Skip to main content
SpringerLink
Log in

Metal Ion-Dependent DNAzymes and Their Applications as Biosensors

  • Chapter
  • First Online:
Book cover Interplay between Metal Ions and Nucleic Acids

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

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.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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. K. Kruger, P. J. Grabowski, A. J. Zaug, J. Sands, D. E. Gottschling, T. R. Cech, Cell 1982, 31, 147–157.

    Article  CAS  PubMed  Google Scholar 

  2. C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, S. Altman, Cell 1983, 35, 849–857.

    Article  CAS  PubMed  Google Scholar 

  3. R. R. Breaker, G. F. Joyce, Chem. Biol. 1994, 1, 223–229.

    Article  CAS  PubMed  Google Scholar 

  4. S. W. Santoro, G. F. Joyce, Proc. Natl. Acad. Sci. USA 1997, 94, 4262–4266.

    Article  CAS  PubMed  Google Scholar 

  5. J. Li, W. Zheng, A. H. Kwon, Y. Lu, Nucleic Acids Res. 2000, 28, 481–488.

    Article  CAS  PubMed  Google Scholar 

  6. C. R. Geyer, D. Sen, Chem. Biol. 1997, 4, 579–593.

    Article  CAS  PubMed  Google Scholar 

  7. D. Faulhammer, M. Famulok, Angew. Chem., Int. Ed. Engl. 1996, 35, 2837–2841.

    Article  CAS  Google Scholar 

  8. A. R. Feldman, D. Sen, J. Mol. Biol. 2001, 313, 283–294.

    Article  CAS  PubMed  Google Scholar 

  9. R. P. G. Cruz, J. B. Withers, Y. Li, Chem. Biol. 2004, 11, 57–67.

    CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  11. N. Carmi, L. A. Shultz, R. R. Breaker, Chem. Biol. 1996, 3, 1039–1046.

    Article  CAS  PubMed  Google Scholar 

  12. N. Carmi, H. R. Balkhi, R. R. Breaker, Proc. Natl. Acad. Sci. USA 1998, 95, 2233–2237.

    Article  CAS  PubMed  Google Scholar 

  13. N. Carmi, R. R. Breaker, Bioorg. Med. Chem. 2001, 9, 2589–2600.

    Article  CAS  PubMed  Google Scholar 

  14. M. Chandra, A. Sachdeva, S. K. Silverman, Nat. Chem. Biol. 2009, 5, 718–720.

    Article  CAS  PubMed  Google Scholar 

  15. Y. Xiao, M. Chandra, S. K. Silverman, Biochemistry 2010.

    Google Scholar 

  16. Y. Xiao, E. C. Allen, S. K. Silverman, Chem. Commun. 2011, 47, 1749–1751.

    Article  CAS  Google Scholar 

  17. J. Burmeister, G. von Kiedrowski, A. D. Ellington, Angew. Chem., Int. Ed. Engl. 1997, 36, 1321–1324.

    Article  CAS  Google Scholar 

  18. B. Cuenoud, J. W. Szostak, Nature 1995, 375, 611–614.

    Article  CAS  PubMed  Google Scholar 

  19. A. Sreedhara, Y. Li, R. R. Breaker, J. Am. Chem. Soc. 2004, 126, 3454–3460.

    Article  CAS  PubMed  Google Scholar 

  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. W. E. Purtha, R. L. Coppins, M. K. Smalley, S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 13124–13125.

