Critical Reviews in Oncology / Hematology
Volume 74, Issue 1 , Pages 1-15 , April 2010

Semiconductor quantum dots for multiplexed bio-detection on solid-state microarrays

  • Gilles Rousserie

      Affiliations

    • EA n°3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France
  • ,
  • Alyona Sukhanova

      Affiliations

    • EA n°3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France
  • ,
  • Klervi Even-Desrumeaux

      Affiliations

    • Laboratoire d’anticorps thérapeutiques et immunociblage, INSERM U624 Stress cellulaire, 13288 Marseille, France
  • ,
  • Fabrice Fleury

      Affiliations

    • Unité de Biotechnologie, Biocatalyse et Biorégulation, UMR6204, 44332 Nantes, France
  • ,
  • Patrick Chames

      Affiliations

    • Laboratoire d’anticorps thérapeutiques et immunociblage, INSERM U624 Stress cellulaire, 13288 Marseille, France
  • ,
  • Daniel Baty

      Affiliations

    • Laboratoire d’anticorps thérapeutiques et immunociblage, INSERM U624 Stress cellulaire, 13288 Marseille, France
  • ,
  • Vladimir Oleinikov

      Affiliations

    • Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
  • ,
  • Michel Pluot

      Affiliations

    • EA n°3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France
  • ,
  • Jacques H.M. Cohen

      Affiliations

    • EA n°3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France
  • ,
  • Igor Nabiev

      Affiliations

    • EA n°3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France
    • CIC nanoGUNE Consolider Research Centre, E-20018 Donostia-San Sebastian, Spain
    • Corresponding Author InformationCorresponding author at: EA n°3798 Détection et Approches Thérapeutiques Nanotechnologiques dans les Mécanismes Biologiques de Défense, Université de Reims Champagne-Ardenne, 51100 Reims, France. Tel.: +33 326918127; fax: +33 326918127.

,Accepted 17 April 2009.

