Advertisement

The Use of Functional Nucleic Acids in Solid-Phase Fluorimetric Assays

  • Nicholas Rupcich
  • Razvan Nutiu
  • Yutu Shen
  • Yingfu Li
  • John D. Brennan
Part of the Integrated Analytical Systems book series (ANASYS)

Abstract

The past 15 years have seen a revolution in the area of functional nucleic acid (FNA) research since the demonstration that single-stranded RNA and DNA species can be used for both ligand binding and catalysis. An emerging area of application for such species is in the development of solid-phase fluorimetric assays for biosensing, proteomics, and drug screening purposes. In this chapter, the methods for immobilization of functional nucleic acids are briefly reviewed, with emphasis on emerging technologies such as sol-gel encapsulation. Methods for generating fluorescence signals from aptamers and nucleic acid enzymes are then described, and the use of such species in solid-phase fluorimetric assays is then discussed. Unique features of sol-gel based materials for the development of solid-phase assays are highlighted, and some emerging applications of immobilized FNA species are discussed.

Keywords

Molecular Beacon Aptamer Sequence Lateral Flow Device Biological Recognition Element Aptamer Beacon 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Luderer, F. and Walschus, U. (2005) Immobilization of oligonucleotides for biochemical sensing by self-assembled monolayers: thiol-organic bonding on gold and silanization on silica surfaces. Top. Curr. Chem. 260:37–56.Google Scholar
  2. 2.
    Smith, C.L., Milea, J.S. and Nguyen, G.H. (2006) Immobilization of nucleic acids using biotin-strept(avidin) systems. Top. Curr. Chem. 261:63–90.Google Scholar
  3. 3.
    Fang, X., Liu, X., Schuster, S. and Tan, W. (1999) Designing a novel molecular beacon for surface-immobilized DNA hybridization studies. J. Am. Chem. Soc. 121:2921–2922.Google Scholar
  4. 4.
    Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature (Lond.) 346:818–822.Google Scholar
  5. 5.
    Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–510.Google Scholar
  6. 6.
    Wilson, D.S. and Szostak, J.W. (1999) In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68:611–647.Google Scholar
  7. 7.
    Famulok, M. (1999) Oligonucleotide aptamers that recognize small molecules. Curr. Opin. Struct. Biol. 9:324–329.Google Scholar
  8. 8.
    Green, L.S., Jellinek, D., Bell, C., Beebe, L.A., Fesitner, B.D., Gill, S.C., Jucker, F.M. and Janjic, N. (1995) Nuclease-resistant nucleic acid ligands to vascular permeability factor/ vascular endothelial growth factor. Chem. Biol. 2:683–695.Google Scholar
  9. 9.
    Pagratis, N.C., Bell, C., Chang, Y.-F., Jennings, S., Fitzwater, T., Jellinek, D. and Dang, C. (1997) Potent 2′-amino-, and 2′-fluoro-2′-deoxyribonucleotide RNA inhibitors of keratinocyte growth factor. Nat. Biotechnol. 15:68–73.Google Scholar
  10. 10.
    Jenison, R.D., Gill, S.C., Pardi, A. and Polisky, B. (1994) High-resolution molecular discrimination by RNA. Science 263:1425–1429.Google Scholar
  11. 11.
    Geiger, A., Burgstaller, P., von der Eltz, H., Roeder, A. and Famulok, M. (1996) RNA aptamers that bind L-arginine with sub-micromolar dissociation constants and high enantioselectivity. Nucleic Acids Res. 24:1029–1036.Google Scholar
  12. 12.
    Achenbach, J.C., Chiuman, W., Cruz, R.P. and Li, Y. (2004) DNAzymes: from creation in vitro to application in vivo. Curr. Pharm. Biotechnol. 5:321–336.Google Scholar
  13. 13.
    Silverman, S.K. (2004) Deoxyribozymes: DNA catalysts for bioorganic chemistry. Org. Biomol. Chem. 2:2701–2706.Google Scholar
  14. 14.
    Joyce, G.F. (2004) Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73: 791–836.Google Scholar
  15. 15.
    Breaker, R.R. (2004) Natural and engineered nucleic acids as tools to explore biology. Nature (Lond.) 432:838–845.Google Scholar
  16. 16.
