Discuss 149:125–135

    CAS  CrossRef  Google Scholar 

  46. Li D, Wieckowska A, Willner I (2008) Optical analysis of Hg2+ ions by oligonucleotide-gold-nanoparticle hybrids and DNA-based machines. Angew Chem Int Ed 47:3927–3931

    CAS  CrossRef  Google Scholar 

  47. Liu CW, Hsieh YT, Huang CC, Lin ZH, Chang HT (2008) Detection of mercury(II) based on Hg2+-DNA complexes inducing the aggregation of gold nanoparticles. Chem Commun: 2242–2244

    Google Scholar 

  48. Wang L, Zhang J, Wang X, Huang Q, Pan D, Song S, Fan C (2008) Gold nanoparticle based optical probes for target-responsive DNA structures. Gold Bull 41:37–41

    CrossRef  Google Scholar 

  49. Liu J, Lu Y (2006) Fast colorimetric sensing of adenosine and cocaine based on a general sensor design involving aptamers and nanoparticles. Angew Chem Int Ed 45:90–94

    CAS  CrossRef  Google Scholar 

  50. Liu J, Lu Y (2006) Smart nanomaterials responsive to multiple chemical stimuli with controllable cooperativity. Adv Mater 18:1667–1671

    CAS  CrossRef  Google Scholar 

  51. Zhao W, Chiuman W, Brook MA, Li Y (2007) Simple and rapid colorimetric biosensors based on DNA aptamer and noncrosslinking gold nanoparticle aggregation. Chembiochem 8:727–731

    CAS  CrossRef  Google Scholar 

  52. Zhao W, Chiuman W, Lam JC, McManus SA, Chen W, Cui Y, Pelton R, Brook MA, Li Y (2008) DNA aptamer folding on gold nanoparticles: from colloid chemistry to biosensors. J Am Chem Soc 130:3610–3618

    CAS  CrossRef  Google Scholar 

  53. Chen SJ, Huang YF, Huang CC, Lee KH, Lin ZH, Chang HT (2008) Colorimetric determination of urinary adenosine using aptamer-modified gold nanoparticles. Biosens Bioelectron 23:1749–1753

    CAS  CrossRef  Google Scholar 

  54. Huang C, Huang Y, Cao Z, Tan W, Chang H (2005) Aptamer-modified gold nanoparticles for colorimetric determination of platelet-derived growth factors and their receptors. Anal Chem 77:5735–5741

    CAS  CrossRef  Google Scholar 

  55. Wang Y, Li D, Ren W, Liu Z, Dong S, Wang E (2008) Ultrasensitive colorimetric detection of protein by aptamer-Au nanoparticles conjugates based on a dot-blot assay. Chem Commun: 2520–2522

    Google Scholar 

  56. Wei H, Li B, Li J, Wang E, Dong S (2007) Simple and sensitive aptamer-based colorimetric sensing of protein using unmodified gold nanoparticle probes. Chem Commun: 3735–3737

    Google Scholar 

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

    Google Scholar 

  58. Wang J, Wang L, Liu X, Liang Z, Song S, Li W, Li G, Fan C (2007) A gold nanoparticle-based aptamer target binding readout for ATP assay. Adv Mater 19:3943–3946

    CAS  CrossRef  Google Scholar 

  59. Zhang J, Wang L, Pan D, Song S, Boey FYC, Zhang H, Fan C (2008) Visual cocaine detection with gold nanoparticles and rationally engineered aptamer structures. Small 4:1196–1200

    CAS  CrossRef  Google Scholar 

  60. Chan CP, Cheung YC, Renneberg R, Seydack M (2008) New trends in immunoassays. Adv Biochem Eng Biotechnol 109:123–154

    CAS  Google Scholar 

  61. Glynou K, Ioannou PC, Christopoulos TK, Syriopoulou V (2003) Oligonucleotide-functionalized gold nanoparticles as probes in a dry-reagent strip biosensor for DNA analysis by hybridization. Anal Chem 75:4155–4160

    CAS  CrossRef  Google Scholar 

  62. Liu J, Mazumdar D, Lu Y (2006) A simple and sensitive “dipstick” test in serum based on lateral flow separation of aptamer-linked nanostructures. Angew Chem Int Ed 45:7955–7959

    CAS  CrossRef  Google Scholar 

  63. Zhao W, Ali MM, Aguirre SD, Brook MA, Li Y (2008) Paper-based bioassays using gold nanoparticle colorimetric probes. Anal Chem 80:8431–8437