    Article  CAS  PubMed  Google Scholar 

  22. Y. Wang, S. K. Silverman, Biochemistry 2003, 42, 15252–15263.

    Article  CAS  PubMed  Google Scholar 

  23. Y. Wang, S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 6880–6881.

    Article  CAS  PubMed  Google Scholar 

  24. R. L. Coppins, S. K. Silverman, Nat. Struct. Mol. Biol. 2004, 11, 270–274.

    Article  CAS  PubMed  Google Scholar 

  25. R. L. Coppins, S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 2900–2907.

    Article  CAS  PubMed  Google Scholar 

  26. E. D. Pratico, Y. Wang, S. K. Silverman, Nucleic Acids Res. 2005, 33, 3503–3512.

    Article  CAS  PubMed  Google Scholar 

  27. Y. Wang, S. K. Silverman, Angew. Chem., Int. Ed. Engl. 2005, 44, 5863–5866.

    Article  CAS  Google Scholar 

  28. P. I. Pradeepkumar, C. Hoebartner, D. A. Baum, S. K. Silverman, Angew. Chem., Int. Ed. Engl. 2008, 47, 1753–1757.

    Article  CAS  Google Scholar 

  29. W. Wang, L. P. Billen, Y. Li, Chem. Biol. 2002, 9, 507–517.

    Article  CAS  PubMed  Google Scholar 

  30. Y. Li, Y. Liu, R. R. Breaker, Biochemistry 2000, 39, 3106–3114.

    Article  CAS  PubMed  Google Scholar 

  31. C. Höbartner, P. I. Pradeepkumar, S. K. Silverman, Chem. Commun. 2007, 2255–2257.

    Google Scholar 

  32. T. L. Sheppard, P. Ordoukhanian, G. F. Joyce, Proc. Natl. Acad. Sci. USA 2000, 97, 7802–7807.

    Article  CAS  PubMed  Google Scholar 

  33. M. Chandra, S. K. Silverman, J. Am. Chem. Soc. 2008, 130, 2936–2937.

    Article  CAS  PubMed  Google Scholar 

  34. Y. Li, D. Sen, Nat. Struct. Biol. 1996, 3, 743–747.

    Article  CAS  PubMed  Google Scholar 

  35. Y. Li, D. Sen, Biochemistry 1997, 36, 5589–5599.

    Article  CAS  PubMed  Google Scholar 

  36. T. Lan, K. Furuya, Y. Lu, Chem. Commun. 2010, 46, 3896–3898.

    Article  CAS  Google Scholar 

  37. A. K. Brown, J. Liu, Y. He, Y. Lu, ChemBioChem 2009, 10, 486–492.

    Article  CAS  PubMed  Google Scholar 

  38. J. Li, Y. Lu, J. Am. Chem. Soc. 2000, 122, 10466–10467.

    Article  CAS  Google Scholar 

  39. J. Liu, Y. Lu, Anal. Chem. 2003, 75, 6666–6672.

    Article  CAS  PubMed  Google Scholar 

  40. N. Nagraj, J. Liu, S. Sterling, J. Wu, Y. Lu, Chem. Commun. 2009, 4103–4105.

    Google Scholar 

  41. J. Liu, Y. Lu, Angew. Chem., Int. Ed. Engl. 2007, 46, 7587–7590.

    Article  CAS  Google Scholar 

  42. J. Liu, Y. Lu, J. Am. Chem. Soc. 2007, 129, 9838–9839.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  45. T. Li, S. Dong, E. Wang, J. Am. Chem. Soc. 2010, 132, 13156–13157.

    Article  CAS  PubMed  Google Scholar 

  46. X. B. Zhang, Z. Wang, H. Xing, Y. Xiang, Y. Lu, Anal. Chem. 2010, 82, 5005–5011.

    Article  CAS  PubMed  Google Scholar 

  47. J. Liu, Y. Lu, J. Am. Chem. Soc. 2003, 125, 6642–6643.

    Article  CAS  PubMed  Google Scholar 

  48. J. H. Lee, Z. Wang, J. Liu, Y. Lu, J. Am. Chem. Soc. 2008, 130, 14217–14226.

    Article  CAS  PubMed  Google Scholar 

  49. Z. Wang, J. H. Lee, Y. Lu, Adv. Mater. 2008, 20, 3263–3267.

    Article  CAS  Google Scholar 

  50. H. Wei, B. Li, J. Li, S. Dong, E. Wang, Nanotechnology 2008, 19, 095501–095505.

    Article  PubMed  CAS  Google Scholar 

  51. J. W. Liu, Y. Lu, J. Fluoresc. 2004, 14, 343–354.

    Article  CAS  PubMed  Google Scholar 

  52. J. Liu, Y. Lu, Chem. Mater. 2004, 16, 3231–3238.

    Article  CAS  Google Scholar 

  53. D. Mazumdar, J. Liu, G. Lu, J. Zhou, Y. Lu, Chem. Commun. 2009, 46, 1416–1418.

    Article  CAS  Google Scholar 

  54. Y. Xiao, A. A. Rowe, K. W. Plaxco, J. Am. Chem. Soc. 2007, 129, 262–263.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  56. D. A. Baum, S. K. Silverman, Cell. Mol. Life Sci. 2008, 65, 2156–2174.

