Interplay between Metal Ions and Nucleic Acids pp 217-248

Part of the Metal Ions in Life Sciences book series (MILS, volume 10)

| Cite as

Metal Ion-Dependent DNAzymes and Their Applications as Biosensors

Chapter

Abstract

Long considered to serve solely as the genetic information carrier, DNA has been shown in 1994 to be able to act as DNA catalysts capable of catalyzing a trans-esterification reaction similar to the action of ribozymes and protein enzymes. Although not yet found in nature, numerous DNAzymes have been isolated through in vitro selection for catalyzing many different types of reactions in the presence of different metal ions and thus become a new class of metalloenzymes. What remains unclear is how DNA can carry out catalysis with simpler building blocks and fewer functional groups than ribozymes and protein enzymes and how DNA can bind metal ions specifically to perform these functions. In the past two decades, many biochemical and biophysical studies have been carried out on DNAzymes, especially RNA-cleaving DNAzymes. Important insights have been gained regarding their metal-dependent activity, global folding, metal binding sites, and catalytic mechanisms for these DNAzymes. Because of their high metal ion selectivity, one of the most important practical applications for DNAzymes is metal ion detection, resulting in highly sensitive and selective fluorescent, colorimetric, and electrochemical sensors for a wide range of metal ions such as Pb2+, UO2 2 +,\(\rm{Pb}^{2+},\ UO^{2+}_{2},\) including paramagnetic metal ions such as Cu2+. This chapter summarizes recent progresses in in vitro selection of metal ion-selective DNAzymes, their biochemical and biophysical studies and sensing applications.