    CAS  CrossRef  Google Scholar 

  64. Mazumdar D, Liu J, Lu G, Zhou J, Lu Y (2010) Easy-to-use dipstick tests for detection of lead in paints using non-cross-linked gold nanoparticle-DNAzyme conjugates. Chem Commun 46:1416–1418

    CAS  CrossRef  Google Scholar 

  65. Das PC, Puri A (2002) Energy flow and fluorescence near a small metal particle. Phys Rev B 65:155416

    CrossRef  CAS  Google Scholar 

  66. Fan C, Wang S, Hong JW, Bazan GC, Plaxco KW, Heeger AJ (2003) Beyond superquenching: hyper-efficient energy transfer from conjugated polymers to gold nanoparticles. Proc Natl Acad Sci USA 100:6297–6301

    CAS  CrossRef  Google Scholar 

  67. Yun CS, Javier A, Jennings T, Fisher M, Hira S, Peterson S, Hopkins B, Reich NO, Strouse GF (2005) Nanometal surface energy transfer in optical rulers, breaking the FRET barrier. J Am Chem Soc 127:3115–3119

    CAS  CrossRef  Google Scholar 

  68. Dulkeith E, Morteani AC, Niedereichholz T, Klar TA, Feldmann J, Levi SA, van Veggel FC, Reinhoudt DN, Möller M, Gittins DI (2002) Fluorescence quenching of dye molecules near gold nanoparticles: radiative and nonradiative effects. Phys Rev Lett 89:203002

    CAS  CrossRef  Google Scholar 

  69. Dubertret B, Calame M, Libchaber AJ (2001) Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat Biotechnol 19:365–370

    CAS  CrossRef  Google Scholar 

  70. Wang W, Chen C, Qian M, Zhao X (2008) Aptamer biosensor for protein detection using gold nanoparticles. Anal Biochem 373:213–219

    CAS  CrossRef  Google Scholar 

  71. Huang CC, Chiu SH, Huang YF, Chang HT (2007) Aptamer-functionalized gold nanoparticles for turn-on light switch detection of platelet-derived growth factor. Anal Chem 79:4798–4804

    CAS  CrossRef  Google Scholar 

  72. Zheng D, Seferos DS, Giljohann DA, Patel PC, Mirkin CA (2009) Aptamer nano-flares for molecular detection in living cells. Nano Lett 9:3258–3261

    CAS  CrossRef  Google Scholar 

  73. Zhang J, Wang L, Zhang H, Boey F, Song S, Fan C (2010) Aptamer-based multicolor fluorescent gold nanoprobes for multiplex detection in homogeneous solution. Small 6:201–204

    CAS  CrossRef  Google Scholar 

  74. Song S, Liang Z, Zhang J, Wang L, Li G, Fan C (2009) Gold-nanoparticle-based multicolor nanobeacons for sequence-specific DNA analysis. Angew Chem Int Ed 48:8670–8674

    CAS  CrossRef  Google Scholar 

  75. Huang Y, Zhao S, Liang H, Chen Z, Liu Y (2011) Multiplex detection of endonucleases by using a multicolor gold nanobeacon. Chem Eur J 17:7313–7319

    CAS  CrossRef  Google Scholar 

  76. Nie S, Emory SR (1997) Probing single molecules and single nanoparticles by surface-enhanced Raman scattering. Science 275:1102–1106

    CAS  CrossRef  Google Scholar 

  77. Moskovits M (1985) Surface-enhanced spectroscopy. Rev Mod Phys 57:783–826

    CAS  CrossRef  Google Scholar 

  78. Futamata M, Maruyama Y, Ishikawa M (2003) Local electric field and scattering cross section of Ag nanoparticles under surface plasmon resonance by finite difference time domain method. J Phys Chem B 107:7607–7617

    CAS  CrossRef  Google Scholar 

  79. Kneipp K, Kneipp H, Itzkan I, Dasari RR, Feld MS (1999) Ultrasensitive chemical analysis by Raman spectroscopy. Chem Rev 99:2957–2975

    CAS  CrossRef  Google Scholar 

  80. Bell SEJ, Sirimuthu NMS (2006) Surface-enhanced Raman spectroscopy (SERS) for sub-micromolar detection of DNA/RNA mononucleotides. J Am Chem Soc 128:15580–15581

