Skip to main content

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

  • Chapter
Functional Nucleic Acids for Analytical Applications

Part of the book series: Integrated Analytical Systems ((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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  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.

    CAS  Google Scholar 

  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. 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.

    CAS  Google Scholar 

  4. Ellington, A.D. and Szostak, J.W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature (Lond.) 346:818–822.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  6. Wilson, D.S. and Szostak, J.W. (1999) In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68:611–647.

    CAS  Google Scholar 

  7. Famulok, M. (1999) Oligonucleotide aptamers that recognize small molecules. Curr. Opin. Struct. Biol. 9:324–329.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  10. Jenison, R.D., Gill, S.C., Pardi, A. and Polisky, B. (1994) High-resolution molecular discrimination by RNA. Science 263:1425–1429.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  13. Silverman, S.K. (2004) Deoxyribozymes: DNA catalysts for bioorganic chemistry. Org. Biomol. Chem. 2:2701–2706.

    CAS  Google Scholar 

  14. Joyce, G.F. (2004) Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73: 791–836.

    CAS  Google Scholar 

  15. Breaker, R.R. (2004) Natural and engineered nucleic acids as tools to explore biology. Nature (Lond.) 432:838–845.

    CAS  Google Scholar 

  16. Peracchi, A. (2005) DNA catalysis: potential, limitations, open questions. ChemBioChem 6: 1316–1322.

    CAS  Google Scholar 

  17. Breaker, R.R. and Joyce, G.F. (1994) A DNA enzyme that cleaves RNA. Chem. Biol. 1: 223–229.

    CAS  Google Scholar 

  18. Santoro, S.W. and Joyce, G.F. (1997) A general purpose RNA-cleaving DNA enzyme. Proc. Natl. Acad. Sci. USA 94:4262–4266.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  20. Wang, Y. and Silverman, S.K. (2003) Deoxyribozymes that synthesize branched and lariat RNA. J. Am. Chem. Soc. 125:6880–6881.

    CAS  Google Scholar 

  21. Carmi, N., Balkhi, S.R. and Breaker, R.R. (1998) Cleaving DNA with DNA. Proc. Natl. Acad. Sci. USA 95:2233–2237.

    CAS  Google Scholar 

  22. Cuenoud, B. and Szostak, J.W. (1995) A DNA metalloenzyme with DNA ligase activity. Nature (Lond.) 375:611–614.

    CAS  Google Scholar 

  23. Sreedhara, A., Li, Y. and Breaker, R.R. (2004) Ligating DNA with DNA. J. Am. Chem. Soc. 126: 3454–3460.

    CAS  Google Scholar 

  24. Li, Y. and Breaker, R.R. (1999) Phosphorylating DNA with DNA. Proc. Natl. Acad. Sci. USA 96:2746–2751.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  28. Camarero, J.A. (2006) New developments for the site-specific attachment of protein to surfaces. Biophys. Rev. Lett. 1:1–28.

    CAS  Google Scholar 

  29. Weetall, H.H. (1993) Preparation of immobilized proteins covalently coupled through silane coupling agents to inorganic supports. Appl. Biochem. Biotechnol. 41:157–188.

    CAS  Google Scholar 

  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. 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. Gill, I. (2001) Bio-doped nanocomposite polymers: sol-gel bioencapsulates. Chem. Mater. 13:3404–3421.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  34. Pierre, A.C. (2004) The sol-gel encapsulation of enzymes. Biocat. Biotrans. 22:145–170.

    CAS  Google Scholar 

  35. Avnir, D., Coradin, T., Lev. O. and Livage, J. (2006) Recent bio-applications of sol-gel materials. J. Mater. Chem. 16:1013–1030.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  39. Gill, I., Ballesteros, A. (2000) Bioencapsulation within synthetic polymers (part 1): sol-gel encapsulated biologicals. Trends Biotechnol. 18:282–296.

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  44. Dick, L.W. and McGown, L.B. (2004) Aptamer-enhanced laser desorption/ionization for affinity mass spectrometry. Anal. Chem. 76:3037–3041.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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. 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. 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.

    CAS  Google Scholar 

  50. Liss, M., Petersen, B., Wolf, H. and Prohaska, E. (2002) An aptamer-based quartz crystal protein biosensor. Anal. Chem. 74:4488–4495.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  53. Rosi, N.L. and Mirkin, C.A. (2005) Nanostructures in biodiagnostics. Chem. Rev. 105: 1547–1562.

    CAS  Google Scholar 

  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. 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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  59. Levy, M., Cater, S.F. and Ellington, A.D. (2005) Quantum-dot aptamer beacons for the detection of proteins. ChemBioChem 6:2163–2166.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  62. Tyagi, S. and Kramer, F.R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14:303–308.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  64. Nutiu, R. and Li, Y. (2002) Tripartite molecular beacons. Nucleic Acids Res. 30:e94.

    Google Scholar 

  65. Hamaguchi, N., Ellington, A. and Stanton, M. (2001) Aptamer beacons for the direct detection of proteins. Anal. Biochem. 294:126–131.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

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

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  70. Stojanovic, M.N., de Prada, P. and Landry, D.W. (2001) Catalytic molecular beacons. ChemBioChem 2:411–415.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  72. Achenbach, J.C., Nutiu, R. and Li, Y. (2005) Structure-switching allosteric deoxyribozymes. Anal. Chim. Acta 534:41–51.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  75. Liu, X., Tan, W. (1999) A fiber-optic evanescent wave DNA biosensor based on novel molecular beacons. Anal. Chem. 71:5054–5059.

    CAS  Google Scholar 

  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. Lee, M. and Walt, D.R. (2000) A fiber-optic microarray biosensor using aptamers as receptors. Anal. Biochem. 282:142–146.

    CAS  Google Scholar 

  78. Heise, C. and Bier, F.F. (2006) Immobilization of DNA on microarrays. Top. Curr. Chem. 261: 1–25.

    Google Scholar 

  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. Yao, G. and Tan, W. (2004) Molecular-beacon-based array for sensitive DNA analysis. Anal. Biochem. 331:216–223.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  86. Stadtherr, K., Wolf, H. and Lindner, P. (2005) An aptamer-based protein biochip. Anal. Chem. 77:4548–4554.

    Google Scholar 

  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.

    CAS  Google Scholar 

  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. Collett, J.R., Cho, E.J. and Ellington, A.D. (2005) Production and processing of aptamer microarrays. Methods 37:4–15.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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. 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. 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. 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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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. 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. 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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  110. Agarwal, R.P. (1982) Inhibitors of adenosine deaminase. Pharmacol. Ther. 17:399–429.

    CAS  Google Scholar 

  111. Nutiu, R. and Li, Y. (2005). In vitro selection of structure-switching signaling aptamers. Angew. Chem. Int. Ed. Engl. 44:1061–1065.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  117. Lin, C., Liu, Y. and Yan, H. (2007) Self-assembled combinatorial encoding nanoarrays for multiplexed biosensing. Nano Lett. 7:507–512.

    CAS  Google Scholar 

  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.

    CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer Science+Business Media, LLC

About this chapter

Cite this chapter

Rupcich, N., Nutiu, R., Shen, Y., Li, Y., Brennan, J.D. (2009). The Use of Functional Nucleic Acids in Solid-Phase Fluorimetric Assays. In: Yingfu, L., Yi, L. (eds) Functional Nucleic Acids for Analytical Applications. Integrated Analytical Systems. Springer, New York, NY. https://doi.org/10.1007/978-0-387-73711-9_12

Download citation

Publish with us

Policies and ethics