Keywords

biosensor catalysis DNA DNAzyme metalloenzyme metal sensing 

References

  1. 1.
    K. Kruger, P. J. Grabowski, A. J. Zaug, J. Sands, D. E. Gottschling, T. R. Cech, Cell 1982, 31, 147–157.CrossRefPubMedGoogle Scholar
  2. 2.
    C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, S. Altman, Cell 1983, 35, 849–857.CrossRefPubMedGoogle Scholar
  3. 3.
    R. R. Breaker, G. F. Joyce, Chem. Biol. 1994, 1, 223–229.CrossRefPubMedGoogle Scholar
  4. 4.
    S. W. Santoro, G. F. Joyce, Proc. Natl. Acad. Sci. USA 1997, 94, 4262–4266.CrossRefPubMedGoogle Scholar
  5. 5.
    J. Li, W. Zheng, A. H. Kwon, Y. Lu, Nucleic Acids Res. 2000, 28, 481–488.CrossRefPubMedGoogle Scholar
  6. 6.
    C. R. Geyer, D. Sen, Chem. Biol. 1997, 4, 579–593.CrossRefPubMedGoogle Scholar
  7. 7.
    D. Faulhammer, M. Famulok, Angew. Chem., Int. Ed. Engl. 1996, 35, 2837–2841.CrossRefGoogle Scholar
  8. 8.
    A. R. Feldman, D. Sen, J. Mol. Biol. 2001, 313, 283–294.CrossRefPubMedGoogle Scholar
  9. 9.
    R. P. G. Cruz, J. B. Withers, Y. Li, Chem. Biol. 2004, 11, 57–67.PubMedGoogle Scholar
  10. 10.
    J. Liu, A. K. Brown, X. Meng, D. M. Cropek, J. D. Istok, D. B. Watson, Y. Lu, Proc. Natl. Acad. Sci. USA 2007, 104, 2056–2061.CrossRefPubMedGoogle Scholar
  11. 11.
    N. Carmi, L. A. Shultz, R. R. Breaker, Chem. Biol. 1996, 3, 1039–1046.CrossRefPubMedGoogle Scholar
  12. 12.
    N. Carmi, H. R. Balkhi, R. R. Breaker, Proc. Natl. Acad. Sci. USA 1998, 95, 2233–2237.CrossRefPubMedGoogle Scholar
  13. 13.
    N. Carmi, R. R. Breaker, Bioorg. Med. Chem. 2001, 9, 2589–2600.CrossRefPubMedGoogle Scholar
  14. 14.
    M. Chandra, A. Sachdeva, S. K. Silverman, Nat. Chem. Biol. 2009, 5, 718–720.CrossRefPubMedGoogle Scholar
  15. 15.
    Y. Xiao, M. Chandra, S. K. Silverman, Biochemistry 2010.Google Scholar
  16. 16.
    Y. Xiao, E. C. Allen, S. K. Silverman, Chem. Commun. 2011, 47, 1749–1751.CrossRefGoogle Scholar
  17. 17.
    J. Burmeister, G. von Kiedrowski, A. D. Ellington, Angew. Chem., Int. Ed. Engl. 1997, 36, 1321–1324.CrossRefGoogle Scholar
  18. 18.
    B. Cuenoud, J. W. Szostak, Nature 1995, 375, 611–614.CrossRefPubMedGoogle Scholar
  19. 19.
    A. Sreedhara, Y. Li, R. R. Breaker, J. Am. Chem. Soc. 2004, 126, 3454–3460.CrossRefPubMedGoogle Scholar
  20. 20.
    R. L. Coppins, W. E. Purtha, Y. Wang, S. K. Silverman “Synthesis of native 3’-5’ RNA linkages by deoxyribozymes”, 229th ACS National Meeting, San Diego, CA, USA, 2005, ORGN–653.Google Scholar
  21. 21.
    W. E. Purtha, R. L. Coppins, M. K. Smalley, S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 13124–13125.CrossRefPubMedGoogle Scholar
  22. 22.
    Y. Wang, S. K. Silverman, Biochemistry 2003, 42, 15252–15263.CrossRefPubMedGoogle Scholar
  23. 23.
    Y. Wang, S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 6880–6881.CrossRefPubMedGoogle Scholar
  24. 24.
    R. L. Coppins, S. K. Silverman, Nat. Struct. Mol. Biol. 2004, 11, 270–274.CrossRefPubMedGoogle Scholar
  25. 25.
    R. L. Coppins, S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 2900–2907.CrossRefPubMedGoogle Scholar
  26. 26.
    E. D. Pratico, Y. Wang, S. K. Silverman, Nucleic Acids Res. 2005, 33, 3503–3512.CrossRefPubMedGoogle Scholar
  27. 27.
    Y. Wang, S. K. Silverman, Angew. Chem., Int. Ed. Engl. 2005, 44, 5863–5866.CrossRefGoogle Scholar
  28. 28.
    P. I. Pradeepkumar, C. Hoebartner, D. A. Baum, S. K. Silverman, Angew. Chem., Int. Ed. Engl. 2008, 47, 1753–1757.CrossRefGoogle Scholar
  29. 29.
    W. Wang, L. P. Billen, Y. Li, Chem. Biol. 2002, 9, 507–517.CrossRefPubMedGoogle Scholar
  30. 30.
    Y. Li, Y. Liu, R. R. Breaker, Biochemistry 2000, 39, 3106–3114.CrossRefPubMedGoogle Scholar