    Article  CAS  PubMed  Google Scholar 

  57. C. R. Dass, P. F. Choong, L. M. Khachigian, Mol. Cancer. Ther. 2008, 7, 243–251.

    Article  CAS  PubMed  Google Scholar 

  58. S. Chakraborti, A. C. Banerjea, Mol. Ther. 2003, 7, 817–826.

    Article  CAS  PubMed  Google Scholar 

  59. R. Goila, A. C. Banerjea, Biochem. J. 2001, 353, 701–708.

    Article  CAS  PubMed  Google Scholar 

  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. 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.

    Article  CAS  PubMed  Google Scholar 

  62. J. Nowakowski, P. J. Shim, G. F. Joyce, C. D. Stout, Acta Crystallogr. D. Biol. Crystallogr. 1999, D55, 1885–1892.

    Article  CAS  Google Scholar 

  63. J. Nowakowski, P. J. Shim, G. S. Prasad, C. D. Stout, G. F. Joyce, Nat. Struct. Biol. 1999, 6, 151–156.

    Article  CAS  PubMed  Google Scholar 

  64. C. Tuerk, L. Gold, Science 1990, 249, 505–510.

    Article  CAS  PubMed  Google Scholar 

  65. A. D. Ellington, J. W. Szostak, Nature 1990, 346, 818–822.

    Article  CAS  PubMed  Google Scholar 

  66. A. A. Beaudry, G. F. Joyce, Science 1992, 257, 635–641.

    Article  CAS  PubMed  Google Scholar 

  67. M. Zuker, Nucleic Acids Res. 2003, 31, 3406–3415.

    Article  CAS  PubMed  Google Scholar 

  68. A. K. Brown, J. Li, C. M. B. Pavot, Y. Lu, Biochemistry 2003, 42, 7152–7161.

    Article  CAS  PubMed  Google Scholar 

  69. S. W. Santoro, G. F. Joyce, Biochemistry 1998, 37, 13330–13342.

    Article  CAS  PubMed  Google Scholar 

  70. A. Peracchi, J. Biol. Chem. 2000, 275, 11693–11697.

    Article  CAS  PubMed  Google Scholar 

  71. Q.-C. He, J.-M. Zhou, D.-M. Zhou, Y. Nakamatsu, T. Baba, K. Taira, Biomacromolecules 2002, 3, 69–83.

    Article  CAS  PubMed  Google Scholar 

  72. R. R. Breaker, G. M. Emilsson, D. Lazarev, S. Nakamura, I. J. Puskarz, A. Roth, N. Sudarsan, RNA 2003, 9, 949–957.

    Article  CAS  PubMed  Google Scholar 

  73. G. M. Emilsson, S. Nakamura, A. Roth, R. R. Breaker, RNA 2003, 9, 907–918.

    Article  CAS  PubMed  Google Scholar 

  74. K. Schlosser, Y. Li, Biochemistry 2004, 43, 9695–9707.

    Article  CAS  PubMed  Google Scholar 

  75. K. Schlosser, J. Gu, L. Sule, Y. Li, Nucleic Acids Res. 2008, 36, 1472–1481.

    Article  CAS  PubMed  Google Scholar 

  76. K. Schlosser, Y. Li, ChemBioChem 2010, 11, 866–879.

    Article  CAS  PubMed  Google Scholar 

  77. S. Sando, T. Sasaki, K. Kanatani, Y. Aoyama, J. Am. Chem. Soc. 2003, 125, 15720–15721.

    Article  CAS  PubMed  Google Scholar 

  78. S. Sando, A. Narita, T. Sasaki, Y. Aoyama, Org. Biomol. Chem. 2005, 3, 1002–1007.

    Article  CAS  PubMed  Google Scholar 

  79. J. Liu, Z. Cao, Y. Lu, Chem. Rev. 2009, 109, 1948–1998.

    Article  CAS  PubMed  Google Scholar 

  80. X. Zhang, R. Kong, Y. Lu, Annu. Rev. Anal. Chem. 2011, 4, DOI: 10.1146/annurev.anchem.111808.073617.

    Google Scholar 

  81. Y. Lu, J. Liu, J. Li, P. J. Bruesehoff, C. M. B. Pavot, A. K. Brown, Biosens. Bioelectron. 2003, 18, 529–540.

    Article  CAS  PubMed  Google Scholar 

  82. M. N. Stojanovic, T. E. Mitchell, D. Stefanovic, J. Am. Chem. Soc. 2002, 124, 3555–3561.

    Article  CAS  PubMed  Google Scholar 

  83. M. N. Stojanovic, D. Stefanovic, J. Am. Chem. Soc. 2003, 125, 6673–6676.

    Article  CAS  PubMed  Google Scholar 

  84. M. N. Stojanovic, S. Semova, D. Kolpashchikov, J. Macdonald, C. Morgan, D. Stefanovic, J. Am. Chem. Soc. 2005, 127, 6914–6915.

