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Aptamer-based optical switch for biosensors

압타머 광학 바이오센서

  • Lee, Joo-Woon (Chemistry - School of Liberal Arts and Sciences, Korea National University of Transportation) ;
  • Cho, Jeong Hwan (Department of Chemistry and Advanced Materials, Kosin University) ;
  • Cho, Eun Jeong (The Texas Institute for Drug and Diagnostic Development, The University of Texas at Austin)
  • 이주운 (한국교통대학교 교양학부-화학) ;
  • 조정환 (고신대학교 화학신소재학과) ;
  • 조은정 (텍사스대학교-오스틴캠퍼스, 신약개발 연구소)
  • Received : 2014.03.07
  • Accepted : 2014.06.16
  • Published : 2014.06.25

Abstract

In this review, we will discuss aptamer technologies including in vitro selection, signal transduction mechanisms, and designing aptamers and aptazyme for label-free biosensors and catalysts. Dye-displacement, a typical label-less method, is described here which allows avoiding relatively complex labeling steps and extending this application to any aptamers without specific conformational changes, in a more simple, sensitive and cost effective way. We will also describe most recent and advanced technologies of signaling aptamer and aptazyme for the various analytical and clinical applications. Quantum dot biosensor (QDB) is explained in detail covering designing and adaptations for multiplexed protein detection. Application to aptamer array utilizing self-assembled signaling aptamer DNA tile and the novel methods that can directly select smart aptamer or aptazyme experimentally and computationally will also be finally discussed, respectively.