  31. 31.
    C. Höbartner, P. I. Pradeepkumar, S. K. Silverman, Chem. Commun. 2007, 2255–2257.Google Scholar
  32. 32.
    T. L. Sheppard, P. Ordoukhanian, G. F. Joyce, Proc. Natl. Acad. Sci. USA 2000, 97, 7802–7807.CrossRefPubMedGoogle Scholar
  33. 33.
    M. Chandra, S. K. Silverman, J. Am. Chem. Soc. 2008, 130, 2936–2937.CrossRefPubMedGoogle Scholar
  34. 34.
    Y. Li, D. Sen, Nat. Struct. Biol. 1996, 3, 743–747.CrossRefPubMedGoogle Scholar
  35. 35.
    Y. Li, D. Sen, Biochemistry 1997, 36, 5589–5599.CrossRefPubMedGoogle Scholar
  36. 36.
    T. Lan, K. Furuya, Y. Lu, Chem. Commun. 2010, 46, 3896–3898.CrossRefGoogle Scholar
  37. 37.
    A. K. Brown, J. Liu, Y. He, Y. Lu, ChemBioChem 2009, 10, 486–492.CrossRefPubMedGoogle Scholar
  38. 38.
    J. Li, Y. Lu, J. Am. Chem. Soc. 2000, 122, 10466–10467.CrossRefGoogle Scholar
  39. 39.
    J. Liu, Y. Lu, Anal. Chem. 2003, 75, 6666–6672.CrossRefPubMedGoogle Scholar
  40. 40.
    N. Nagraj, J. Liu, S. Sterling, J. Wu, Y. Lu, Chem. Commun. 2009, 4103–4105.Google Scholar
  41. 41.
    J. Liu, Y. Lu, Angew. Chem., Int. Ed. Engl. 2007, 46, 7587–7590.CrossRefGoogle Scholar
  42. 42.
    J. Liu, Y. Lu, J. Am. Chem. Soc. 2007, 129, 9838–9839.CrossRefPubMedGoogle Scholar
  43. 43.
    T. S. Dalavoy, D. P. Wernette, M. Gong, J. V. Sweedler, Y. Lu, B. R. Flachsbart, M. A. Shannon, P. W. Bohn, D. M. Cropek, Lab Chip 2008, 8, 786–793.CrossRefPubMedGoogle Scholar
  44. 44.
    I.-H. Chang, J. J. Tulock, J. Liu, W.-S. Kim, D. M. Cannon, Jr., Y. Lu, P. W. Bohn, J. V. Sweedler, D. M. Cropek, Environ. Sci. Technol. 2005, 39, 3756–3761.CrossRefPubMedGoogle Scholar
  45. 45.
    T. Li, S. Dong, E. Wang, J. Am. Chem. Soc. 2010, 132, 13156–13157.CrossRefPubMedGoogle Scholar
  46. 46.
    X. B. Zhang, Z. Wang, H. Xing, Y. Xiang, Y. Lu, Anal. Chem. 2010, 82, 5005–5011.CrossRefPubMedGoogle Scholar
  47. 47.
    J. Liu, Y. Lu, J. Am. Chem. Soc. 2003, 125, 6642–6643.CrossRefPubMedGoogle Scholar
  48. 48.
    J. H. Lee, Z. Wang, J. Liu, Y. Lu, J. Am. Chem. Soc. 2008, 130, 14217–14226.CrossRefPubMedGoogle Scholar
  49. 49.
    Z. Wang, J. H. Lee, Y. Lu, Adv. Mater. 2008, 20, 3263–3267.CrossRefGoogle Scholar
  50. 50.
    H. Wei, B. Li, J. Li, S. Dong, E. Wang, Nanotechnology 2008, 19, 095501–095505.CrossRefPubMedGoogle Scholar
  51. 51.
    J. W. Liu, Y. Lu, J. Fluoresc. 2004, 14, 343–354.CrossRefPubMedGoogle Scholar
  52. 52.
    J. Liu, Y. Lu, Chem. Mater. 2004, 16, 3231–3238.CrossRefGoogle Scholar
  53. 53.
    D. Mazumdar, J. Liu, G. Lu, J. Zhou, Y. Lu, Chem. Commun. 2009, 46, 1416–1418.CrossRefGoogle Scholar
  54. 54.
    Y. Xiao, A. A. Rowe, K. W. Plaxco, J. Am. Chem. Soc. 2007, 129, 262–263.CrossRefPubMedGoogle Scholar
  55. 55.
    L. Shen, Z. Chen, Y. Li, S. He, S. Xie, X. Xu, Z. Liang, X. Meng, Q. Li, Z. Zhu, M. Li, X. C. Le, Y. Shao, Anal. Chem. 2008, 80, 6323–6328.CrossRefPubMedGoogle Scholar
  56. 56.
    D. A. Baum, S. K. Silverman, Cell. Mol. Life Sci. 2008, 65, 2156–2174.CrossRefPubMedGoogle Scholar
  57. 57.
    C. R. Dass, P. F. Choong, L. M. Khachigian, Mol. Cancer. Ther. 2008, 7, 243–251.CrossRefPubMedGoogle Scholar
  58. 58.
    S. Chakraborti, A. C. Banerjea, Mol. Ther. 2003, 7, 817–826.CrossRefPubMedGoogle Scholar
  59. 59.
    R. Goila, A. C. Banerjea, Biochem. J. 2001, 353, 701–708.CrossRefPubMedGoogle Scholar
  60. 60.
    S. W. Santoro, in Synthetic Nucleic Acids as Inhibitors of Gene Expression, Ed L. M. Khachigian, CRC Press, Boca Raton, 2005, pp. 53–68.Google Scholar
  61. 61.
    T. Toyoda, Y. Imamura, H. Takaku, T. Kashiwagi, K. Hara, J. Iwahashi, Y. Ohtsu, N. Tsumura, H. Kato, N. Hamada, FEBS Lett. 2000, 481, 113–116.CrossRefPubMedGoogle Scholar