    Peracchi, A. (2005) DNA catalysis: potential, limitations, open questions. ChemBioChem 6: 1316–1322.Google Scholar
  17. 17.
    Breaker, R.R. and Joyce, G.F. (1994) A DNA enzyme that cleaves RNA. Chem. Biol. 1: 223–229.Google Scholar
  18. 18.
    Santoro, S.W. and Joyce, G.F. (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94:4262–4266.Google Scholar
  19. 19.
    Flynn-Charlebois, A., Wang, Y., Prior, T.K., Rashid, I., Hoadley, K.A., Coppins, R.L., Wolf, A.C. and Silverman, S.K. (2003) Deoxyribozymes with 2′-5′ RNA ligase activity. J. Am. Chem. Soc. 125:2444–2454.Google Scholar
  20. 20.
    Wang, Y. and Silverman, S.K. (2003) Deoxyribozymes that synthesize branched and lariat RNA. J. Am. Chem. Soc. 125:6880–6881.Google Scholar
  21. 21.
    Carmi, N., Balkhi, S.R. and Breaker, R.R. (1998) Cleaving DNA with DNA. Proc. Natl. Acad. Sci. USA 95:2233–2237.Google Scholar
  22. 22.
    Cuenoud, B. and Szostak, J.W. (1995) A DNA metalloenzyme with DNA ligase activity. Nature (Lond.) 375:611–614.Google Scholar
  23. 23.
    Sreedhara, A., Li, Y. and Breaker, R.R. (2004) Ligating DNA with DNA. J. Am. Chem. Soc. 126: 3454–3460.Google Scholar
  24. 24.
    Li, Y. and Breaker, R.R. (1999) Phosphorylating DNA with DNA. Proc. Natl. Acad. Sci. USA 96:2746–2751.Google Scholar
  25. 25.
    Achenbach, J.C., Jeffries, G.A., McManus, S.A., Billen, L.P. and Li, Y. (2005) Secondary-structure characterization of two proficient kinase deoxyribozymes. Biochemistry 44:3765–3774.Google Scholar
  26. 26.
    Nutiu, R., Mei, S.H.J., Liu, Z. and Li, Y. (2004) Engineering DNA aptamers and DNA enzymes with fluorescence-signaling properties. Pure Appl. Chem. 76:1547–1561.Google Scholar
  27. 27.
    Liu, Z., Mei, S.H.J., Brennan J.D. and Li, Y. (2003) An assemblage of signaling DNA enzymes with intriguing metal-ion specificities and pH dependences. J. Am. Chem. Soc. 125: 7539–7545.Google Scholar
  28. 28.
    Camarero, J.A. (2006) New developments for the site-specific attachment of protein to surfaces. Biophys. Rev. Lett. 1:1–28.Google Scholar
  29. 29.
    Weetall, H.H. (1993) Preparation of immobilized proteins covalently coupled through silane coupling agents to inorganic supports. Appl. Biochem. Biotechnol. 41:157–188.Google Scholar
  30. 30.
    Vandenberg, E.T., Brown, R.S. and Krull, U.J. (1994) Immobilization of proteins for biosensor development. In: Veliky, I.A. and Mclean, R.J.C. (eds.) Immobilized biosystems in theory and practical applications. Blackie, Glasgow, pp. 129–231.Google Scholar
  31. 31.
    Di Giusto, D.A. and King, G.C. (2006) Special-purpose modifications and immobilized functional nucleic acids for biomolecular interactions. Top. Curr. Chem. 261:131–168.Google Scholar
  32. 32.
    Gill, I. (2001) Bio-doped nanocomposite polymers: sol-gel bioencapsulates. Chem. Mater. 13:3404–3421.Google Scholar
  33. 33.
    Jin, W. and Brennan, J.D. (2002) Properties and applications of proteins encapsulated within sol-gel derived materials. Anal. Chim. Acta 461:1–36.Google Scholar
  34. 34.
    Pierre, A.C. (2004) The sol-gel encapsulation of enzymes. Biocat. Biotrans. 22:145–170.Google Scholar
  35. 35.
    Avnir, D., Coradin, T., Lev. O. and Livage, J. (2006) Recent bio-applications of sol-gel materials. J. Mater. Chem. 16:1013–1030.Google Scholar
  36. 36.