Keywords

optical;sensor;aptamer;fluorescence

Acknowledgement

Supported by : Kosin University

References

  1. Y. He, Y. Chen, H. Liu, A. E. Ribbe and C. Mao, J. Am. Chem. Soc., 127(35), 12202-12203 (2005). https://doi.org/10.1021/ja0541938
  2. E. Winfree, F. Liu, L. A. Wenzler and N. C. Seeman, Nature, 394(6693), 539-544 (1998). https://doi.org/10.1038/28998
  3. H. Yan, S. H. Park, G. Finkelstein, J. H. Reif and T. H. LaBean, Science, 301(5641), 1882-1884 (2003). https://doi.org/10.1126/science.1089389
  4. T. S. Romig, C. Bell and D. W. Drolet, J. Chromatogr. B Biomed. Sci. Appl., 731(2), 275-284 (1999). https://doi.org/10.1016/S0378-4347(99)00243-1
  5. T. G. McCauley, N. Hamaguchi and M. Stanton, Anal. Biochem., 319(2), 244-250 (2003). https://doi.org/10.1016/S0003-2697(03)00297-5
  6. M. Lee and D. R. Walt, Anal Biochem, 282(1), 142-146 (2000). https://doi.org/10.1006/abio.2000.4595
  7. R. A. Potyrailo, R. C. Conrad, A. D. Ellington and G. M. Hieftje, Anal. Chem., 70(16), 3419-3425 (1998). https://doi.org/10.1021/ac9802325
  8. G. Ramsay, Nat. Biotechnol., 16(1), 40-44 (1998). https://doi.org/10.1038/nbt0198-40
  9. R. F. Macaya, J. A. Waldron, B. A. Beutel, H. Gao, M. E. Joesten, M. Yang, R. Patel, A. H. Bertelsen and A. F. Cook, Biochemistry, 34(13), 4478-4492 (1995). https://doi.org/10.1021/bi00013a041
  10. S. Su, R. Nutiu, C. D. Filipe, Y. Li and R. Pelton, Langmuir, 23(3), 1300-1302 (2007). https://doi.org/10.1021/la060961c
  11. L. M. Ellerby, C. R. Nishida, F. Nishida, S. A. Yamanaka, B. Dunn, J. S. Valentine, and J. I. Zink, Science, 255(5048), 1113-1115 (1992). https://doi.org/10.1126/science.1312257
  12. I. Gill and A. Ballesteros, Trends Biotechnol., 18(7), 282-296 (2000). https://doi.org/10.1016/S0167-7799(00)01457-8
  13. C. Lin, E. Katilius, Y. Liu, J. Zhang and H. Yan, Angew. Chem. Int. Ed. Engl., 45(32), 5296-5301 (2006). https://doi.org/10.1002/anie.200600438
  14. C. Lin, Y. Liu and H. Yan, Nano Lett., 7(2), 507-512 (2007). https://doi.org/10.1021/nl062998n
  15. N. C. Seeman, Nature, 421(6921), 427-431 (2003). https://doi.org/10.1038/nature01406
  16. C. Lin, Y. Liu, S. Rinker and H. Yan, Chemphyschem, 7(8), 1641-1647 (2006). https://doi.org/10.1002/cphc.200600260
  17. U. Feldkamp and C. M. Niemeyer, Angew. Chem. Int. Ed. Engl., 45(12), 1856-1876 (2006). https://doi.org/10.1002/anie.200502358
  18. Y. He, Y. Tian, Y. Chen, Z. Deng, A. E. Ribbe and C. Mao, Angew. Chem. Int. Ed. Engl., 44(41), 6694-6696 (2005). https://doi.org/10.1002/anie.200502193
  19. J. J. Harvey, S. P. Lee, E. K. Chan, J. H. Kim, E. S. Hwang, C. Y. Cha, J. R. Knutson and M. K. Han, Anal. Biochem., 333(2), 246-255 (2004). https://doi.org/10.1016/j.ab.2004.05.037
  20. I. V. Smolina, V. V. Demidov, C. R. Cantor and N. E. Broude, Anal. Biochem., 335(2), 326-329 (2004). https://doi.org/10.1016/j.ab.2004.07.022
  21. M. P. Robertson and A. D. Ellington, Nat. Biotechnol., 17(1), 62-66 (1999). https://doi.org/10.1038/5236
  22. M. Levy and A. D. Ellington, Chem. Biol., 9(4), 417-426 (2002). https://doi.org/10.1016/S1074-5521(02)00123-0
  23. M. Levy and A. D. Ellington, J. Mol. Evol., 54(2), 180-190 (2002). https://doi.org/10.1007/s00239-001-0066-1