  62. 62.
    J. Nowakowski, P. J. Shim, G. F. Joyce, C. D. Stout, Acta Crystallogr. D. Biol. Crystallogr. 1999, D55, 1885–1892.CrossRefGoogle Scholar
  63. 63.
    J. Nowakowski, P. J. Shim, G. S. Prasad, C. D. Stout, G. F. Joyce, Nat. Struct. Biol. 1999, 6, 151–156.CrossRefPubMedGoogle Scholar
  64. 64.
    C. Tuerk, L. Gold, Science 1990, 249, 505–510.CrossRefPubMedGoogle Scholar
  65. 65.
    A. D. Ellington, J. W. Szostak, Nature 1990, 346, 818–822.CrossRefPubMedGoogle Scholar
  66. 66.
    A. A. Beaudry, G. F. Joyce, Science 1992, 257, 635–641.CrossRefPubMedGoogle Scholar
  67. 67.
    M. Zuker, Nucleic Acids Res. 2003, 31, 3406–3415.CrossRefPubMedGoogle Scholar
  68. 68.
    A. K. Brown, J. Li, C. M. B. Pavot, Y. Lu, Biochemistry 2003, 42, 7152–7161.CrossRefPubMedGoogle Scholar
  69. 69.
    S. W. Santoro, G. F. Joyce, Biochemistry 1998, 37, 13330–13342.CrossRefPubMedGoogle Scholar
  70. 70.
    A. Peracchi, J. Biol. Chem. 2000, 275, 11693–11697.CrossRefPubMedGoogle Scholar
  71. 71.
    Q.-C. He, J.-M. Zhou, D.-M. Zhou, Y. Nakamatsu, T. Baba, K. Taira, Biomacromolecules 2002, 3, 69–83.CrossRefPubMedGoogle Scholar
  72. 72.
    R. R. Breaker, G. M. Emilsson, D. Lazarev, S. Nakamura, I. J. Puskarz, A. Roth, N. Sudarsan, RNA 2003, 9, 949–957.CrossRefPubMedGoogle Scholar
  73. 73.
    G. M. Emilsson, S. Nakamura, A. Roth, R. R. Breaker, RNA 2003, 9, 907–918.CrossRefPubMedGoogle Scholar
  74. 74.
    K. Schlosser, Y. Li, Biochemistry 2004, 43, 9695–9707.CrossRefPubMedGoogle Scholar
  75. 75.
    K. Schlosser, J. Gu, L. Sule, Y. Li, Nucleic Acids Res. 2008, 36, 1472–1481.CrossRefPubMedGoogle Scholar
  76. 76.
    K. Schlosser, Y. Li, ChemBioChem 2010, 11, 866–879.CrossRefPubMedGoogle Scholar
  77. 77.
    S. Sando, T. Sasaki, K. Kanatani, Y. Aoyama, J. Am. Chem. Soc. 2003, 125, 15720–15721.CrossRefPubMedGoogle Scholar
  78. 78.
    S. Sando, A. Narita, T. Sasaki, Y. Aoyama, Org. Biomol. Chem. 2005, 3, 1002–1007.CrossRefPubMedGoogle Scholar
  79. 79.
    J. Liu, Z. Cao, Y. Lu, Chem. Rev. 2009, 109, 1948–1998.CrossRefPubMedGoogle Scholar
  80. 80.
    X. Zhang, R. Kong, Y. Lu, Annu. Rev. Anal. Chem. 2011, 4, DOI: 10.1146/annurev.anchem.111808.073617.Google Scholar
  81. 81.
    Y. Lu, J. Liu, J. Li, P. J. Bruesehoff, C. M. B. Pavot, A. K. Brown, Biosens. Bioelectron. 2003, 18, 529–540.CrossRefPubMedGoogle Scholar
  82. 82.
    M. N. Stojanovic, T. E. Mitchell, D. Stefanovic, J. Am. Chem. Soc. 2002, 124, 3555–3561.CrossRefPubMedGoogle Scholar
  83. 83.
    M. N. Stojanovic, D. Stefanovic, J. Am. Chem. Soc. 2003, 125, 6673–6676.CrossRefPubMedGoogle Scholar
  84. 84.
    M. N. Stojanovic, S. Semova, D. Kolpashchikov, J. Macdonald, C. Morgan, D. Stefanovic, J. Am. Chem. Soc. 2005, 127, 6914–6915.CrossRefPubMedGoogle Scholar
  85. 85.
    H. Lederman, J. Macdonald, D. Stefanovic, M. N. Stojanovic, Biochemistry 2006, 45, 1194–1199.CrossRefPubMedGoogle Scholar
  86. 86.
    I. Willner, B. Shlyahovsky, M. Zayats, B. Willner, Chem. Soc. Rev. 2008, 37, 1153–1165.CrossRefPubMedGoogle Scholar
  87. 87.
    J. Elbaz, O. Lioubashevski, F. Wang, F. Remacle, R. D. Levine, I. Willner, Nature Nanotech. 2010, 5, 417–422.CrossRefGoogle Scholar
  88. 88.
    A. Flynn-Charlebois, Y. Wang, T. K. Prior, I. Rashid, K. A. Hoadley, R. L. Coppins, A. C. Wolf, S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 2444–2454.CrossRefPubMedGoogle Scholar
  89. 89.
    A. Flynn-Charlebois, T. K. Prior, K. A. Hoadley, S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 5346–5350.CrossRefPubMedGoogle Scholar
  90. 90.