    Besanger, T.R. and Brennan, J.D. (2006) Entrapment of membrane proteins in sol-gel derived silica. J. Sol-gel Sci. Technol. 40:209–225.Google Scholar
  37. 37.
    Pierre, A., Bonnet, J., Vekris, A. and Portier, J. (2001) Encapsulation of deoxyribonucleic acid molecules in silica and hybrid organic-silica gels. J. Mater. Sci. Mater. Med. 12:51–55.Google Scholar
  38. 38.
    Numata, M., Sugiyasu, K., Hasegawa, T. and Shinkai, S. (2004) Sol-gel reaction using DNA as a template: an attempt toward transcription of DNA into inorganic materials. Angew. Chem. Int. Ed. Engl. 43:3279–3283.Google Scholar
  39. 39.
    Gill, I., Ballesteros, A. (2000) Bioencapsulation within synthetic polymers (part 1): sol-gel encapsulated biologicals. Trends Biotechnol. 18:282–296.Google Scholar
  40. 40.
    Li, J., Tan, W., Wang, K., Yang, X., Tang, Z. and He, X. (2001) Optical DNA biosensor based on molecular beacon immobilized on sol-gel membrane. Proc. SPIE 4414 (International Conference on Sensor Technology: ISTC 2001) 2001:27–30.Google Scholar
  41. 41.
    Navani, N.K. and Li, Y. (2006) Nucleic acid aptamers and enzymes as sensors. Curr. Opin. Chem. Biol. 10:272–281.Google Scholar
  42. 42.
    Deng, Q., German, I., Buchanan, D. and Kennedy, R.T. (2001) Retention and separation of adenosine and analogues by affinity chromatography with an aptamer stationary phase. Anal. Chem. 73:5415–5421.Google Scholar
  43. 43.
    Rehder, M.A. and McGown, L.B. (2001) Open-tubular capillary electrochromatography of bovine b-lactoglobulin variants A and B using an aptamer stationary phase. Electrophoresis 22:3759–3764.Google Scholar
  44. 44.
    Dick, L.W. and McGown, L.B. (2004) Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry. Anal. Chem. 76:3037–3041.Google Scholar
  45. 45.
    Elghanian, R., Storhoff, J.J., Mucic, R.C., Letsinger, R.L. and Mirkin, C.A. (1997) Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science 277:1078–1080.Google Scholar
  46. 46.
    Liu, J. and Lu, Y. (2003) A colorimetric lead biosensor using DNAzyme-directed assembly of gold nanoparticles. J. Am. Chem. Soc. 125:6642–6643.Google Scholar
  47. 47.
    Di Giusto, D.A., Wlassoff, W.A., Giesebrecht, S., Gooding, J.J. and King, G.C. (2004) Multipotential electrochemical detection of primer extension reactions on DNA self-assembled monolayers. J. Am. Chem. Soc. 126:4120–4121.Google Scholar
  48. 48.
    Rodriguez, M.C., Kawde, A.N. and Wang, J. (2005) Aptamer biosensor for label-free impedance spectroscopy detection of proteins based on recognition-induced switching of the surface charge. Chem. Commun. 34:4267–4269.Google Scholar
  49. 49.
    Li, Y., Lee, H.J. and Corn, R.M. (2006) Fabrication and characterization of RNA aptamer microarrays for the study of protein—aptamer interactions with SPR imaging. Nucleic Acids Res. 34:6416–6424.Google Scholar
  50. 50.
    Liss, M., Petersen, B., Wolf, H. and Prohaska, E. (2002) An aptamer-based quartz crystal protein biosensor. Anal. Chem. 74:4488–4495.Google Scholar
  51. 51.
    Savran, C.A., Knudsen, S.M., Ellington, A.D. and Manalis, S.R. (2004) Micromechanical detection of proteins using aptamer-based receptor molecules. Anal. Chem. 76:3194–3198.Google Scholar
  52. 52.
    Lu, Y. and Liu, J. (2006) Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers. Curr. Opin. Biotechnol. 17:580–588.Google Scholar
  53. 53.
    Rosi, N.L. and Mirkin, C.A. (2005) Nanostructures in biodiagnostics. Chem. Rev. 105: 1547–1562.Google Scholar
  54. 54.