    CAS  CrossRef  Google Scholar 

  81. Barhoumi A, Zhang D, Tam F, Halas NJ (2008) Surface-enhanced Raman spectroscopy of DNA. J Am Chem Soc 130:5523–5529

    CAS  CrossRef  Google Scholar 

  82. Bailo E, Deckert V (2008) Tip-enhanced Raman spectroscopy of single RNA strands: towards a novel direct-sequencing method. Angew Chem Int Ed 47:1658–1661

    CAS  CrossRef  Google Scholar 

  83. Qian XM, Zhou X, Nie S (2008) Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling. J Am Chem Soc 130:14934–14935

    CrossRef  Google Scholar 

  84. Faulds K, Smith WE, Graham D (2004) Evaluation of surface-enhanced resonance Raman scattering for quantitative DNA analysis. Anal Chem 76:412–417

    CAS  CrossRef  Google Scholar 

  85. Lim DK, Jeon KS, Kim HM, Nam JM, Suh YD (2010) Nanogap-engineerable Raman-active nanodumbbells for single-molecule detection. Nat Mater 9:60–67

    CAS  CrossRef  Google Scholar 

  86. Wang Y, Wei H, Li B, Ren W, Guo S, Dong S, Wang E (2007) SERS opens a new way in aptasensor for protein recognition with high sensitivity and selectivity. Chem Commun: 5220–5222

    Google Scholar 

  87. Wang Y, Lee K, Irudayaraj J (2010) SERS aptasensor from nanorod-nanoparticle junction for protein detection. Chem Commun 46:613–615

    CAS  CrossRef  Google Scholar 

  88. Chen J, Jiang J, Gao X, Liu G, Shen G, Yu R (2008) A new aptameric biosensor for cocaine based on surface-enhanced Raman scattering spectroscopy. Chem Eur J 14:8374–8382

    CAS  CrossRef  Google Scholar 

  89. Chen JW, Liu XP, Feng KJ, Liang Y, Jiang JH, Shen GL, Yu RQ (2008) Detection of adenosine using surface-enhanced Raman scattering based on structure-switching signaling aptamer. Biosens Bioelectron 24:66–71

    CAS  CrossRef  Google Scholar 

  90. Li M, Zhang J, Suri S, Sooter LJ, Ma D, Wu N (2012) Detection of adenosine triphosphate with an aptamer biosensor based on surface-enhanced Raman scattering. Anal Chem 84:2837–2842

    CAS  CrossRef  Google Scholar 

  91. Wang Y, Irudayaraj J (2011) A SERS DNAzyme biosensor for lead ion detection. Chem Commun 47:4394–4396

    CAS  CrossRef  Google Scholar 

  92. Li J, Lu Y (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J Am Chem Soc 122:10466–10467

    CAS  CrossRef  Google Scholar 

  93. Liu J, Brown AK, Meng X, Cropek DM, Istok JD, Watson DB, Lu Y (2007) A catalytic beacon sensor for uranium with parts-per-trillion sensitivity and millionfold selectivity. Proc Natl Acad Sci U S A 104:2056–2061

    CAS  CrossRef  Google Scholar 

  94. Liu J, Lu Y (2007) Rational design of “turn-on” allosteric DNAzyme catalytic beacons for aqueous mercury ions with ultrahigh sensitivity and selectivity. Angew Chem Int Ed 46:7587–7590

    CAS  CrossRef  Google Scholar 

  95. Liu J, Lu Y (2007) A DNAzyme catalytic beacon sensor for paramagnetic Cu2+ ions in aqueous solution with high sensitivity and selectivity. J Am Chem Soc 129:9838–9839

    CAS  CrossRef  Google Scholar 

  96. Zhang X, Wang Z, Xing H, Xiang Y, Lu Y (2010) Catalytic and molecular beacons for amplified detection of metal ions and organic molecules with high sensitivity. Anal Chem 82:5005–5011

    CAS  CrossRef  Google Scholar 

  97. Xu W, Lu Y (2010) Label-free fluorescent aptamer sensor based on regulation of malachite green fluorescence. Anal Chem 82:574–578

    CAS  CrossRef  Google Scholar 

  98. Xiang Y, Tong A, Lu Y (2009) Abasic site-containing DNAzyme and aptamer for label-free fluorescent detection of Pb2+ and adenosine with high sensitivity, selectivity, and tunable dynamic range. J Am Chem Soc 131:15352–15357

    CAS  CrossRef  Google Scholar 

  99. Huang CC, Chang HT (2008) Aptamer-based fluorescence sensor for rapid detection of potassium ions in urine. Chem Commun: 1461–1463

    Google Scholar 

  100. Nutiu R, Li Y (2005) A DNA-protein nanoengine for “on-demand” release and precise delivery of molecules. Angew Chem Int Ed 44:5464–5467