  24. M. Levy and A. D. Ellington, Bioorg. Med. Chem., 9(10), 2581-2587 (2001). https://doi.org/10.1016/S0968-0896(01)00033-5
  25. Y. Xu and E. T. Kool, Nucleic Acids Res, 27(3), 875-881 (1999). https://doi.org/10.1093/nar/27.3.875
  26. O. Soderberg, M. Gullberg, M. Jarvius, K. Ridderstrale, K. J. Leuchowius, J. Jarvius, K. Wester, P. Hydbring, F. Bahram, L. G. Larsson, and U. Landegren, Nat. Methods, 3(12), 995-1000 (2006). https://doi.org/10.1038/nmeth947
  27. S. Fredriksson, M. Gullberg, J. Jarvius, C. Olsson, K. Pietras, S. M. Gustafsdottir, A. Ostman and U. Landegren, Nat Biotechnol, 20(5), 473-477 (2002). https://doi.org/10.1038/nbt0502-473
  28. L. Yang, C. W. Fung, E. J. Cho and A. D. Ellington, Anal. Chem., 79(9), 3320-3329 (2007). https://doi.org/10.1021/ac062186b
  29. T. S. Bayer and C. D. Smolke, Nat. Biotechnol., 23(3), 337-343 (2005). https://doi.org/10.1038/nbt1069
  30. J. Liu and Y. Lu, Angew. Chem. Int. Ed. Engl., 45(1), 90-94 (2005).
  31. L. Yang and A. D. Ellington, Anal. Biochem., 380(2), 164-173 (2008). https://doi.org/10.1016/j.ab.2008.05.018
  32. R. Nutiu, J. M. Yu and Y. Li, Chembiochem, 5(8), 1139-1144 (2004). https://doi.org/10.1002/cbic.200400026
  33. Q. Deng, C. J. Watson and R. T. Kennedy, J. Chromatogr. A, 1005(1-2), 123-130 (2003). https://doi.org/10.1016/S0021-9673(03)00812-4
  34. H. Zhou, K. Bouwman, M. Schotanus, C. Verweij, J. A. Marrero, D. Dillon, J. Costa, P. Lizardi and B. B. Haab, Genome Biol., 5(4), R28 (2004). https://doi.org/10.1186/gb-2004-5-4-r28
  35. N. H. Elowe, R. Nutiu, A. Allali-Hassani, J. D. Cechetto, D. W. Hughes, Y. Li and E. D. Brown, Angew. Chem. Int. Ed. Engl., 45(34), 5648-5652 (2006). https://doi.org/10.1002/anie.200601695
  36. J. Barletta, Mol. Aspects. Med., 27(2-3), 224-253 (2006). https://doi.org/10.1016/j.mam.2005.12.008
  37. P. M. Lizardi, X. Huang, Z. Zhu, P. Bray-Ward, D. C. Thomas and D. C. Ward, Nat. Genet., 19(3), 225-232 (1998). https://doi.org/10.1038/898
  38. G. Nallur, C. Luo, L. Fang, S. Cooley, V. Dave, J. Lambert, K. Kukanskis, S. Kingsmore, R. Lasken and B. Schweitzer, Nucleic Acids Res., 29(23), E118 (2001). https://doi.org/10.1093/nar/29.23.e118
  39. M. J. Espy, J. R. Uhl, L. M. Sloan, S. P. Buckwalter, M. F. Jones, E. A. Vetter, J. D. Yao, N. L. Wengenack, J. E. Rosenblatt, F. R. Cockerill, 3rd and T. F. Smith, Clin. Microbiol. Rev., 19(1), 165-256 (2006). https://doi.org/10.1128/CMR.19.1.165-256.2006
  40. G. A. Blab, T. Schmidt and M. Nilsson, Anal. Chem., 76(2), 495-498 (2004). https://doi.org/10.1021/ac034987+
  41. M. Nilsson, M. Gullberg, F. Dahl, K. Szuhai and A. K. Raap, Nucleic Acids Res., 30(14), e66 (2002). https://doi.org/10.1093/nar/gnf065
  42. B. Schweitzer, S. Wiltshire, J. Lambert, S. O'Malley, K. Kukanskis, Z. Zhu, S. F. Kingsmore, P. M. Lizardi and D. C. Ward, Proc. Natl. Acad. Sci. USA, 97(18), 10113-10119 (2000). https://doi.org/10.1073/pnas.170237197
  43. B. Schweitzer, S. Roberts, B. Grimwade, W. Shao, M. Wang, Q. Fu, Q. Shu, I. Laroche, Z. Zhou, V. T. Tchernev, J. Christiansen, M. Velleca and S. F. Kingsmore, Nat. Biotechnol., 20(4), 359-365 (2002). https://doi.org/10.1038/nbt0402-359