    Y. Wang, S. K. Silverman, Biochemistry 2005, 44, 3017–3023.CrossRefPubMedGoogle Scholar
  91. 91.
    C. Hobartner, S. K. Silverman, Biopolymers 2007, 87, 279–292.CrossRefPubMedGoogle Scholar
  92. 92.
    Y. Li, C. R. Geyer, D. Sen, Biochemistry 1996, 35, 6911–6922.CrossRefPubMedGoogle Scholar
  93. 93.
    P. Travascio, Y. Li, D. Sen, Chem. Biol. 1998, 5, 505–517.CrossRefPubMedGoogle Scholar
  94. 94.
    P. Travascio, A. J. Bennet, D. Y. Wang, D. Sen, Chem. Biol. 1999, 6, 779–787.CrossRefPubMedGoogle Scholar
  95. 95.
    P. Travascio, D. Sen, A. J. Bennet, Can. J. Chem. 2006, 84, 613–619.CrossRefGoogle Scholar
  96. 96.
    H.-W. Lee, D. J. F. Chinnapen, D. Sen, Pure Appl. Chem. 2004, 76, 1537–1545.CrossRefGoogle Scholar
  97. 97.
    B. Seelig, A. Jaschke, Chem.Biol. 1999, 6, 167–176.CrossRefPubMedGoogle Scholar
  98. 98.
    N. Sugimoto, Y. Okumoto, T. Ohmichi, J. Chem. Soc., Perkin Trans. 2 1999, 1381–1386.Google Scholar
  99. 99.
    Z. Zaborowska, J. P. Fuerste, V. A. Erdmann, J. Kurreck, J. Biol. Chem. 2002, 277, 40617–40622.CrossRefPubMedGoogle Scholar
  100. 100.
    Z. Zaborowska, S. Schubert, J. Kurreck, V. A. Erdmann, FEBS Lett. 2004, 579, 554–558.CrossRefGoogle Scholar
  101. 101.
    G. F. Joyce, Methods Enzymol. 2001, 341, 503–517.CrossRefPubMedGoogle Scholar
  102. 102.
    A. Peracchi, M. Bonaccio, M. Clerici, J. Mol. Biol. 2005, 352, 783–794.CrossRefPubMedGoogle Scholar
  103. 103.
    B. Wang, L. Cao, W. Chiuman, Y. Li, Z. Xi, Biochemistry 2010, 49, 7553–7562.CrossRefPubMedGoogle Scholar
  104. 104.
    Y. Liu, D. Sen, J. Mol. Biol. 2008, 381, 845–859.CrossRefPubMedGoogle Scholar
  105. 105.
    Y. Liu, D. Sen, J. Mol. Biol. 2010, 395, 234.CrossRefPubMedGoogle Scholar
  106. 106.
    G. S. Sekhon, D. Sen, Biochemistry 2010, 49, 9072–9077.CrossRefPubMedGoogle Scholar
  107. 107.
    C. J. Burrows, J. G. Muller, Chem. Rev. 1998, 98, 1109–1151.CrossRefPubMedGoogle Scholar
  108. 108.
    H. K. Kim, J. Liu, J. Li, N. Nagraj, M. Li, C. M. B. Pavot, Y. Lu, J. Am. Chem. Soc. 2007, 129, 6896–6902.CrossRefPubMedGoogle Scholar
  109. 109.
    H. K. Kim, I. Rasnik, J. Liu, T. Ha, Y. Lu, Nat. Chem. Biol. 2007, 3, 763–768.CrossRefPubMedGoogle Scholar
  110. 110.
    E. K. Y. Leung, D. Sen, Chem. Biol. 2007, 14, 41–51.CrossRefPubMedGoogle Scholar
  111. 111.
    D. Faulhammer, M. Famulok, J. Mol. Biol. 1997, 269, 188–202.CrossRefPubMedGoogle Scholar
  112. 112.
    K. Schlosser, J. Gu, J. C. Lam, Y. Li, Nucleic Acids Res. 2008, 36, 4768–4777.CrossRefPubMedGoogle Scholar
  113. 113.
    M. Bonaccio, A. Credali, A. Peracchi, Nucleic Acids Res. 2004, 32, 916–925.CrossRefPubMedGoogle Scholar
  114. 114.
    K. Schlosser, Y. Li, Nucleic Acids Res. 2009, 37, 413–420.CrossRefPubMedGoogle Scholar
  115. 115.
    J. A. Cowan, J. Inorg. Biochem. 1993, 49, 171–175.CrossRefPubMedGoogle Scholar
  116. 116.
    D. Mazumdar, N. Nagraj, H. K. Kim, X. Meng, A. K. Brown, Q. Sun, W. Li, Y. Lu, J. Am. Chem. Soc. 2009, 131, 5506–5515.CrossRefPubMedGoogle Scholar
  117. 117.
    B. Nawrot, K. Widera, M. Wojcik, B. Rebowska, G. Nowak, W. J. Stec, FEBS Lett. 2007, 274, 1062–1072.Google Scholar
  118. 118.
    R. M. Clegg, Methods Enzymol. 1992, 211, 353–388.CrossRefPubMedGoogle Scholar
  119. 119.
    M. Lorenz, A. Hillisch, S. Diekmann, Rev. Mol. Biotechnol. 2002, 82, 197–209.CrossRefGoogle Scholar
  120. 120.
    D. M. J. Lilley, T. J. Wilson, Curr. Opin. Chem. Biol. 2000, 4, 507–517.CrossRefPubMedGoogle Scholar
  121. 121.
    N. G. Walter, Methods 2001, 25, 19–30.CrossRefPubMedGoogle Scholar
  122. 122.
    C. Gohlke, A. I. H. Murchie, D. M. J. Lilley, R. M. Clegg, Proc. Natl. Acad. Sci. USA 1994, 91, 11660–11664.CrossRefPubMedGoogle Scholar