    CAS  CrossRef  Google Scholar 

  101. Nutiu R, Li Y (2003) Structure-switching signaling aptamers. J Am Chem Soc 125:4771–4778

    CAS  CrossRef  Google Scholar 

  102. Medintz IL, Uyeda HT, Goldman ER, Mattoussi H (2005) Quantum dot bioconjugates for imaging, labelling and sensing. Nat Mater 4:435–446

    CAS  CrossRef  Google Scholar 

  103. Gao XH, Yang LL, Petros JA, Marshal FF, Simons JW, Nie S (2005) In vivo molecular and cellular imaging with quantum dots. Curr Opin Biotechnol 16:63–72

    CAS  CrossRef  Google Scholar 

  104. Medintz IL, Clapp AR, Mattoussi H, Goldman ER, Fisher B, Mauro JM (2003) Self-assembled nanoscale biosensors based on quantum dot FRET donors. Nat Mater 2:630–638

    CAS  CrossRef  Google Scholar 

  105. Medintz IL, Clapp AR, Brunel FM, Tiefenbrunn T, Uyeda HT, Chang EL, Deschamps JR, Dawson PE, Mattoussi H (2006) Proteolytic activity monitored by fluorescence resonance energy transfer through quantum-dot-peptide conjugates. Nat Mater 5:581–589

    CAS  CrossRef  Google Scholar 

  106. Shi LF, De Paoli V, Rosenzweig N, Rosenzweig Z (2006) Synthesis and application of quantum dots FRET-based protease sensors. J Am Chem Soc 128:10378–10379

    CAS  CrossRef  Google Scholar 

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

    CAS  CrossRef  Google Scholar 

  108. Peng H, Zhang L, Kjallman THM, Soeller C, Travas-Sejdic J (2007) DNA hybridization detection with blue luminescent quantum dots and dye-labeled single-stranded DNA. J Am Chem Soc 129:3048–3049

    CAS  CrossRef  Google Scholar 

  109. Yuan J, Guo W, Yang X, Wang E (2009) Anticancer drug-DNA interactions measured using a photoinduced electron-transfer mechanism based on luminescent quantum dots. Anal Chem 81:362–368

    CAS  CrossRef  Google Scholar 

  110. Levy M, Cater SF, Ellington AD (2005) Quantum-dot aptamer beacons for the detection of proteins. Chembiochem 6:2163–2166

    CAS  CrossRef  Google Scholar 

  111. Choi JH, Chen KH, Strano MS (2006) Aptamer-capped nanocrystal quantum dots: a new method for label-free protein detection. J Am Chem Soc 128:15584–15585

    CAS  CrossRef  Google Scholar 

  112. Liu J, Lee JH, Lu Y (2007) Quantum dot encoding of aptamer-linked nanostructures for one-pot simultaneous detection of multiple analytes. Anal Chem 79:4120–4125

    CAS  CrossRef  Google Scholar 

  113. Wu CS, Oo MKK, Fan X (2010) Highly sensitive multiplexed heavy metal detection using quantum-dot-labeled DNAzymes. ACS Nano 4:5897–5904

    CAS  CrossRef  Google Scholar 

  114. Wang F, Liu X (2009) Recent advances in the chemistry of lanthanide-doped upconversion nanocrystals. Chem Soc Rev 38:976–989

    CAS  CrossRef  Google Scholar 

  115. Haase M, Schäfer H (2011) Upconverting nanoparticles. Angew Chem Int Ed 50:5808–5829

    CAS  CrossRef  Google Scholar 

  116. Auzel F (2003) Upconversion and anti-stokes processes with f and d ions in solids. Chem Rev 104:139–174

    CrossRef  CAS  Google Scholar 

  117. Feng W, Sun L, Zhang Y, Yan C (2010) Synthesis and assembly of rare earth nanostructures directed by the principle of coordination chemistry in solution-based process. Coord Chem Rev 254:1038–1053

    CAS  CrossRef  Google Scholar 

  118. Wang G, Peng Q, Li Y (2011) Lanthanide-doped nanocrystals: synthesis, optical-magnetic properties, and applications. Acc Chem Res 44:322–332

    CrossRef  CAS  Google Scholar 

  119. Mader HS, Kele P, Saleh SM, Wolfbeis OS (2010) Upconverting luminescent nanoparticles for use in bioconjugation and bioimaging. Curr Opin Chem Biol 14:582–596