References 

  1. Ehrenreich A. DNA microarray technology for the microbiologist: an overview. Appl Microbiol Biotechnol. 2006;73:255–273
  2. Stoll D, Templin MF, Schrenk M, Traub PC, Vöhringer CF, Joos TO. Protein microarray technology. Front Biosci. 2002;7:c13–32
  3. Gracey AY, Cossins AR. Application of microarray technology in environmental and comparative physiology. Annu Rev Physiol. 2003;65:231–259
  4. Park HG, Song JY, Park KH, Kim MH. Fluorescence-based assay formats and signal amplification strategies for DNA microarray analysis. Chem Engen Sci. 2006;61:954–965
  5. Zajac A, Song D, Qian W, Zhukov T. Protein microarrays and quantum dot probes for early cancer detection. Colloids Surf B Biointerfaces. 2007;58:309–314
  6. Resch-Genger U, Grabolle M, Cavaliere-Jaricot S, Nitschke R, Nann T. Quantum dots versus organic dyes as fluorescent labels. Nat Methods. 2008;5:763–775
  7. Nabiev I, Sukhanova A, Artemyev M, Oleinikov V. Fluorescent colloidal particles as a detection tools in biotechnology systems. In:  Elaissari A editors. Colloidal Nanoparticles in Biotechnology, pp. 376. Wiley & Sons Inc.; 2008;p. 133–168
  8. Sukhanova A, Nabiev I. Fluorescent nanocrystal quantum dots as medical diagnostic tools. Exp Opin Med Diagn. 2008;2:429–447
  9. Sukhanova A, Nabiev I. Liquid-phase chips based on the fluorescent nanocrystal-encoded microbeads for cancer diagnostics. Crit Rev Oncol Hematol. 2008;68:39–59
  10. Ling MM, Ricks C, Lea P. Multiplexing molecular diagnostics and immunoassays using emerging microarray technologies. Expert Rev Mol Diagn. 2007;7:87–98
  11. Blohm DH, Guiseppi-Elie A. New developments in microarray technology. Curr Opin Biotechnol. 2001;12:41–47
  12. McGall G, Labadie J, Brock P, Wallraff G, Nguyen T, Hinsberg W. Light-directed synthesis of high-density oligonucleotide arrays using semiconductor photoresists. Proc Natl Acad Sci U S A. 1996;93:13555–13560
  13. Hoek KS. DNA microarray analyses of melanoma gene expression: a decade in the mines. Pigment Cell Res. 2007;20:466–484
  14. Duncan R. DNA microarray analysis of protozoan parasite gene expression: outcomes correlate with mechanisms of regulation. Trends Parasitol. 2004;20:211–215
  15. Yamakawa H, Hirose T, Kuroda M, Yamaguchi T. Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol. 2007;144:258–277
  16. Wakamatsu E, Nakamura Y, Matsumoto I, et al. DNA microarray analysis of labial salivary glands of patients with Sjogren's syndrome. Ann Rheum Dis. 2007;66:844–845
  17. Feferman T, Aricha R, Menon R, Souroujon MC, Berrih-Aknin S, Fuchs S. DNA microarray in search of new drug targets for myasthenia gravis. Ann N Y Acad Sci. 2007;1107:111–117
  18. Dorrell N, Hinchliffe SJ, Wren BW. Comparative phylogenomics of pathogenic bacteria by microarray analysis. Curr Opin Microbiol. 2005;8:620–626
  19. Tao SC, Chen CS, Zhu H. Applications of protein microarray technology. Comb Chem High Throughput Screen. 2007;10:706–718
  20. Lee Y, Lee EK, Cho YW, et al. ProteoChip: a highly sensitive protein microarray prepared by a novel method of protein immobilization for application of protein–protein interaction studies. Proteomics. 2003;3:2289–2304
  21. Sasakura Y, Kanda K, Yoshimura-Suzuki T, Matsui T, Fukuzono S, Shimizu T. Investigation of the relationship between protein–protein interaction and catalytic activity of a heme-regulated phosphodiesterase from Escherichia coli (Ec DOS) by protein microarray. Biochemistry. 2005;44:9598–9605
  22. Zha H, Raffeld M, Charboneau L, et al. Similarities of prosurvival signals in Bcl-2-positive and Bcl-2-negative follicular lymphomas identified by reverse phase protein microarray. Lab Invest. 2004;84:235–244
  23. Chan SM, Weng AP, Tibshirani R, Aster JC, Utz PJ. Notch signals positively regulate activity of the mTOR pathway in T-cell acute lymphoblastic leukemia. Blood. 2007;110:278–286