    Article  CAS  PubMed  Google Scholar 

  85. H. Lederman, J. Macdonald, D. Stefanovic, M. N. Stojanovic, Biochemistry 2006, 45, 1194–1199.

    Article  CAS  PubMed  Google Scholar 

  86. I. Willner, B. Shlyahovsky, M. Zayats, B. Willner, Chem. Soc. Rev. 2008, 37, 1153–1165.

    Article  CAS  PubMed  Google Scholar 

  87. J. Elbaz, O. Lioubashevski, F. Wang, F. Remacle, R. D. Levine, I. Willner, Nature Nanotech. 2010, 5, 417–422.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  89. A. Flynn-Charlebois, T. K. Prior, K. A. Hoadley, S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 5346–5350.

    Article  CAS  PubMed  Google Scholar 

  90. Y. Wang, S. K. Silverman, Biochemistry 2005, 44, 3017–3023.

    Article  CAS  PubMed  Google Scholar 

  91. C. Hobartner, S. K. Silverman, Biopolymers 2007, 87, 279–292.

    Article  CAS  PubMed  Google Scholar 

  92. Y. Li, C. R. Geyer, D. Sen, Biochemistry 1996, 35, 6911–6922.

    Article  CAS  PubMed  Google Scholar 

  93. P. Travascio, Y. Li, D. Sen, Chem. Biol. 1998, 5, 505–517.

    Article  CAS  PubMed  Google Scholar 

  94. P. Travascio, A. J. Bennet, D. Y. Wang, D. Sen, Chem. Biol. 1999, 6, 779–787.

    Article  CAS  PubMed  Google Scholar 

  95. P. Travascio, D. Sen, A. J. Bennet, Can. J. Chem. 2006, 84, 613–619.

    Article  CAS  Google Scholar 

  96. H.-W. Lee, D. J. F. Chinnapen, D. Sen, Pure Appl. Chem. 2004, 76, 1537–1545.

    Article  CAS  Google Scholar 

  97. B. Seelig, A. Jaschke, Chem.Biol. 1999, 6, 167–176.

    Article  CAS  PubMed  Google Scholar 

  98. N. Sugimoto, Y. Okumoto, T. Ohmichi, J. Chem. Soc., Perkin Trans. 2 1999, 1381–1386.

    Google Scholar 

  99. Z. Zaborowska, J. P. Fuerste, V. A. Erdmann, J. Kurreck, J. Biol. Chem. 2002, 277, 40617–40622.

    Article  CAS  PubMed  Google Scholar 

  100. Z. Zaborowska, S. Schubert, J. Kurreck, V. A. Erdmann, FEBS Lett. 2004, 579, 554–558.

    Article  CAS  Google Scholar 

  101. G. F. Joyce, Methods Enzymol. 2001, 341, 503–517.

    Article  CAS  PubMed  Google Scholar 

  102. A. Peracchi, M. Bonaccio, M. Clerici, J. Mol. Biol. 2005, 352, 783–794.

    Article  CAS  PubMed  Google Scholar 

  103. B. Wang, L. Cao, W. Chiuman, Y. Li, Z. Xi, Biochemistry 2010, 49, 7553–7562.

    Article  CAS  PubMed  Google Scholar 

  104. Y. Liu, D. Sen, J. Mol. Biol. 2008, 381, 845–859.

    Article  CAS  PubMed  Google Scholar 

  105. Y. Liu, D. Sen, J. Mol. Biol. 2010, 395, 234.

    Article  CAS  PubMed  Google Scholar 

  106. G. S. Sekhon, D. Sen, Biochemistry 2010, 49, 9072–9077.

    Article  CAS  PubMed  Google Scholar 

  107. C. J. Burrows, J. G. Muller, Chem. Rev. 1998, 98, 1109–1151.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  109. H. K. Kim, I. Rasnik, J. Liu, T. Ha, Y. Lu, Nat. Chem. Biol. 2007, 3, 763–768.