    CAS  CrossRef  Google Scholar 

  120. Wang F, Han Y, Lim CS, Lu YH, Wang J, Xu J, Chen HY, Zhang C, Hong M, Liu X (2010) Simultaneous phase and size control of upconversion nanocrystals through lanthanide doping. Nature 463:1061–1065

    CAS  CrossRef  Google Scholar 

  121. Wang F, Deng R, Wang J, Wang Q, Han Y, Zhu H, Chen X, Liu X (2011) Tuning upconversion through energy migration in core-shell nanoparticles. Nat Mater 10:968–973

    CAS  CrossRef  Google Scholar 

  122. Li LL, Zhang R, Yin L, Zheng K, Qin W, Selvin PR, Lu Y (2012) Biomimetic surface engineering of lanthanide-doped upconversion nanoparticles as versatile bioprobes. Angew Chem Int Ed 51:6121–6125

    CAS  CrossRef  Google Scholar 

  123. Wang M, Hou W, Mi CC, Wang WX, Xu ZR, Teng HH, Mao CB, Xu SK (2009) Immunoassay of goat antihuman immunoglobulin G antibody based on luminescence resonance energy transfer between near-infrared responsive NaYF4:Yb, Er upconversion fluorescent nanoparticles and gold nanoparticles. Anal Chem 81:8783–8789

    CAS  CrossRef  Google Scholar 

  124. Rantanen T, Järvenpää ML, Vuojola J, Kuningas K, Soukka T (2008) Fluorescence-quenching-based enzyme-activity assay by using photon upconversion. Angew Chem Int Ed 47:3811–3813

    CAS  CrossRef  Google Scholar 

  125. Chen Z, Chen H, Hu H, Yu M, Li F, Zhang Q, Zhou Z, Yi T, Huang C (2008) Versatile synthesis strategy for carboxylic acid-functionalized upconverting nanophosphors as biological labels. J Am Chem Soc 130:3023–3029

    CAS  CrossRef  Google Scholar 

  126. Zhang P, Rogelj S, Nguyen K, Wheeler D (2006) Design of a highly sensitive and specific nucleotide sensor based on photon upconverting particles. J Am Chem Soc 128:12410–12411

    CAS  CrossRef  Google Scholar 

  127. Liu Q, Peng J, Sun L, Li F (2011) High-efficiency upconversion luminescent sensing and bioimaging of Hg(II) by chromophoric ruthenium complex-assembled nanophosphors. ACS Nano 5:8040–8048

    CAS  CrossRef  Google Scholar 

  128. Liu C, Wang Z, Jia H, Li Z (2011) Efficient fluorescence resonance energy transfer between upconversion nanophosphors and graphene oxide: a highly sensitive biosensing platform. Chem Commun 47:4661–4663

    CAS  CrossRef  Google Scholar 

  129. Wang Y, Bao L, Liu Z, Pang D (2011) Aptamer biosensor based on fluorescence resonance energy transfer from upconverting phosphors to carbon nanoparticles for thrombin detection in human plasma. Anal Chem 83:8130–8137

    CAS  CrossRef  Google Scholar 

  130. Song K, Kong X, Liu X, Zhang Y, Zeng Q, Tu L, Shi Z, Zhang H (2012) Aptamer optical biosensor without bio-breakage using upconversion nanoparticles as donors. Chem Commun 48:1156–1158

    CAS  CrossRef  Google Scholar 

  131. Na HB, Song IC, Hyeon T (2009) Inorganic nanoparticles for MRI contrast agents. Adv Mater 21:2133–2148

    CAS  CrossRef  Google Scholar 

  132. Bulte JWM, Kraitchman DL (2004) Iron oxide MR contrast agents for molecular and cellular imaging. NMR Biomed 17:484–499

    CAS  CrossRef  Google Scholar 

  133. Harisinghani MG, Barentsz J, Hahn PF, Deserno WM, Tabatabaei S, van de Kaa CH, de la Rosette J, Weissleder R (2003) Noninvasive detection of clinically occult lymph-node metastases in prostate cancer. N Engl J Med 348:2491–2499

    CrossRef  Google Scholar 

  134. Lee J, Zylka MJ, Anderson DJ, Burdette JE, Woodruff TK, Meade TJ (2005) A steroid-conjugated contrast agent for magnetic resonance imaging of cell signaling. J Am Chem Soc 127:13164–13166

    CAS  CrossRef  Google Scholar 

  135. Gupta AK, Gupta M (2005) Synthesis and surface engineering of iron oxide nanoparticles for biomedical applications. Biomaterials 26:3995–4021