    Nutiu, R., Billen, L.P. and Li, Y. (2006). Fluorescence-signaling nucleic acid-based sensors. In: Silverman, S.K. (ed.) Nucleic acid switches and sensors. Landes Bioscience/Springer, New York, pp. 49–74.Google Scholar
  55. 55.
    Cho, E.J., Collett, J.R., Szafranska, A.E. and Ellington, A.D. (2006) Optimization of aptamer microarray technology for multiple protein targets. Anal. Chim. Acta 564:82–90.Google Scholar
  56. 56.
    Bock, C., Coleman, M., Collins, B., Davis, J., Foulds, G., Gold, L., Greef, C., Heil, J., Heilig, J.S., Hicke, B., Nelson Hurst, M., Husar, G., Miller, D., Ostroff, R., Petach, H., Schneider, D., Vant-Hull, B., Waugh, S., Weiss, A. and Wilcox, S.K. (2004) Photoaptamer arrays applied to multiplexed proteomic analysis. Proteomics 4:609–618.Google Scholar
  57. 57.
    Potyrailo, R.A., Conrad, R.C., Ellington, A.D. and Hieftje, G.M. (1998) Adapting selected nucleic acid ligands (aptamers) to biosensors. Anal. Chem. 70:3419–3425.Google Scholar
  58. 58.
    Jhaveri, S., Kirby, R., Conrad, R., Maglott, E., Bowser, M., Kennedy, R.T., Glick, G. and Ellington, A.D. (2000) Designed signaling aptamers that transducer molecular recognition to changes in fluorescence intensity. J. Am. Chem. Soc. 122:2469–2473.Google Scholar
  59. 59.
    Levy, M., Cater, S.F. and Ellington, A.D. (2005) Quantum-dot aptamer beacons for the detection of proteins. ChemBioChem 6:2163–2166.Google Scholar
  60. 60.
    Liu, J. and Lu, Y. (2007) Quantum dot encoding of aptamer-linked nanostructures for one-pot simultaneous detection of multiple analytes. Anal. Chem. 79:4120–4125.Google Scholar
  61. 61.
    Du, H., Disney, M.D., Miller, B.L. and Krauss, T.D. (2003) Hybridization-based unquenching of DNA hairpins on Au surfaces: prototypical “molecular beacon” biosensors. J. Am. Chem. Soc. 125:4012–4013.Google Scholar
  62. 62.
    Tyagi, S. and Kramer, F.R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303–308.Google Scholar
  63. 63.
    Tan, W., Fang, X., Li, J. and Liu, X. (2000) Molecular beacons: a novel DNA probe for nucleic acid and protein studies. Chem. Eur. J. 6:1107–1111.Google Scholar
  64. 64.
    Nutiu, R. and Li, Y. (2002) Tripartite molecular beacons. Nucleic Acids Res. 30:e94.Google Scholar
  65. 65.
    Hamaguchi, N., Ellington, A. and Stanton, M. (2001) Aptamer beacons for the direct detection of proteins. Anal. Biochem. 294:126–131.Google Scholar
  66. 66.
    Li, J.J., Fang, X. and Tan, W. (2002) Molecular aptamer beacons for real-time protein recognition. Biochem. Biophys. Res. Commun. 292:31–40.Google Scholar
  67. 67.
    Nutiu, R. and Li, Y. (2003) Structure-switching signaling aptamers. J. Am. Chem. Soc. 125: 4771–4778.Google Scholar
  68. 68.
    Li, J. and Lu, Y. (2000) A highly sensitive and selective catalytic DNA biosensor for lead ions. J. Am. Chem. Soc. 122:10466–10467.Google Scholar
  69. 69.
    Liu, J., Brown, A.K., Meng, X., Cropek, D.M., Istok, J.D., Watson, D.B. and Lu, Y. (2007) A catalytic beacon sensor for uranium with parts-per trillion sensitivity and millionfold selectivity. Proc. Natl. Acad. Sci. USA 104:2056–2061.Google Scholar
  70. 70.
    Stojanovic, M.N., de Prada, P. and Landry, D.W. (2001) Catalytic molecular beacons. ChemBioChem 2:411–415.Google Scholar
  71. 71.