    Article  CAS  PubMed  Google Scholar 

  110. E. K. Y. Leung, D. Sen, Chem. Biol. 2007, 14, 41–51.

    Article  CAS  PubMed  Google Scholar 

  111. D. Faulhammer, M. Famulok, J. Mol. Biol. 1997, 269, 188–202.

    Article  CAS  PubMed  Google Scholar 

  112. K. Schlosser, J. Gu, J. C. Lam, Y. Li, Nucleic Acids Res. 2008, 36, 4768–4777.

    Article  CAS  PubMed  Google Scholar 

  113. M. Bonaccio, A. Credali, A. Peracchi, Nucleic Acids Res. 2004, 32, 916–925.

    Article  CAS  PubMed  Google Scholar 

  114. K. Schlosser, Y. Li, Nucleic Acids Res. 2009, 37, 413–420.

    Article  CAS  PubMed  Google Scholar 

  115. J. A. Cowan, J. Inorg. Biochem. 1993, 49, 171–175.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  117. B. Nawrot, K. Widera, M. Wojcik, B. Rebowska, G. Nowak, W. J. Stec, FEBS Lett. 2007, 274, 1062–1072.

    CAS  Google Scholar 

  118. R. M. Clegg, Methods Enzymol. 1992, 211, 353–388.

    Article  CAS  PubMed  Google Scholar 

  119. M. Lorenz, A. Hillisch, S. Diekmann, Rev. Mol. Biotechnol. 2002, 82, 197–209.

    Article  CAS  Google Scholar 

  120. D. M. J. Lilley, T. J. Wilson, Curr. Opin. Chem. Biol. 2000, 4, 507–517.

    Article  CAS  PubMed  Google Scholar 

  121. N. G. Walter, Methods 2001, 25, 19–30.

    Article  CAS  PubMed  Google Scholar 

  122. C. Gohlke, A. I. H. Murchie, D. M. J. Lilley, R. M. Clegg, Proc. Natl. Acad. Sci. USA 1994, 91, 11660–11664.

    Article  CAS  PubMed  Google Scholar 

  123. F. Stuehmeier, J. B. Welch, A. I. H. Murchie, D. M. J. Lilley, R. M. Clegg, Biochemistry 1997, 36, 13530–13538.

    Article  CAS  Google Scholar 

  124. R. M. Clegg, A. I. H. Murchie, D. M. J. Lilley, Biophys. J. 1994, 66, 99–109.

    Article  CAS  PubMed  Google Scholar 

  125. G. S. Bassi, A. I. H. Murchie, F. Walter, R. M. Clegg, D. M. J. Lilley, EMBO J. 1997, 16, 7481–7489.

    Article  CAS  PubMed  Google Scholar 

  126. J. B. Murray, A. A. Seyhan, N. G. Walter, J. M. Burke, W. G. Scott, Chem. Biol. 1998, 5, 587–595.

    Article  CAS  PubMed  Google Scholar 

  127. N. G. Walter, J. M. Burke, D. P. Millar, Nat. Struct. Biol. 1999, 6, 544–549.

    Article  CAS  PubMed  Google Scholar 

  128. K. J. Hampel, J. M. Burke, Biochemistry 2001, 40, 3723–3729.

    Article  CAS  PubMed  Google Scholar 

  129. M. J. B. Pereira, D. A. Harris, D. Rueda, N. G. Walter, Biochemistry 2002, 41, 730–740.

    Article  CAS  PubMed  Google Scholar 

  130. A. Jenne, W. Gmelin, N. Raffler, M. Famulok, Angew.Chem., Int. Ed. 1999, 38, 1300–1303.

    Article  CAS  Google Scholar 

  131. X.-w. Fang, T. Pan, T. R. Sosnick, Nat. Struct. Biol. 1999, 6, 1091–1095.

    Article  CAS  PubMed  Google Scholar 

  132. M. I. Wallace, L. Ying, S. Balasubramanian, D. Klenerman, Proc. Natl. Acad. Sci. USA 2001, 98, 5584–5589.

    Article  CAS  PubMed  Google Scholar 

  133. K. M. Parkhurst, M. Brenowitz, L. J. Parkhurst, Biochemistry 1996, 35, 7459–7465.

    Article  CAS  PubMed  Google Scholar 

  134. V. V. Didenko, BioTechniques 2001, 31, 1106–1121.

    CAS  PubMed  Google Scholar 

  135. J. Liu, Y. Lu, J. Am. Chem. Soc. 2002, 124, 15208–15216.

    Article  CAS  PubMed  Google Scholar 

  136. W. H. Sawyer, R. Y. S. Chan, J. F. Eccleston, B. E. Davidson, S. A. Samat, Y. Yan, Biochemistry 2000, 39, 5653–5661.