    CAS  CrossRef  Google Scholar 

  136. Ito A, Kuga Y, Honda H, Kikkawa H, Horiuchi A, Watanabe Y, Kobayashi T (2004) Magnetite nanoparticle-loaded anti-HER2 immunoliposomes for combination of antibody therapy with hyperthermia. Cancer Lett 212:167–175

    CAS  CrossRef  Google Scholar 

  137. Kohler N, Sun C, Wang J, Zhang M (2005) Methotrexate-modified superparamagnetic nanoparticles and their intracellular uptake into human cancer cells. Langmuir 21:8858–8864

    CAS  CrossRef  Google Scholar 

  138. Perez JM, Josephson L, O’Loughlin T, Hogemann D, Weissleder R (2002) Magnetic relaxation switches capable of sensing molecular interactions. Nat Biotechnol 20:816–820

    CAS  Google Scholar 

  139. Josephson L, Perez JM, Weissleder R (2001) Magnetic nanosensors for the detection of oligonucleotide sequences. Angew Chem Int Ed 40:3204–3206

    CAS  CrossRef  Google Scholar 

  140. Zhao M, Josephson L, Tang Y, Weissleder R (2003) Magnetic sensors for protease assays. Angew Chem Int Ed 42:1375–1378

    CAS  CrossRef  Google Scholar 

  141. Kaittanis C, Naser SA, Perez JM (2007) One-step, nanoparticle-mediated bacterial detection with magnetic relaxation. Nano Lett 7:380–383

    CAS  CrossRef  Google Scholar 

  142. Perez JM, Simeone FJ, Saeki Y, Josephson L, Weissleder R (2003) Viral-induced self-assembly of magnetic nanoparticles allows the detection of viral particles in biological media. J Am Chem Soc 125:10192–10193

    CAS  CrossRef  Google Scholar 

  143. Tsourkas A, Hofstetter O, Hofstetter H, Weissleder R, Josephson L (2004) Magnetic relaxation switch immunosensors detect enantiomeric impurities. Angew Chem Int Ed 43:2395–2399

    CAS  CrossRef  Google Scholar 

  144. Yigit MV, Mazumdar D, Kim HK, Lee JH, Dintsov B, Lu Y (2007) Smart “turn-on” magnetic resonance contrast agents based on aptamer-functionalized superparamagnetic iron oxide nanoparticles. Chembiochem 8:1675–1678

    CAS  CrossRef  Google Scholar 

  145. Yigit MV, Mazumdar D, Lu Y (2008) MRI detection of thrombin with aptamer functionalized superparamagnetic iron oxide nanoparticles. Bioconjug Chem 19:412–417

    CAS  CrossRef  Google Scholar 

  146. Bamrungsap S, Shukoor MI, Chen T, Sefah K, Tan W (2011) Detection of lysozyme magnetic relaxation switches based on aptamer-functionalized superparamagnetic nanoparticles. Anal Chem 83:7795–7799

    CAS  CrossRef  Google Scholar 

  147. Novoselov KS, Geim AK, Morozov SV, Jiang D, Zhang Y, Dubonos SV, Grigorieva IV, Firsov AA (2004) Electric field effect in atomically thin carbon films. Science 306:666–669

    CAS  CrossRef  Google Scholar 

  148. Geim AK, Novoselov KS (2007) The rise of graphene. Nat Mater 6:183–191

    CAS  CrossRef  Google Scholar 

  149. Allen MJ, Tung VC, Kaner RB (2009) Honeycomb carbon: a review of graphene. Chem Rev 110:132–145

    CrossRef  CAS  Google Scholar 

  150. Rao CNR, Sood AK, Subrahmanyam KS, Govindaraj A (2009) Graphene: the new two-dimensional nanomaterial. Angew Chem Int Ed 48:7752–7777

    CAS  CrossRef  Google Scholar 

  151. Yang WR, Ratinac KR, Ringer SP, Thordarson P, Gooding JJ, Braet F (2010) Carbon nanomaterials in biosensors: should you use nanotubes or graphene? Angew Chem Int Ed 49:2114–2138

    CAS  CrossRef  Google Scholar 

  152. Shao YY, Wang J, Wu H, Liu J, Aksay IA, Lin YH (2010) Graphene based electrochemical sensors and biosensors: a review. Electroanalysis 22:1027–1036

    CAS  CrossRef  Google Scholar 

  153. Wang Y, Li ZH, Wang J, Li JH, Lin YH (2011) Graphene and graphene oxide: biofunctionalization and applications in biotechnology. Trends Biotechnol 29:205–212