  123. 123.
    F. Stuehmeier, J. B. Welch, A. I. H. Murchie, D. M. J. Lilley, R. M. Clegg, Biochemistry 1997, 36, 13530–13538.CrossRefGoogle Scholar
  124. 124.
    R. M. Clegg, A. I. H. Murchie, D. M. J. Lilley, Biophys. J. 1994, 66, 99–109.CrossRefPubMedGoogle Scholar
  125. 125.
    G. S. Bassi, A. I. H. Murchie, F. Walter, R. M. Clegg, D. M. J. Lilley, EMBO J. 1997, 16, 7481–7489.CrossRefPubMedGoogle Scholar
  126. 126.
    J. B. Murray, A. A. Seyhan, N. G. Walter, J. M. Burke, W. G. Scott, Chem. Biol. 1998, 5, 587–595.CrossRefPubMedGoogle Scholar
  127. 127.
    N. G. Walter, J. M. Burke, D. P. Millar, Nat. Struct. Biol. 1999, 6, 544–549.CrossRefPubMedGoogle Scholar
  128. 128.
    K. J. Hampel, J. M. Burke, Biochemistry 2001, 40, 3723–3729.CrossRefPubMedGoogle Scholar
  129. 129.
    M. J. B. Pereira, D. A. Harris, D. Rueda, N. G. Walter, Biochemistry 2002, 41, 730–740.CrossRefPubMedGoogle Scholar
  130. 130.
    A. Jenne, W. Gmelin, N. Raffler, M. Famulok, Angew.Chem., Int. Ed. 1999, 38, 1300–1303.CrossRefGoogle Scholar
  131. 131.
    X.-w. Fang, T. Pan, T. R. Sosnick, Nat. Struct. Biol. 1999, 6, 1091–1095.CrossRefPubMedGoogle Scholar
  132. 132.
    M. I. Wallace, L. Ying, S. Balasubramanian, D. Klenerman, Proc. Natl. Acad. Sci. USA 2001, 98, 5584–5589.CrossRefPubMedGoogle Scholar
  133. 133.
    K. M. Parkhurst, M. Brenowitz, L. J. Parkhurst, Biochemistry 1996, 35, 7459–7465.CrossRefPubMedGoogle Scholar
  134. 134.
    V. V. Didenko, BioTechniques 2001, 31, 1106–1121.PubMedGoogle Scholar
  135. 135.
    J. Liu, Y. Lu, J. Am. Chem. Soc. 2002, 124, 15208–15216.CrossRefPubMedGoogle Scholar
  136. 136.
    W. H. Sawyer, R. Y. S. Chan, J. F. Eccleston, B. E. Davidson, S. A. Samat, Y. Yan, Biochemistry 2000, 39, 5653–5661.CrossRefPubMedGoogle Scholar
  137. 137.
    A. Bhattacharyya, B. Bhattacharyya, S. Roy, Eur. J. Biochem. 1993, 216, 757–761.CrossRefPubMedGoogle Scholar
  138. 138.
    A. K. Tong, S. Jockusch, Z. Li, H.–R. Zhu, D. L. Akins, N. J. Turro, J. Ju, J. Am. Chem. Soc. 2001, 123, 12923–12924.CrossRefPubMedGoogle Scholar
  139. 139.
    J. C. F. Lam, Y. Li, ChemBioChem 2010, 11, 1710–1719.CrossRefPubMedGoogle Scholar
  140. 140.
    N. K. Lee, H. R. Koh, K. Y. Han, S. K. Kim, J. Am. Chem. Soc. 2007, 129, 15526–15534.CrossRefPubMedGoogle Scholar
  141. 141.
    N. K. Lee, H. R. Koh, K. Y. Han, J. Lee, S. K. Kim, Chem. Commun. 2010, 46, 4683–4685.CrossRefGoogle Scholar
  142. 142.
    Y.-J. Choi, H.-J. Han, J.-H. Lee, S.-W. Suh, B.-S. Choi, Bull. Korean Chem. Soc. 2000, 21, 955–956.Google Scholar
  143. 143.
    D. E. Draper, Biophys.Chem. 1985, 21, 91–101.CrossRefPubMedGoogle Scholar
  144. 144.
    A. L. Feig, W. G. Scott, O. C. Uhlenbeck, Science 1998, 279, 81–84.CrossRefPubMedGoogle Scholar
  145. 145.
    A. L. Feig, M. Panek, W. D. Horrocks, Jr., O. C. Uhlenbeck, Chem. Biol. 1999, 6, 801–810.CrossRefPubMedGoogle Scholar
  146. 146.
    D. S. Gross, H. Simpkins, J. Biol. Chem. 1981, 256, 9593–9598.PubMedGoogle Scholar
  147. 147.
    M. D. Topal, J. R. Fresco, Biochemistry 1980, 19, 5531–5537.CrossRefPubMedGoogle Scholar
  148. 148.
    R. K. O. Sigel, A. M. Pyle, Met. Ions Biol. Syst. 2003, 40, 477–512.PubMedGoogle Scholar
  149. 149.
    N. L. Greenbaum, C. Mundoma, D. R. Peterman, Biochemistry 2001, 40, 1124–1134.CrossRefPubMedGoogle Scholar
  150. 150.
    H. K. Kim, J. Li, N. Nagraj, Y. Lu, Chem. Eur. J. 2008, 232, 8696.CrossRefGoogle Scholar
  151. 151.
    C. R. Geyer, D. Sen, J. Mol. Biol. 1998, 275, 483–489.CrossRefPubMedGoogle Scholar
  152. 152.
    F. M. Pohl, T. M. Jovin, J. Mol. Biol. 1972, 67, 375–396.CrossRefPubMedGoogle Scholar