    Article  CAS  PubMed  Google Scholar 

  137. A. Bhattacharyya, B. Bhattacharyya, S. Roy, Eur. J. Biochem. 1993, 216, 757–761.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  139. J. C. F. Lam, Y. Li, ChemBioChem 2010, 11, 1710–1719.

    Article  CAS  PubMed  Google Scholar 

  140. N. K. Lee, H. R. Koh, K. Y. Han, S. K. Kim, J. Am. Chem. Soc. 2007, 129, 15526–15534.

    Article  CAS  PubMed  Google Scholar 

  141. N. K. Lee, H. R. Koh, K. Y. Han, J. Lee, S. K. Kim, Chem. Commun. 2010, 46, 4683–4685.

    Article  CAS  Google Scholar 

  142. Y.-J. Choi, H.-J. Han, J.-H. Lee, S.-W. Suh, B.-S. Choi, Bull. Korean Chem. Soc. 2000, 21, 955–956.

    CAS  Google Scholar 

  143. D. E. Draper, Biophys.Chem. 1985, 21, 91–101.

    Article  CAS  PubMed  Google Scholar 

  144. A. L. Feig, W. G. Scott, O. C. Uhlenbeck, Science 1998, 279, 81–84.

    Article  CAS  PubMed  Google Scholar 

  145. A. L. Feig, M. Panek, W. D. Horrocks, Jr., O. C. Uhlenbeck, Chem. Biol. 1999, 6, 801–810.

    Article  CAS  PubMed  Google Scholar 

  146. D. S. Gross, H. Simpkins, J. Biol. Chem. 1981, 256, 9593–9598.

    CAS  PubMed  Google Scholar 

  147. M. D. Topal, J. R. Fresco, Biochemistry 1980, 19, 5531–5537.

    Article  CAS  PubMed  Google Scholar 

  148. R. K. O. Sigel, A. M. Pyle, Met. Ions Biol. Syst. 2003, 40, 477–512.

    CAS  PubMed  Google Scholar 

  149. N. L. Greenbaum, C. Mundoma, D. R. Peterman, Biochemistry 2001, 40, 1124–1134.

    Article  CAS  PubMed  Google Scholar 

  150. H. K. Kim, J. Li, N. Nagraj, Y. Lu, Chem. Eur. J. 2008, 232, 8696.

    Article  CAS  Google Scholar 

  151. C. R. Geyer, D. Sen, J. Mol. Biol. 1998, 275, 483–489.

    Article  CAS  PubMed  Google Scholar 

  152. F. M. Pohl, T. M. Jovin, J. Mol. Biol. 1972, 67, 375–396.

    Article  CAS  PubMed  Google Scholar 

  153. T. J. Thamann, R. C. Lord, A. H. Wang, A. Rich, Nucleic Acids Res. 1981, 9, 5443–5457.

    Article  CAS  PubMed  Google Scholar 

  154. M. W. Germann, K. H. Schoenwaelder, J. H. Van de Sande, Biochemistry 1985, 24, 5698–5702.

    Article  CAS  PubMed  Google Scholar 

  155. Y. Wang, G. A. Thomas, W. L. Peticolas, Biochemistry 1987, 26, 5178–5186.

    Article  CAS  PubMed  Google Scholar 

  156. L. E. Xodo, G. Manzini, F. Quadrifoglio, G. A. Van der Marel, J. H. Van Boom, Biochemistry 1988, 27, 6327–6331.

    Article  CAS  PubMed  Google Scholar 

  157. B. Hernandez, V. Baumruk, C. Gouyette, M. Ghomi, Biopolymers 2005, 78, 21–34.

    Article  CAS  PubMed  Google Scholar 

  158. M. Cieslak, J. Szymanski, R. W. Adamiak, C. S. Cierniewski, J. Biol. Chem. 2003, 278, 47987–47996.

    Article  CAS  PubMed  Google Scholar 

  159. G. W. Ewing, Analytical Instrumentation Handbook, M. Dekker, New York, 1997.

    Google Scholar 

  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.