    CrossRef  CAS  Google Scholar 

  154. Gulbakan B, Yasun E, Shukoor MI, Zhu Z, You M, Tan X, Sanchez H, Powell DH, Dai H, Tan W (2010) A dual platform for selective analyte enrichment and ionization in mass spectrometry using aptamer-conjugated graphene oxide. J Am Chem Soc 132:17408–17410

    CAS  CrossRef  Google Scholar 

  155. Liu Z, Robinson JT, Sun X, Dai H (2008) PEGylated nanographene oxide for delivery of water-insoluble cancer drugs. J Am Chem Soc 130:10876–10877

    CAS  CrossRef  Google Scholar 

  156. Sun X, Liu Z, Welsher K, Robinson JT, Goodwin A, Zaric S, Dai H (2008) Nano-graphene oxide for cellular imaging and drug delivery. Nano Res 1:203–212

    CAS  CrossRef  Google Scholar 

  157. Li JL, Bao HC, Hou XL, Sun L, Wang XG, Gu M (2012) Graphene oxide nanoparticles as a nonbleaching optical probe for two-photon luminescence imaging and cell therapy. Angew Chem Int Ed 51:1830–1834

    CAS  CrossRef  Google Scholar 

  158. Swathi RS, Sebastiana KL (2008) Resonance energy transfer from a dye molecule to graphene. J Chem Phys 129:054703

    CAS  CrossRef  Google Scholar 

  159. Swathi RS, Sebastiana KL (2009) Long range resonance energy transfer from a dye molecule to graphene has (distance)-4 dependence. J Chem Phys 130:086101

    CAS  CrossRef  Google Scholar 

  160. Husale BS, Sahoo S, Radenovic A, Traversi F, Annibale P, Kis A (2010) ssDNA binding reveals the atomic structure of graphene. Langmuir 26:18078–18082

    CAS  CrossRef  Google Scholar 

  161. Lu CH, Yang HH, Zhu CL, Chen X, Chen GN (2009) A graphene platform for sensing biomolecules. Angew Chem Int Ed 48:4785–4787

    CAS  CrossRef  Google Scholar 

  162. Dong HF, Gao WC, Yan F, Ji HX, Ju HX (2010) Fluorescence resonance energy transfer between quantum dots and graphene oxide for sensing biomolecules. Anal Chem 82:5511–5517

    CAS  CrossRef  Google Scholar 

  163. Li F, Huang Y, Yang Q, Zhong Z, Li D, Wang LH, Song S, Fan C (2010) A graphene-enhanced molecular beacon for homogeneous DNA detection. Nanoscale 2:1021–1026

    CAS  CrossRef  Google Scholar 

  164. Zhou M, Zhai Y, Dong S (2009) Electrochemical sensing and biosensing platform based on chemically reduced graphene oxide. Anal Chem 81:5603–5613

    CAS  CrossRef  Google Scholar 

  165. Huang PJJ, Liu J (2012) DNA-length-dependent fluorescence signaling on graphene oxide surface. Small 8:977–983

    CAS  CrossRef  Google Scholar 

  166. Wu W, Hu H, Li F, Wang L, Gao J, Lu J, Fan C (2011) A graphene oxide-based nano-beacon for DNA phosphorylation analysis. Chem Commun 47:1201–1203

    CAS  CrossRef  Google Scholar 

  167. Wen Y, Xing F, He S, Song S, Wang L, Long Y, Li D, Fan C (2010) A graphene-based fluorescent nanoprobe for silver(I) ions detection by using graphene oxide and a silver-specific oligonucleotide. Chem Commun 46:2596–2598

    CAS  CrossRef  Google Scholar 

  168. He S, Song B, Li D, Zhu C, Qi W, Wen Y, Wang L, Song S, Fang H, Fan C (2010) A graphene nanoprobe for rapid, sensitive, and multicolor fluorescent DNA analysis. Adv Funct Mater 20:453–459

    CAS  CrossRef  Google Scholar 

  169. Lin L, Liu Y, Zhao X, Li J (2011) Sensitive and rapid screening of T4 polynucleotide kinase activity and inhibition based on coupled exonuclease reaction and graphene oxide platform. Anal Chem 83:8396–8402

    CAS  CrossRef  Google Scholar 

  170. Yang R, Jin J, Chen Y, Shao N, Kang H, Xiao Z, Tang Z, Wu Y, Zhu Z, Tan W (2008) Carbon nanotube-quenched fluorescent oligonucleotides: probes that fluoresce upon hybridization. J Am Chem Soc 130:8351–8358