  44. D. A. Di Giusto, W. A. Wlassoff, J. J. Gooding, B. A. Messerle and G. C. King, Nucleic Acids Res., 33(6), e64 (2005). https://doi.org/10.1093/nar/gni063
  45. M. N. Stojanovic and D. W. Landry, J. Am. Chem. Soc., 124(33), 9678-9679 (2002). https://doi.org/10.1021/ja0259483
  46. A. N. Glazer and H. S. Rye, Nature, 359(6398), 859-861 (1992). https://doi.org/10.1038/359859a0
  47. S. Laib and S. Seeger, J. Fluoresc., 14(2), 187-191 (2004). https://doi.org/10.1023/B:JOFL.0000016290.34070.ee
  48. Y. Liu and B. Danielsson, Anal. Chem., 77(8), 2450-2454 (2005). https://doi.org/10.1021/ac048449o
  49. M. N. Stojanovic and D. M. Kolpashchikov, J. Am. Chem. Soc., 126(30), 9266-9670 (2004). https://doi.org/10.1021/ja032013t
  50. J. R. Babendure, S. R. Adams and R. Y. Tsien, J. Am. Chem. Soc., 125(48), 14716-14717 (2003). https://doi.org/10.1021/ja037994o
  51. D. Grate and C. Wilson, Proc. Natl. Acad. Sci. U S A, 96(11), 6131-6136 (1999). https://doi.org/10.1073/pnas.96.11.6131
  52. H. A. Ho and M. Leclerc, J. Am. Chem. Soc., 126(5), 1384-1387 (2004). https://doi.org/10.1021/ja037289f
  53. I. L. Medintz, A. R. Clapp, H. Mattoussi, E. R. Goldman, B. Fisher, and J. M. Mauro, Nat. Mater., 2(9), 630-638 (2003). https://doi.org/10.1038/nmat961
  54. P. S. Nelson, Ann. N Y Acad. Sci., 975, 232-246 (2002). https://doi.org/10.1111/j.1749-6632.2002.tb05955.x
  55. S. E. Lupold, B. J. Hicke, Y. Lin and D. S. Coffey, Cancer Res., 62(14), 4029-4033 (2002).
  56. O. C. Farokhzad, S. Jon, A. Khademhosseini, T. N. Tran, D. A. Lavan and R. Langer, Cancer Res., 64(21), 7668-7672 (2004). https://doi.org/10.1158/0008-5472.CAN-04-2550
  57. T. C. Chu, F. Shieh, L. A. Lavery, M. Levy, R. Richards-Kortum, B. A. Korgel and A. D. Ellington, Biosens. Bioelectron., 21(10), 1859-1866 (2006). https://doi.org/10.1016/j.bios.2005.12.015
  58. J. K. Herr, J. E. Smith, C. D. Medley, D. Shangguan and W. Tan, Anal. Chem., 78(9), 2918-2924 (2006). https://doi.org/10.1021/ac052015r
  59. J. Srinivasan, S. T. Cload, N. Hamaguchi, J. Kurz, S. Keene, M. Kurz, R. M. Boomer, J. Blanchard, D. Epstein, C. Wilson and J. L. Diener, Chem. Biol., 11(4), 499-508 (2004). https://doi.org/10.1016/j.chembiol.2004.03.014
  60. R. Nutiu and Y. Li, J. Am. Chem. Soc., 125(16), 4771-4778 (2003). https://doi.org/10.1021/ja028962o
  61. Z. Tang, P. Mallikaratchy, R. Yang, Y. Kim, Z. Zhu, H. Wang and W. Tan, J Am Chem Soc, 130(34), 11268-11269 (2008). https://doi.org/10.1021/ja804119s
  62. J. J. Li, X. Fang and W. Tan, Biochem. Biophys. Res. Commun., 292(1), 31-40 (2002). https://doi.org/10.1006/bbrc.2002.6581
  63. M. N. Stojanovic, P. de Prada and D. W. Landry, J. Am. Chem. Soc., 122(46), 11547-11548 (2000). https://doi.org/10.1021/ja0022223
  64. E. J. Merino and K. M. Weeks, J. Am. Chem. Soc., 125(41), 12370-12371 (2003). https://doi.org/10.1021/ja035299a
  65. C. J. Yang, S. Jockusch, M. Vicens, N. J. Turro and W. Tan, Proc Natl Acad Sci USA, 102(48), 17278-17283 (2005). https://doi.org/10.1073/pnas.0508821102
  66. E. Heyduk and T. Heyduk, Anal Chem, 77(4), 1147-1156 (2005). https://doi.org/10.1021/ac0487449