    Chapter  Google Scholar 

  161. A. W. Czarnik, Chem. Biol. 1995, 2, 423–428.

    Article  CAS  PubMed  Google Scholar 

  162. A. W. Czarnik, Acc. Chem. Res. 1994, 27, 302–308.

    Article  CAS  Google Scholar 

  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.

    Chapter  Google Scholar 

  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. S. K. Silverman, Chem. Commun. 2008, 30, 3467–3485.

    Article  CAS  Google Scholar 

  166. S. K. Silverman, Acc. Chem. Res. 2009, 42, 1521–1531.

    Article  CAS  PubMed  Google Scholar 

  167. Y. Lu, Chem. Eur. J. 2002, 8, 4589–4596.

    Article  PubMed  Google Scholar 

  168. H. Wang, Y. Kim, H. Liu, Z. Zhu, S. Bamrungsap, W. Tan, J. Am. Chem. Soc. 2009, 131, 8221–8226.

    Article  CAS  PubMed  Google Scholar 

  169. D. W. Boomer, M. J. Powell, Anal. Chem. 1987, 59, 2810–2813.

    Article  CAS  PubMed  Google Scholar 

  170. W. Chiuman, Y. Li, Nucleic Acids Res. 2007, 35, 401–405.

    Article  CAS  PubMed  Google Scholar 

  171. S. H. J. Mei, Z. Liu, J. D. Brennan, Y. Li, J. Am. Chem. Soc. 2003, 125, 412–420.

    Article  CAS  PubMed  Google Scholar 

  172. Z. Liu, S. H. J. Mei, J. D. Brennan, Y. Li, J. Am. Chem. Soc. 2003, 125, 7539–7545.

    Article  CAS  PubMed  Google Scholar 

  173. S. Hohng, T. Ha, ChemPhysChem 2005, 6, 956–960.

    Article  CAS  PubMed  Google Scholar 

  174. D. M. Willard, A. Van Orden, Nature Mater. 2003, 2, 575–576.

    Article  CAS  Google Scholar 

  175. C. S. Wu, M. K. Khaing Oo, X. Fan, ACS Nano 2010, 4, 5897–5904.

    Article  CAS  PubMed  Google Scholar 

  176. R. A. Reynolds, III, C. A. Mirkin, R. L. Letsinger, J. Am. Chem. Soc. 2000, 122, 3795–3796.

    Article  CAS  Google Scholar 

  177. J. Yguerabide, E. E. Yguerabide, Anal. Biochem. 1998, 262, 137–156.

    Article  CAS  PubMed  Google Scholar 

  178. J. H. Kim, S. H. Han, B. H. Chung, Biosens. Bioelectron. 2011, 26, 2125–2129.

    Article  CAS  PubMed  Google Scholar 

  179. Y. Xiang, A. Tong, Y. Lu, J. Am. Chem. Soc. 2009, 131, 15352–15357.

    Article  CAS  PubMed  Google Scholar 

  180. Y. Xiang, Z. Wang, H. Xing, N. Y. Wong, Y. Lu, Anal. Chem. 2010, 82, 4122–4129.

    Article  CAS  PubMed  Google Scholar 

  181. L. Zhang, B. Han, T. Li, E. Wang, Chem. Commun. 2011, 47, 3099–3101.

    Article  CAS  Google Scholar 

  182. J. Liu, Y. Lu, Nat. Protoc. 2006, 1, 246–252.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  184. C. A. Mirkin, R. L. Letsinger, R. C. Mucic, J. J. Storhoff, Nature 1996, 382, 607–609.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  186. H. Li, L. Rothberg, Proc. Natl. Acad. Sci. USA 2004, 101, 14036–14039.