  24. Li B, Zhou D, Wang Z, et al. Antibody profiling in plague patients by protein microarray. Microbes Infect. 2008;10:45–51
  25. Xu R, Gan X, Fang Y, Zheng S, Dong Q. A simple, rapid, and sensitive integrated protein microarray for simultaneous detection of multiple antigens and antibodies of five human hepatitis viruses (HBV, HCV, HDV, HEV, and HGV). Anal Biochem. 2007;362:69–75
  26. Yuk CS, Lee HK, Kim HT, Choi YK, Lee BC, Chun BH, et al. Development and evaluation of a protein microarray chip for diagnosis of hepatitis C virus. Biotechnol Lett. 2004;26:1563–1568
  27. Zhu H, Hu S, Jona G, et al. Severe acute respiratory syndrome diagnostics using a coronavirus protein microarray. Proc Natl Acad Sci U S A. 2006;103:4011–4016
  28. Smith AM, Dave S, Nie S, True L, Gao X. Multicolor quantum dots for molecular diagnostics of cancer. Expert Rev Mol Diagn. 2006;6(March):231–244
  29. Brown PO, Botstein D. Exploring the new world of the genome with DNA microarrays. Nat Genet. 1999;21:33–37
  30. Granjeaud S, Bertucci F, Jordan BR. Expression profiling: DNA arrays in many guises. Bioessays. 1999;21:781–790
  31. Saitou M, Yabuta Y, Kurimoto K. Single-cell cDNA high-density oligonucleotide microarray analysis: detection of individual cell types and properties in complex biological processes. Reprod Biomed Online. 2008;16:26–40
  32. Zekri AR, Hafez MM, Bahnassy AA, et al. Genetic profile of Egyptian hepatocellular-carcinoma associated with hepatitis C virus Genotype 4 by 15 K cDNA microarray: preliminary study. BMC Res Notes. 2008;1:106
  33. Liang RQ, Li W, Li Y, et al. An oligonucleotide microarray for microRNA expression analysis based on labeling RNA with quantum dot and nanogold probe. Nucleic Acids Res. 2005;33:e17
  34. Williams BA, Gwirtz RM, Wold BJ. Genomic DNA as a cohybridization standard for mammalian microarray measurements. Nucleic Acids Res. 2004;32:e81
  35. Kader HA, Tchernev VT, Satyaraj E, et al. Protein microarray analysis of disease activity in pediatric inflammatory bowel disease demonstrates elevated serum PLGF, IL-7, TGF-beta1, and IL-12p40 levels in Crohn's disease and ulcerative colitis patients in remission versus active disease. Am J Gastroenterol. 2005;100:414–423
  36. Geho D, Lahar N, Gurnani P, et al. Pegylated, steptavidin-conjugated quantum dots are effective detection elements for reverse-phase protein microarrays. Bioconjug Chem. 2005;16:559–566
  37. Hall DA, Ptacek J, Snyder M. Protein microarray technology. Mech Ageing Dev. 2007;128:161–167
  38. Zhu H, Bilgin M, Bangham R, et al. Global analysis of protein activities using proteome chips. Science. 2001;293:2101–2105
  39. Angenendt P, Glökler J, Murphy D, Lehrach H, Cahill DJ. Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal Biochem. 2002;309:253–260
  40. Wingren C, Ingvarsson J, Dexlin L, Szul D, Borrebaeck CA. Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling tag and solid support. Proteomics. 2007;7:3055–3065
  41. Seurynck-Servoss SL, White AM, Baird CL, Rodland KD, Zangar RC. Evaluation of surface chemistries for antibody microarrays. Anal Biochem. 2007;371:105–115
  42. Wingren C, Steinhauer C, Ingvarsson J, Persson E, Larsson K, Borrebaeck CA. Microarrays based on affinity-tagged single-chain Fv antibodies: sensitive detection of analyte in complexe proteomes. Proteomics. 2005;5:1281–1291
  43. Grainger DW, Greef CH, Gong P, Lochhead MJ. Current microarray surface chemistries. Methods Mol Biol. 2007;381:37–57
  44. Arenkov P, Kukhtin A, Gemmell A, Voloshchuk S, Chupeeva V, Mirzabekov A. Protein microchips: use for immunoassay and enzymatic reactions. Anal Biochem. 2000;278:123–131
  45. Mircean C, Shmulevich I, Cogdell D, et al. Robust estimation of protein expression ratios with lysate microarray technology. Bioinformatics. 2005;21:1935–1942