  67. E. Katilius, Z. Katiliene and N. W. Woodbury, Anal. Chem., 78(18), 6484-6489 (2006). https://doi.org/10.1021/ac060859k
  68. R. D. Jenison, S. C. Gill, A. Pardi and B. Polisky, Science, 263(5152), 1425-1429 (1994). https://doi.org/10.1126/science.7510417
  69. S. Seetharaman, M. Zivarts, N. Sudarsan and R. R. Breaker, Nat. Biotechnol., 19(4), 336-341 (2001). https://doi.org/10.1038/86723
  70. R. R. Breaker and G. F. Joyce, Trends Biotechnol., 12(7), 268-275 (1994). https://doi.org/10.1016/0167-7799(94)90138-4
  71. R. R. Breaker, Chem. Rev., 97(2), 371-390 (1997). https://doi.org/10.1021/cr960008k
  72. A. Ferguson, R. M. Boomer, M. Kurz, S. C. Keene, J. L. Diener, A. D. Keefe, C. Wilson and S. T. Cload, Nucleic Acids Res., 32(5), 1756-1766 (2004). https://doi.org/10.1093/nar/gkh336
  73. R. Nutiu and Y. Li, Angew. Chem. Int. Ed. Engl., 44(34), 5464-5467 (2005). https://doi.org/10.1002/anie.200501214
  74. J. Bunkenborg, N. I. Gadjev, T. Deligeorgiev and J. P. Jacobsen, Bioconjug. Chem., 11(6), 861-867 (2000). https://doi.org/10.1021/bc000042c
  75. G. A. Soukup and R. R. Breaker, Proc. Natl. Acad. Sci. U S A, 96(7), 3584-3589 (1999). https://doi.org/10.1073/pnas.96.7.3584
  76. L. C. Bock, L. C. Griffin, J. A. Latham, E. H. Vermaas and J. J. Toole, Nature, 355(6360), 564-566 (1992). https://doi.org/10.1038/355564a0
  77. N. Hamaguchi, A. Ellington and M. Stanton, Anal. Biochem., 294(2), 126-131 (2001). https://doi.org/10.1006/abio.2001.5169
  78. S. D. Seiwert, T. Stines Nahreini, S. Aigner, N. G. Ahn and O. C. Uhlenbeck, Chem. Biol., 7(11), 833-843 (2000). https://doi.org/10.1016/S1074-5521(00)00032-6
  79. A. Roth and R. R. Breaker, Methods Mol. Biol., 252, 145-164 (2004).
  80. J. Tang and R. R. Breaker, Chem. Biol., 4(6), 453-459 (1997). https://doi.org/10.1016/S1074-5521(97)90197-6
  81. B. Hall, J. R. Hesselberth and A. D. Ellington, Biosens. Bioelectron., 22(9-10), 1939-1947 (2007). https://doi.org/10.1016/j.bios.2006.08.019
  82. M. P. Robertson, S. M. Knudsen and A. D. Ellington, RNA, 10(1), 114-127 (2004). https://doi.org/10.1261/rna.5900204
  83. M. Zuker, Curr. Opin. Struct. Biol., 10(3), 303-310 (2000). https://doi.org/10.1016/S0959-440X(00)00088-9
  84. D. Proske, M. Blank, R. Buhmann, and A. Resch, Appl. Microbiol. Biotechnol., 69(4), 367-374 (2005). https://doi.org/10.1007/s00253-005-0193-5
  85. D. H. Bunka and P. G. Stockley, Nat. Rev. Microbiol., 4(8), 588-596 (2006). https://doi.org/10.1038/nrmicro1458
  86. A. C. Yan, K. M. Bell, M. M. Breeden and A. D. Ellington, Front. Biosci., 10, 1802-1827 (2005). https://doi.org/10.2741/1663
  87. J. F. Lee, G. M. Stovall and A. D. Ellington, Curr. Opin. Chem. Biol., 10(3), 282-289 (2006). https://doi.org/10.1016/j.cbpa.2006.03.015
  88. X. Fang, A. Sen, M. Vicens and W. Tan, Chembiochem, 4(9), 829-834 (2003). https://doi.org/10.1002/cbic.200300615
  89. R. Nutiu and Y. Li, Methods, 37(1), 16-25 (2005). https://doi.org/10.1016/j.ymeth.2005.07.001
  90. R. L. Nutiu, Y., Chem. Eur. J., 10(8), 1868-1876 (2004). https://doi.org/10.1002/chem.200305470
  91. T. H. LaBean, H. Yan, J. Kopatsch, F. Liu, E. Winfree, J. H. Relf and N. C. Seeman, J. Am. Chem. Soc., 407(9), 1848-1860 (2000).