    Hartig, J.S., Najafi-Shoushtari, S.H., Gruene, I., Yan, A., Ellington, A.D. and Famulok, M. (2002) Protein-dependent ribozymes report molecular interactions in real time. Nat. Biotechnol. 20: 717–722.Google Scholar
  72. 72.
    Achenbach, J.C., Nutiu, R. and Li, Y. (2005) Structure-switching allosteric deoxyribozymes. Anal. Chim. Acta 534:41–51.Google Scholar
  73. 73.
    Mei, S.H., Liu, Z., Brennan, J.D. and Li, Y. (2003) An efficient RNA-cleaving DNA enzyme the synchronized catalysis with fluorescence signaling. J. Am. Chem. Soc. 125:412–420.Google Scholar
  74. 74.
    Chiuman, W. and Li, Y. (2007) Efficient signaling platforms built from a small catalytic DNA and doubly labeled fluorogenic substrates. Nucleic Acids Res. 35:401–405.Google Scholar
  75. 75.
    Liu, X., Tan, W. (1999) A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons. Anal. Chem. 71:5054–5059.Google Scholar
  76. 76.
    Yu, S., Cai, X., Tan, X., Zhu, Y. and Lu, B. (2001) Fiber optic biosensor using aptamer as receptors. Proc. SPIE 4414 (International Conference on Sensor Technology: ISTC 2001) 2001:35–37.Google Scholar
  77. 77.
    Lee, M. and Walt, D.R. (2000) A fiber-optic microarray biosensor using aptamers as receptors. Anal. Biochem. 282:142–146.Google Scholar
  78. 78.
    Heise, C. and Bier, F.F. (2006) Immobilization of DNA on microarrays. Top. Curr. Chem. 261: 1–25.Google Scholar
  79. 79.
    Wang, H., Li, J., Liu, Q., Liu, H. and Lu, Z. (2001) Label-free DNA hybridization detection with molecular beacon immobilized in photopolymerized acrylamide gel microarray. Proc. SPIE 4601 (Micromachining and Microfabrication Process Technology and Devices), 256–259.Google Scholar
  80. 80.
    Yao, G. and Tan, W. (2004) Molecular-beacon-based array for sensitive DNA analysis. Anal. Biochem. 331:216–223.Google Scholar
  81. 81.
    Ramachandran, A., Flinchbaugh, J., Ayoubi, P., Olah, G.A. and Malayer, J.R. (2004) Target discrimination by surface-immobilized molecular beacons designed to detect Francisella tularensis. Biosens. Bioelectron. 19:727–736.Google Scholar
  82. 82.
    Kim, H., Kane, M.D., Kim, S., Dominguez, W., Applegate, B.M. and Savikhin, S. (2007) A molecular beacon DNA microarray system for rapid detection of E. coli O157:H7 that eliminates the risk of a false negative signal. Biosens. Bioelectron. 22:1041–1047.Google Scholar
  83. 83.
    Maxwell, D.J., Taylor, J.R. and Nie, S. (2002) Self-assembled nanoparticle probes for recognition and detection of biomolecules. J. Am. Chem. Soc. 124:9606–9612.Google Scholar
  84. 84.
    Du, H., Strohsahl, C.M., Camera, J., Miller, B.L. and Krauss, T.D. (2005) Sensitivity and specificity of metal surface-immobilized “molecular beacon” biosensors. J. Am. Chem. Soc. 127: 7932–7940.Google Scholar
  85. 85.
    Swearingen, C.B., Wernette, D.P., Cropek, D.M., Lu, Y., Sweedler, J.V. and Bohn, P.W. (2005) Immobilization of a catalytic DNA molecular beacon on Au for Pb(II) detection. Anal. Chem. 77:442–448.Google Scholar
  86. 86.
    Stadtherr, K., Wolf, H. and Lindner, P. (2005) An aptamer-based protein biochip. Anal. Chem. 77:4548–4554.Google Scholar
  87. 87.
    Kirby, R., Cho, E.J., Gehrke, B., Bayer, T., Park, Y.S., Neikirk, D.P., McDevitt, J.T. and Ellington, A.D. (2004) Aptamer-based sensor arrays for the detection and quantitation of proteins. Anal. Chem. 76:4066–4078.Google Scholar
  88. 88.