  46. Sakanyan V. High-throughput and multiplexed protein array technology: protein–DNA and protein–protein interactions. J Chromatogr B Analyt Technol Biomed Life Sci. 2005;815:77–95
  47. Wingren C, Borrebaeck CA. Progress in miniaturization of protein arrays-a step closer to high-density nanoarrays. Drug Discov Today. 2007;12:813–819
  48. Lesaicherre ML, Uttamchandani M, Chen GY, Yao SQ. Developing site specific immobilization strategies of peptides in a microarray. Bioorg Med Chem Lett. 2002;12:2079–2083
  49. Evans D, Johnson S, Laurenson S, Davies AG, Ferrigno PK, Wälti C. Electrical protein detection in cell lysates using high-density peptide-aptamer microarrays. J Biol. 2008;7:3
  50. Houseman BT, Huh JH, Kron SJ, Mrksich M. Peptide chips for the quantitative evaluation of protein kinase activity. Nat Biotechnol. 2002;20:270–274
  51. Carlsson A, Wingren C, Ingvarsson J, et al. Serum proteome profiling of metastatic breast cancer using recombinant antibody microarrays. Eur J Cancer. 2008;44:472–480
  52. Renberg B, Nordin J, Merca A, et al. Affibody molecules in protein capture microarrays: evaluation of multidomain ligands and different detection formats. J Proteome Res. 2007;6:171–179
  53. Harmsen MM, De Haard HJ. Properties, production, and applications of camelid single-domain antibody fragments. Appl Microbiol Technol. 2007;77:13–22
  54. Van der Linden RH, Frenken LG, de Geus B, et al. Comparison of physical chemical properties of llama VHH antibody fragments and mouse monoclonal antibodies. Biochim Biophys Acta. 1999;1431:37–46
  55. Kingsmore SF. Multiplexed protein measurement: technologies and applications of protein and antibody arrays. Nat Rev Drug Discov. 2006;5:310–320
  56. Robinson WH, DiGennaro C, Hueber W, et al. Autoantigen microarrays for multiplexed characterization of autoantibody responses. Nat Med. 2002;8:295–301
  57. Fang Y, Frutos AG, Lahiri J. Membrane protein microarrays. J Am Chem Soc. 2002;124:2394–2395
  58. Sieber SA, Mondala TS, Head SR, Cravatt BF. Microarray platform for profiling enzyme activities in complex proteomes. J Am Chem Soc. 2004;126:15640–15641
  59. Ramachandran N, Raphael JV, Hainsworth E, et al. Next-generation high-density self-assembling functional protein arrays. Nat Methods. 2008;5:535–538
  60. Situma C, Hashimoto M, Soper SA. Merging microfluidics with microarray-based bioassays. Biomol Eng. 2006;23:213–231
  61. Lee KB, Park SJ, Mirkin CA, Smith JC, Mrksich M. Protein nanoarrays generated by dip-pen nanolithography. Science. 2002;295:1702–1705
  62. Yan J, Estévez MJ, Smith JE, et al. Dye-doped nanoparticles for bioanalysis. Nanotoday. 2007;2:44–50
  63. Huber F, Hegner M, Gerber C, Güntherodt HJ, Lang HP. Label free analysis of transcription factors using microcantilever arrays. Biosens Bioelectron. 2006;21:1599–1605
  64. Klenkar G, Liedberg B. A microarray chip for label-free detection of narcotics. Anal Bioanal Chem. 2008;391:1679–1688
  65. Cheng MMC, Cuda G, Bunimovich YL, et al. Nanotechnologies for biomolecular detection and medical diagnostics. Curr Opin Chem Biol. 2006;10:11–19
  66. Backmann N, Zahnd C, Huber F, et al. A label-free immunosensor array using single-chain antibody fragments. Proc Natl Acad Sci U S A. 2005;102:14587–14592
  67. Yuan J, Sueda S, Somazawa R, Matsumoto K, Matsumoto K. Structure and luminescence properties of the tetradentate β-diketonate–europium(III) complexes. Chem Lett. 2003;32:492–493
  68. Wang F, Tan WB, Zhang Y, Fan X, Wang M. Luminescent nanomaterials for biological labelling. Nanotechnology. 2006;17:1–13
  69. Bruchez M, Moronne M, Gin P, Weiss S, Alivisatos AP. Semiconductor nanocrystals as fluorescent biological labels. Science. 1998;281(5385):2013–2016
  70. Chan WC, Nie S. Quantum dot bioconjugates for ultrasensitive nonisotopic detection. Science. 1998;25(281 (5385)):2016–2018
  71. Baranov AV, Rakovich YP, Donegan JF, et al. Effect of ZnS shell thickness on the phonon spectra in CdSe quantum dots. Phys Rev B. 2003;68:1653061–1653067