  153. 153.
    T. J. Thamann, R. C. Lord, A. H. Wang, A. Rich, Nucleic Acids Res. 1981, 9, 5443–5457.CrossRefPubMedGoogle Scholar
  154. 154.
    M. W. Germann, K. H. Schoenwaelder, J. H. Van de Sande, Biochemistry 1985, 24, 5698–5702.CrossRefPubMedGoogle Scholar
  155. 155.
    Y. Wang, G. A. Thomas, W. L. Peticolas, Biochemistry 1987, 26, 5178–5186.CrossRefPubMedGoogle Scholar
  156. 156.
    L. E. Xodo, G. Manzini, F. Quadrifoglio, G. A. Van der Marel, J. H. Van Boom, Biochemistry 1988, 27, 6327–6331.CrossRefPubMedGoogle Scholar
  157. 157.
    B. Hernandez, V. Baumruk, C. Gouyette, M. Ghomi, Biopolymers 2005, 78, 21–34.CrossRefPubMedGoogle Scholar
  158. 158.
    M. Cieslak, J. Szymanski, R. W. Adamiak, C. S. Cierniewski, J. Biol. Chem. 2003, 278, 47987–47996.CrossRefPubMedGoogle Scholar
  159. 159.
    G. W. Ewing, Analytical Instrumentation Handbook, M. Dekker, New York, 1997.Google Scholar
  160. 160.
    R. Y. Tsien, A. W. Czarnik, in Fluorescenct Chemosensors for Ion and Molecule Recognization, Vol. 538 of ACS Symposium Series, Ed A. W. Czarnik, American Chemical Society, Washington, DC, 1993, pp. 130–146.CrossRefGoogle Scholar
  161. 161.
    A. W. Czarnik, Chem. Biol. 1995, 2, 423–428.CrossRefPubMedGoogle Scholar
  162. 162.
    A. W. Czarnik, Acc. Chem. Res. 1994, 27, 302–308.CrossRefGoogle Scholar
  163. 163.
    K. Schlosser, S. A. McManus, Y. Li, in The Aptamer Handbook: Functional Oligonucleotides and Their Applications, Ed S. Klussmann, Wiley-VCH, Weinheim, 2006, pp. 228–261.CrossRefGoogle Scholar
  164. 164.
    Functional Nucleic Acids for Sensing and Other Analytical Applications, Vol. 8 of Integrated Analytical Systems, Eds Y. Li, Y. Lu, Springer, New York, 2009.Google Scholar
  165. 165.
    S. K. Silverman, Chem. Commun. 2008, 30, 3467–3485.CrossRefGoogle Scholar
  166. 166.
    S. K. Silverman, Acc. Chem. Res. 2009, 42, 1521–1531.CrossRefPubMedGoogle Scholar
  167. 167.
    Y. Lu, Chem. Eur. J. 2002, 8, 4589–4596.CrossRefPubMedGoogle Scholar
  168. 168.
    H. Wang, Y. Kim, H. Liu, Z. Zhu, S. Bamrungsap, W. Tan, J. Am. Chem. Soc. 2009, 131, 8221–8226.CrossRefPubMedGoogle Scholar
  169. 169.
    D. W. Boomer, M. J. Powell, Anal. Chem. 1987, 59, 2810–2813.CrossRefPubMedGoogle Scholar
  170. 170.
    W. Chiuman, Y. Li, Nucleic Acids Res. 2007, 35, 401–405.CrossRefPubMedGoogle Scholar
  171. 171.
    S. H. J. Mei, Z. Liu, J. D. Brennan, Y. Li, J. Am. Chem. Soc. 2003, 125, 412–420.CrossRefPubMedGoogle Scholar
  172. 172.
    Z. Liu, S. H. J. Mei, J. D. Brennan, Y. Li, J. Am. Chem. Soc. 2003, 125, 7539–7545.CrossRefPubMedGoogle Scholar
  173. 173.
    S. Hohng, T. Ha, ChemPhysChem 2005, 6, 956–960.CrossRefPubMedGoogle Scholar
  174. 174.
    D. M. Willard, A. Van Orden, Nature Mater. 2003, 2, 575–576.CrossRefGoogle Scholar
  175. 175.
    C. S. Wu, M. K. Khaing Oo, X. Fan, ACS Nano 2010, 4, 5897–5904.CrossRefPubMedGoogle Scholar
  176. 176.
    R. A. Reynolds, III, C. A. Mirkin, R. L. Letsinger, J. Am. Chem. Soc. 2000, 122, 3795–3796.CrossRefGoogle Scholar
  177. 177.
    J. Yguerabide, E. E. Yguerabide, Anal. Biochem. 1998, 262, 137–156.CrossRefPubMedGoogle Scholar
  178. 178.
    J. H. Kim, S. H. Han, B. H. Chung, Biosens. Bioelectron. 2011, 26, 2125–2129.CrossRefPubMedGoogle Scholar
  179. 179.
    Y. Xiang, A. Tong, Y. Lu, J. Am. Chem. Soc. 2009, 131, 15352–15357.CrossRefPubMedGoogle Scholar
  180. 180.
    Y. Xiang, Z. Wang, H. Xing, N. Y. Wong, Y. Lu, Anal. Chem. 2010, 82, 4122–4129.CrossRefPubMedGoogle Scholar
  181. 181.
    L. Zhang, B. Han, T. Li, E. Wang, Chem. Commun. 2011, 47, 3099–3101.CrossRefGoogle Scholar