    Collett, J.R., Cho, E.J., Lee, J.F., Levy, M., Hood, A.J., Wan, C. and Ellington, A.D. (2004) Functional RNA microarrays for high-throughput screening of antiprotein aptamers. Anal. Biochem. 338:113–123.Google Scholar
  89. 89.
    Collett, J.R., Cho, E.J. and Ellington, A.D. (2005) Production and processing of aptamer microarrays. Methods 37:4–15.Google Scholar
  90. 90.
    Brody, E.N., Willis, M.C., Smith, J.D., Jayasena, S., Zichi, D. and Gold, L. (1999) The use of aptamers in large arrays for molecular diagnostics. Mol. Diagn. 4:381–388.Google Scholar
  91. 91.
    McCauley, T.G., Hamaguchi, N. and Stanton, M. (2003) Aptamer-based biosensor arrays for detection and quantification of biological macromolecules. Anal. Biochem. 319:244–250.Google Scholar
  92. 92.
    Yamamoto-Fujita, R. and Kumar, P.K.R. (2005) Aptamer-derived nucleic acid oligos: application to develop nucleic acid chips to analyze proteins and small ligands. Anal. Chem. 77:5460–5466.Google Scholar
  93. 93.
    Lin, C., Katilius, E., Liu, Y., Zhang, J. and Yan, H. (2006) Self-assembled signalling aptamer DNA arrays for protein detection. Angew. Chem. Int. Ed. 45:5295–5301.Google Scholar
  94. 94.
    Abérem, M.B., Najari, A., Ho, H.-A., Gravel, J.-F., Nobert, P., Boudreau, D. and Leclerc, M. (2006) Protein detecting arrays based on cationic polythiophene—DNA—aptamer complexes. Adv. Mater. 18:2703–2707.Google Scholar
  95. 95.
    Hesselbert, J.R., Robertson, M.P., Knudsen, S.M. and Ellington, A.D. (2003) Simultaneous detection of diverse analytes with an aptazyme ligase array. Anal. Biochem. 312:106–112.Google Scholar
  96. 96.
    Seetharaman, S., Zivarts, M., Sudarsan, N. and Breaker, R.R. (2001) Immobilized RNA switches for the analysis of complex chemical and biological mixtures. Nat. Biotechnol. 19:336–341.Google Scholar
  97. 97.
    Braun, S., Rappoport, S., Zusman, R., Avnir, D. and Ottolenghi, M. (1990) Biochemically active sol-gel-glasses: the trapping of enzymes. Mater. Lett. 10:1–5.Google Scholar
  98. 98.
    Ellerby, L.M., Nishida, C.R., Nishida, F., Yamanaka, S., Dunn, B., Valentine, J.S. and Zink, J.I. (1992) Encapsulation of proteins in transparent porous silicate glasses prepared by the sol-gel method. Science 255:1113–1115.Google Scholar
  99. 99.
    Brook, M.A., Chen, Y., Guo, K., Zhang, Z. and Brennan, J.D. (2004) Sugar-modified silanes: precursors for silica monoliths. J. Mater. Chem. 14:1469–1479.Google Scholar
  100. 100.
    Brinker, C.J. and Scherer, G.W. (1990) Sol-gel science: the physics and chemistry of sol-gel processing. Academic Press, San Diego, CA.Google Scholar
  101. 101.
    Wang, H., Li, J., Liu, Q., Liu, H. and Lu, Z. (2001) Label-free DNA hybridization detection with molecular beacon immobilized in photopolymerized acrylamide gel microarray. Proc. SPIE 4601 (Micromachining and Microfabrication Process Technology and Devices), 256–259.Google Scholar
  102. 102.
    Rupcich, N., Nutiu, R., Li, Y. and Brennan, J.D. (2005) Entrapment of fluorescent signaling DNA aptamers in sol-gel derived silica. Anal. Chem. 77:4300–4307.Google Scholar
  103. 103.
    Sui, X., Cruz-Aguado, J.A., Chen, Y., Zhang, Z., Brook, M.A. and Brennan, J.D. (2005) Properties of human serum albumin entrapped in sol-gel-derived silica bearing covalently tethered sugars. Chem. Mater. 17:1174–1182.Google Scholar
  104. 104.