  72. Azzazy HME, Mansour MMH, Kazmierczak SC. From diagnostics to therapy: prospects of quantum dots. Clin Biochem. 2007;40:917–927
  73. Shi C, Zhu Y, Cerwinka WH, et al. Quantum dots: emerging applications in urologic oncology. Urol Oncol. 2008;26(1):86–92
  74. Alivisatos AP, Gu W, Larabell C. Quantum dots as cellular probes. Annu Rev Biomed Eng. 2005;7:55–76
  75. Karlin-Neumann G, Sedova M, Falkowski M, Wang Z, Lin S, Jain M. Application of quantum dots to multicolor microarray experiments: four-color genotyping. Methods Mol Biol. 2007;374:239–251
  76. Sukhanova A, Devy J, Venteo L, et al. Biocompatible fluorescent nanocrystals for immunolabeling of membrane proteins and cells. Anal Biochem. 2004;324:60–67
  77. Zhong X, Feng Y, Knoll W, Han M. Alloyed ZnxCd1−xS nanocrystals with highly narrow luminescence spectral width. J Am Chem Soc. 2003;125:13559–13563
  78. Nirmal M, Dabbousi BO, Bawendi MG, et al. Fluorescence intermittency in single cadmium selenide nanocrystals. Nature. 1996;383:802–804
  79. Empedocles SA, Neuhauser R, Shimizu K, Bawendi MG. Photoluminescence from single semiconductor nanostructures. Adv Mater. 1999;15(11):243–256
  80. Hohng S, Ha T. Near complete suppression of quantum dot blinking in ambient condition. J Am Chem Soc. 2004;126:1324–1325
  81. Vora GJ, Meador CE, Anderson GP, Taitt CR. Comparison of detection and signal amplification methods for DNA microarrays. Mol Cell Probes. 2008;22(5–6):294–300
  82. Pathak S, Davidson MC, Silva GA. Characterization of the functional binding properties of antibody conjugated quantum dots. Nano Lett. 2007;7:1839–1845
  83. True LD, Gao X. Quantum dots for molecular pathology: their time has arrived. J Mol Diagn. 2007;9:7–11
  84. Shingyoji M, Gerion D, Pinkel D, Gray JW, Chen F. Quantum dots-based reverse phase protein microarray. Talanta. 2005;67:472–478
  85. Ghazani AA, Lee JA, Klostranec J, et al. High throughput quantification of protein expression of cancer antigens in tissue microarray using quantum dot nanocrystals. Nano Lett. 2006;6:2881–2886
  86. Robelek R, Niu L, Schmid EL, Knoll W. Multiplexed hybridization detection of quantum dot-conjugated DNA sequences using surface plasmon enhanced fluorescence microscopy and spectrometry. Anal Chem. 2004;76:6160–6165
  87. Eastman PS, Ruan W, Doctolero M, et al. Qdot nanobarcodes for multiplexed gene expression analysis. Nano Lett. 2006;6:1059–1064
  88. Murata S, Herman P, Mochizuki K, et al. Spatial distribution analysis of AT- and GC-rich regions in nuclei using corrected fluorescence resonance energy transfer. J Histochem Cytochem. 2003;51:951–958
  89. Schwartz DE, Gong P, Shepard KL. Time-resolved Förster-resonance-energy-transfer DNA assay on an active CMOS microarray. Biosens Bioelectron. 2008;24:383–390
  90. Schuler B, Eaton WA. Protein folding studied by single-molecule FRET. Curr Opin Struct Biol. 2008;18:16–26
  91. Gertler A, Biener E, Ramanujan KV, Djiane J, Herman B. Fluorescence resonance energy transfer (FRET) microscopy in living cells as a novel tool for the study of cytokine action. J Dairy Res. 2005;72:14–19
  92. Hallworth R, Currall B, Nichols MG, Wu X, Zuo J. Studying inner ear protein–protein interactions using FRET and FLIM. Brain Res. 2006;1091:122–131
  93. Jain KK. Applications of nanobiotechnology in clinical diagnostics. Clin Chem. 2007;53:2002–2009
  94. Phan JH, Young AN, Wang MD. Selecting clinically-driven biomarkers for cancer nanotechnology. Conf Proc IEEE Eng Med Biol Soc. 2006;1:3317–3320
  95. Goldschmidt MC. The use of biosensor and microarray techniques in the rapid detection and identification of salmonellae. J AOAC Int. 2006;89:530–537

PII: S1040-8428(09)00083-3

doi: 10.1016/j.critrevonc.2009.04.006

Critical Reviews in Oncology / Hematology
Volume 74, Issue 1 , Pages 1-15 , April 2010