  182. 182.
    J. Liu, Y. Lu, Nat. Protoc. 2006, 1, 246–252.CrossRefPubMedGoogle Scholar
  183. 183.
    I. I. Lim, W. Ip, E. Crew, P. N. Njoki, D. Mott, C. J. Zhong, Y. Pan, S. Zhou, Langmuir 2007, 23, 826–833.CrossRefPubMedGoogle Scholar
  184. 184.
    C. A. Mirkin, R. L. Letsinger, R. C. Mucic, J. J. Storhoff, Nature 1996, 382, 607–609.CrossRefPubMedGoogle Scholar
  185. 185.
    J. J. Storhoff, A. A. Lazarides, R. C. Mucic, C. A. Mirkin, R. L. Letsinger, G. C. Schatz, J. Am. Chem. Soc. 2000, 122, 4640–4650.CrossRefGoogle Scholar
  186. 186.
    H. Li, L. Rothberg, Proc. Natl. Acad. Sci. USA 2004, 101, 14036–14039.CrossRefPubMedGoogle Scholar
  187. 187.
    W. Zhao, F. Gonzaga, Y. Li, M. A. Brook, Adv. Mater. 2007, 19, 1766–1771.CrossRefGoogle Scholar
  188. 188.
    K. Sato, K. Hosokawa, M. Maeda, J. Am. Chem. Soc. 2003, 125, 8102–8103.CrossRefPubMedGoogle Scholar
  189. 189.
    J. Liu, Y. Lu, J. Am. Chem. Soc. 2004, 126, 12298–12305.CrossRefPubMedGoogle Scholar
  190. 190.
    J. Liu, D. P. Wernette, Y. Lu, Angew. Chem., Int. Ed. Engl. 2005, 44, 7290–7293.CrossRefGoogle Scholar
  191. 191.
    J. Liu, Y. Lu, Org. Biomol. Chem. 2006, 4, 3435–3441.CrossRefPubMedGoogle Scholar
  192. 192.
    J. Liu, Y. Lu, Chem. Commun. 2007, 4872–4874.Google Scholar
  193. 193.
    H. Li, L. J. Rothberg, J. Am. Chem. Soc. 2004, 126, 10958–10961.CrossRefPubMedGoogle Scholar
  194. 194.
    I. Willner, R. Baron, B. Willner, Biosens. Bioelectron. 2007, 22, 1841–1852.CrossRefPubMedGoogle Scholar
  195. 195.
    I. Willner, B. Willner, E. Katz, Bioelectrochemistry 2007, 70, 2–11.CrossRefPubMedGoogle Scholar
  196. 196.
    Y. Xiao, V. Pavlov, R. Gill, T. Bourenko, I. Willner, ChemBioChem 2004, 5, 374–379.CrossRefPubMedGoogle Scholar
  197. 197.
    T. Niazov, V. Pavlov, Y. Xiao, R. Gill, I. Willner, Nano Letters 2004, 4, 1683–1687.CrossRefGoogle Scholar
  198. 198.
    V. Pavlov, Y. Xiao, R. Gill, A. Dishon, M. Kotler, I. Willner, Anal. Chem. 2004, 76, 2152–2156.CrossRefPubMedGoogle Scholar
  199. 199.
    Y. Xiao, V. Pavlov, T. Niazov, A. Dishon, M. Kotler, I. Willner, J. Am. Chem. Soc. 2004, 126, 7430–7431.CrossRefPubMedGoogle Scholar
  200. 200.
    J. Elbaz, M. Moshe, B. Shlyahovsky, I. Willner, Chem. Eur. J. 2009, 15, 3411–3418.CrossRefPubMedGoogle Scholar
  201. 201.
    C. B. Swearingen, D. P. Wernette, D. M. Cropek, Y. Lu, J. V. Sweedler, P. W. Bohn, Anal. Chem. 2005, 77, 442–448.CrossRefPubMedGoogle Scholar
  202. 202.
    D. P. Wernette, C. B. Swearingen, D. M. Cropek, Y. Lu, J. V. Sweedler, P. W. Bohn, Analyst 2006, 131, 41–47.CrossRefPubMedGoogle Scholar
  203. 203.
    D. P. Wernette, C. Mead, P. W. Bohn, Y. Lu, Langmuir 2007, 23, 9513–9521.CrossRefPubMedGoogle Scholar
  204. 204.
    T.-J. Yim, J. Liu, Y. Lu, R. S. Kane, J. S. Dordick, J. Am. Chem. Soc. 2005, 127, 12200–12201.CrossRefPubMedGoogle Scholar
  205. 205.
    Y. Shen, G. Mackey, N. Rupcich, D. Gloster, W. Chiuman, Y. Li, J. D. Brennan, Anal. Chem. 2007, 79, 3494–3503.CrossRefPubMedGoogle Scholar
  206. 206.
    A. K. Shaikh, K. S. Ryu, E. D. Goluch, J.-M. Nam, J. Liu, C. S. Thaxton, N. T. Chiesl, A. E. Barron, Y. Lu, C. A. Mirkin, C. Liu, Proc. Natl. Acad. Sci. USA 2005, 102, 9745–9750.CrossRefPubMedGoogle Scholar
  207. 207.
    ANDalyze, Inc., 2010, http://www.andalyze.com. (accessed on April 8, 2011).

Copyright information

© Springer Science+Business Media B.V. 2012

Authors and Affiliations

  1. 1.Department of BiochemistryUniversity of Illinois at Urbana-ChampaignUrbanaUSA
  2. 2.Department of ChemistryUniversity of Illinois at Urbana-ChampaignUrbanaUSA

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