    CAS  CrossRef  Google Scholar 

  171. Zhen SJ, Chen LQ, Xiao SJ, Li YF, Hu PP, Zhan L, Peng L, Song EQ, Huang CZ (2010) Carbon nanotubes as a low background signal platform for a molecular aptamer beacon on the basis of long-range resonance energy transfer. Anal Chem 82:8432–8437

    CAS  CrossRef  Google Scholar 

  172. Chen Z, Zhang X, Yang R, Zhu Z, Chen Y, Tan W (2011) Single-walled carbon nanotubes as optical materials for biosensing. Nanoscale 3:1949–1956

    CAS  CrossRef  Google Scholar 

  173. Li H, Tian J, Wang L, Zhang Y, Sun X (2011) Multi-walled carbon nanotubes as an effective fluorescent sensing platform for nucleic acid detection. J Mater Chem 21:824–828

    CAS  CrossRef  Google Scholar 

  174. Li H, Zhang Y, Wu T, Liu S, Wang L, Sun X (2011) Carbon nanospheres for fluorescent biomolecular detection. J Mater Chem 21:4663–4668

    CAS  CrossRef  Google Scholar 

  175. Li H, Zhang Y, Wang L, Tian J, Sun X (2011) Nucleic acid detection using carbon nanoparticles as a fluorescent sensing platform. Chem Commun 47:961–963

    CAS  CrossRef  Google Scholar 

  176. Li H, Zhang Y, Luo Y, Sun X (2011) Nano-C60: a novel, effective, fluorescent sensing platform for biomolecular detection. Small 7:1562–1568

    CAS  CrossRef  Google Scholar 

  177. Chang H, Tang L, Wang Y, Jiang J, Li J (2010) Graphene fluorescence resonance energy transfer aptasensor for the thrombin detection. Anal Chem 82:2341–2346

    CAS  CrossRef  Google Scholar 

  178. Lu CH, Li J, Lin MH, Wang YW, Yang HH, Chen X, Chen GN (2010) Amplified aptamer-based assay through catalytic recycling of the analyte. Angew Chem Int Ed 49:8454–8457

    CAS  CrossRef  Google Scholar 

  179. Wang Y, Li Z, Hu D, Lin CT, Li J, Lin Y (2010) Aptamer/graphene oxide nanocomplex for in situ molecular probing in living cells. J Am Chem Soc 132:9274–9276

    CAS  CrossRef  Google Scholar 

  180. Wen Y, Peng C, Li D, Zhuo L, He S, Wang L, Huang Q, Xu QH, Fan C (2011) Metal ion-modulated graphene-DNAzyme interactions: design of a nanoprobe for fluorescent detection of lead(II) ions with high sensitivity, selectivity and tunable dynamic range. Chem Commun 47:6278–6280

    CAS  CrossRef  Google Scholar 

  181. Zhao XH, Kong RM, Zhang XB, Meng HM, Liu WN, Tan W, Shen GL, Yu RQ (2011) Graphene-DNAzyme based biosensor for amplified fluorescence “turn-on” detection of Pb2+ with a high selectivity. Anal Chem 83:5062–5066

    CAS  CrossRef  Google Scholar 

  182. Mohanty N, Berry V (2008) Graphene-based single-bacterium resolution biodevice and DNA transistor: interfacing graphene derivatives with nanoscale and microscale biocomponents. Nano Lett 8:4469–4476

    CAS  CrossRef  Google Scholar 

  183. Mao S, Lu G, Yu K, Bo Z, Chen J (2010) Specific protein detection using thermally reduced graphene oxide sheet decorated with gold nanoparticle-antibody conjugates. Adv Mater 22:3521–3526

    CAS  CrossRef  Google Scholar 

  184. Ohno Y, Maehashi K, Matsumoto K (2010) Label-free biosensors based on aptamer-modified graphene field-effect transistors. J Am Chem Soc 132:18012–18013

    CAS  CrossRef  Google Scholar 

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Acknowledgments

The research of the Lu group described in this chapter has been generously supported by the US National Institutes of Health, Department of Energy, Department of Defense, Department of Housing and Urban Development, Environmental Protection Agency, National Science Foundation, and the Illinois Sustainable Technology Center.

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Li, L., Lu, Y. (2013). Functional DNA-Integrated Nanomaterials for Biosensing. In: Fan, C. (eds) DNA Nanotechnology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-36077-0_13

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