    Chiuman, W. and Li, Y. (2006) Revitalization of six abandoned catalytic DNA species reveals a common three-way junction framework and diverse catalytic cores. J. Mol. Biol. 357:748–754.Google Scholar
  105. 105.
    Shen, Y., Mackey, G., Rupcich, N., Gloster, N.D., Chiuman, W., Li, Y. and Brennan, J.D. (2007) Entrapment of fluorescence-signaling DNA enzymes in sol-gel derived materials for metal ion sensing. Anal. Chem. 79:3494–3503.Google Scholar
  106. 106.
    Rupcich, N., Chiuman, W., Nutiu, R., Mei, S., Flora, K.K., Li, Y. and Brennan, J.D. (2006) Quenching of fluorophore-labeled DNA oligonucleotides by divalent metal ions: implications for selection, design and applications of signaling aptamers and signaling deoxyribozymes. J. Am. Chem. Soc. 128:780–790.Google Scholar
  107. 107.
    Rupcich, N., Nutiu, R., Li, Y. and Brennan, J.D. (2006) Solid-phase enzyme activity assay utilizing an entrapped fluorescence-signaling DNA aptamer. Angew. Chem. Int. Ed. Engl. 45:3295–3299.Google Scholar
  108. 108.
    Elowe, N.H., Nutiu, R., Allali-Hassani, A., Cechetto, J.D., Hughes, D.W., Li, Y. and Brown, E.D. (2006) Screening made simple for a difficult target with a signaling aptamer for deaminase activity. Angew. Chem. Int. Ed. Engl. 45:5648–5652.Google Scholar
  109. 109.
    Hodgson, R., Besanger, T.R., Brook M.A. and Brennan, J.D. (2005) Inhibitor screening using immobilized enzyme-reactor chromatography/mass spectrometry. Anal. Chem. 77: 7512–7519.Google Scholar
  110. 110.
    Agarwal, R.P. (1982) Inhibitors of adenosine deaminase. Pharmacol. Ther. 17:399–429.Google Scholar
  111. 111.
    Nutiu, R. and Li, Y. (2005). In vitro selection of structure-switching signaling aptamers. Angew. Chem. Int. Ed. Engl. 44:1061–1065.Google Scholar
  112. 112.
    Nutiu, R., Yu, J.M.Y. and Li, Y. (2004a) Signaling aptamers for monitoring enzymatic activity and for inhibitor screening. ChemBioChem 5:1139–1144.Google Scholar
  113. 113.
    Srinivasan, J., Cload, S.T., Hamaguchi, N., Kurz, J., Keene, S., Kurz, M., Boomer, R., Blanchard, J., Epstein, D., Wilson, C. and Diener, J.L. (2004) ADP-specific sensors enable universal assay of protein kinase activity. Chem. Biol. 11:499–508.Google Scholar
  114. 114.
    Liu, J., Mazumdar, D. and 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.Google Scholar
  115. 115.
    Su, S., Nutiu, R., Filipe, C.D.M., Li, Y. and Pelton, R. (2007) Adsorption and covalent coupling of ATP-binding DNA aptamers onto cellulose. Langmuir 23:1300–1302.Google Scholar
  116. 116.
    Zhao, W., Gao, Y., Kandadai, S.A., Brook, M.A. and Li, Y. (2006) DNA polymerization on gold nanoparticles through rolling circle amplification: towards novel scaffolds for three-dimensional periodic nanoassemblies. Angew. Chem. Int. Ed. 45:2409–2413.Google Scholar
  117. 117.
    Lin, C., Liu, Y. and Yan, H. (2007) Self-assembled combinatorial encoding nanoarrays for multiplexed biosensing. Nano Lett. 7:507–512.Google Scholar
  118. 118.
    Jones, R.B., Gordus, A., Krall, J.A. and MacBeath, G. (2006) A quantitative protein interaction network for the ErbB receptors using protein microarrays. Nature (Lond.) 439: 168–174.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2009

Authors and Affiliations

  • Nicholas Rupcich
    • 1
  • Razvan Nutiu
    • 1
  • Yutu Shen
    • 1
  • Yingfu Li
    • 2
  • John D. Brennan
    • 1
  1. 1.Department of ChemistryMcMaster UniversityHamiltonCanada
  2. 2.Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonCanada

Personalised recommendations