    Article  CAS  PubMed  Google Scholar 

  187. W. Zhao, F. Gonzaga, Y. Li, M. A. Brook, Adv. Mater. 2007, 19, 1766–1771.

    Article  CAS  Google Scholar 

  188. K. Sato, K. Hosokawa, M. Maeda, J. Am. Chem. Soc. 2003, 125, 8102–8103.

    Article  CAS  PubMed  Google Scholar 

  189. J. Liu, Y. Lu, J. Am. Chem. Soc. 2004, 126, 12298–12305.

    Article  CAS  PubMed  Google Scholar 

  190. J. Liu, D. P. Wernette, Y. Lu, Angew. Chem., Int. Ed. Engl. 2005, 44, 7290–7293.

    Article  CAS  Google Scholar 

  191. J. Liu, Y. Lu, Org. Biomol. Chem. 2006, 4, 3435–3441.

    Article  CAS  PubMed  Google Scholar 

  192. J. Liu, Y. Lu, Chem. Commun. 2007, 4872–4874.

    Google Scholar 

  193. H. Li, L. J. Rothberg, J. Am. Chem. Soc. 2004, 126, 10958–10961.

    Article  CAS  PubMed  Google Scholar 

  194. I. Willner, R. Baron, B. Willner, Biosens. Bioelectron. 2007, 22, 1841–1852.

    Article  CAS  PubMed  Google Scholar 

  195. I. Willner, B. Willner, E. Katz, Bioelectrochemistry 2007, 70, 2–11.

    Article  CAS  PubMed  Google Scholar 

  196. Y. Xiao, V. Pavlov, R. Gill, T. Bourenko, I. Willner, ChemBioChem 2004, 5, 374–379.

    Article  CAS  PubMed  Google Scholar 

  197. T. Niazov, V. Pavlov, Y. Xiao, R. Gill, I. Willner, Nano Letters 2004, 4, 1683–1687.

    Article  CAS  Google Scholar 

  198. V. Pavlov, Y. Xiao, R. Gill, A. Dishon, M. Kotler, I. Willner, Anal. Chem. 2004, 76, 2152–2156.

    Article  CAS  PubMed  Google Scholar 

  199. Y. Xiao, V. Pavlov, T. Niazov, A. Dishon, M. Kotler, I. Willner, J. Am. Chem. Soc. 2004, 126, 7430–7431.

    Article  CAS  PubMed  Google Scholar 

  200. J. Elbaz, M. Moshe, B. Shlyahovsky, I. Willner, Chem. Eur. J. 2009, 15, 3411–3418.

    Article  CAS  PubMed  Google Scholar 

  201. C. B. Swearingen, D. P. Wernette, D. M. Cropek, Y. Lu, J. V. Sweedler, P. W. Bohn, Anal. Chem. 2005, 77, 442–448.

    Article  CAS  PubMed  Google Scholar 

  202. D. P. Wernette, C. B. Swearingen, D. M. Cropek, Y. Lu, J. V. Sweedler, P. W. Bohn, Analyst 2006, 131, 41–47.

    Article  CAS  PubMed  Google Scholar 

  203. D. P. Wernette, C. Mead, P. W. Bohn, Y. Lu, Langmuir 2007, 23, 9513–9521.

    Article  CAS  PubMed  Google Scholar 

  204. T.-J. Yim, J. Liu, Y. Lu, R. S. Kane, J. S. Dordick, J. Am. Chem. Soc. 2005, 127, 12200–12201.

    Article  CAS  PubMed  Google Scholar 

  205. Y. Shen, G. Mackey, N. Rupcich, D. Gloster, W. Chiuman, Y. Li, J. D. Brennan, Anal. Chem. 2007, 79, 3494–3503.

    Article  CAS  PubMed  Google Scholar 

  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.

    Article  CAS  PubMed  Google Scholar 

  207. ANDalyze, Inc., 2010, http://www.andalyze.com. (accessed on April 8, 2011).

Download references

Acknowledgments

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

Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Tian Lan & Yi Lu

  2. Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA

    Yi Lu

Authors
  1. Tian Lan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yi Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yi Lu .

Editor information

Editors and Affiliations

  1. Inorganic Chemistry, Chemistry, Universität Basel, Spitalstr. 51, Basel, 4056, Basel Stadt, Switzerland

    Astrid Sigel

  2. Inorganic Chemistry, Chemistry, Universität Basel, Spitalstr. 51, Basel, 4056, Basel Stadt, Switzerland

    Helmut Sigel

  3. Organisch-Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, Zürich, 8057, Switzerland

    Roland K. O. Sigel

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Lan, T., Lu, Y. (2012). Metal Ion-Dependent DNAzymes and Their Applications as Biosensors. In: Sigel, A., Sigel, H., Sigel, R. (eds) Interplay between Metal Ions and Nucleic Acids. Metal Ions in Life Sciences, vol 10. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2172-2_8

Download citation

Publish with us

Policies and ethics

Search

Navigation