DNAzymes: From creation in vitro to application in vivo

Current Pharmaceutical Biotechnology

Volumn 5, Issue 4, 2004, Pages 321-336

  Achenbach, J C ^a   Chiuman, W ^a   Cruz, R P G ^a   Li, Ying ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

Allosteric deoxyribozyme; Biosensing; DNAzymes; Flourescence; Gene therapeutics; In vitro selection; Nucleic acids

Indexed keywords

10 23; 16.2 11; 2':15 2; 7 Q10; 8 17; 9 25 11; BIPARTITE II; DEOXYRIBOZYME; DET 22 18; PH 7DZ1; PS 5.M; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

BIOSENSOR; CATALYSIS; DNA SEQUENCE; DRUG RESEARCH; GENE CONTROL; GENE EXPRESSION REGULATION; IN VITRO SELECTION; IN VITRO STUDY; IN VIVO STUDY; LIGAND BINDING; REVIEW; RNA SEQUENCE;

ANIMALS; BIOSENSING TECHNIQUES; DNA, CATALYTIC; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION; GENE TARGETING; GENE THERAPY; GENETIC ENGINEERING; HUMANS;

EID: 4344561755     PISSN: 13892010     EISSN: None     Source Type: Journal    
DOI: 10.2174/1389201043376751     Document Type: Review

References (128)

1. Breaker, R.R. and Joyce, G.F. (1994) Chem. Biol., 1(4), 223-229.
2. Tuerk, C. and Gold, L. (1990) Science, 249(4968), 505-510.
3. Ellington, A.D. and Szostak, J.W. (1990) Nature, 346(6287), 818-822.
4. Breaker, R.R. (1997) Chem. Rev., 97(2), 371-390.
5. Famulok, M. (1999) Curr. Opin. Struct. Biol., 9(3), 324-329.
6. Wilson, D.S. and Szostak, J.W. (1999) Annu. Rev. Biochem., 68, 611-647.
7. Breaker, R.R. (2002) Curr. Opin. Biotechnol., 13(1), 31-39.
8. Osborne, S.E., Matsumura, I. and Ellington, A.D. (1997) Curr. Opin. Chem. Biol., 1(1), 5-9.
9. Brody, E.N. and Gold, L. (2000) J. Biotechnol., 74(1), 5-13.
10. Hesselberth, J., Robertson, M.P., Jhaveri, S. and Ellington, A.D. (2000) J. Biotechnol., 74(1), 15-25.
11. Famulok, M., Blind, M. and Mayer, G. (2001) Chem.Biol., 8(10), 931-939.
12. Soukup, G.A. and Breaker, R.R. (1999) Trends Biotechnol., 17(12), 469-476.
13. Silverman, S.K. (2003) RNA, 9(4), 377-383.
14. Cech, T.R. (2002) Biochem. Soc. Trans., 30(Pt. 6), 1162-1166.
15. Jaeger, L. (1997) Curr. Opin. Struct. Biol., 7(3), 324-335.
16. Rossi, J.J. (1999) Chem. Biol., 6(2), R33-37.
17. Robertson, D.L. and Joyce, G.F. (1990) Nature, 344(6265), 467-468.
18. Santoro, S.W. and Joyce, G.F. (1997) Proc. Natl. Acad. Sci. USA, 94(9), 4262-4266.
19. Santoro, S.W. and Joyce, G.F. (1998) Biochemistry, 37(38), 13330-13342.
20. Mei, S.H., Liu, Z., Brennan, J.D. and Li, Y. (2003) J. Am. Chem. Soc., 125(2), 412-420.
21. Lermer, L., Roupioz, Y., Ting, R. and Perrin, D.M. (2002) J. Am. Chem. Soc., 124(34), 9960-9961.
22. Li, Y. and Sen, D. (1996) Nat. Struct. Biol., 3(9), 743-747.
23. Li, Y., Geyer, C.R. and Sen, D. (1996) Biochemistry, 35(21), 6911-6922.
24. Sheppard, T.L., Ordoukhanian, P. and Joyce, G.F. (2000) Proc. Natl. Acad. Sci. USA, 97(14), 7802-7807.
25. Wang, W., Billen, L.P. and Li, Y. (2002) Chem. Biol., 9(4), 507-517.
26. Li, Y. and Breaker, R.R. (1999) Proc. Natl. Acad. Sci. USA, 96(6), 2746-2751.
27. Breaker, R.R. (2000) Science, 290(5499), 2095-2096.
28. Breaker, R.R. (1997) Nat. Biotechnol., 15(5), 427-431.
29. Breaker, R.R. (1997) Curr. Opin. Chem. Biol., 1(1), 26-31.
30. Emilsson, G.M. and Breaker, R.R. (2002) Cell Mol. Life Sci., 59(4), 596-607.
31. Sen, D. and Geyer, C.R. (1998) Curr. Opin. Chem. Biol., 2(6), 680-687.
32. Li, Y. and Breaker, R.R. (1999) Curr. Opin. Struct. Biol., 9(3), 315-323.
33. Jaschke, A. (2001) Curr. Opin. Struct. Biol., 11(3), 321-326.
34. Breaker, R.R. and Joyce, G.F. (1995) Chem. Biol., 2(10), 655-660.
35. Santoro, S.W., Joyce, G.F., Sakthivel, K., Gramatikova, S. and Barbas, C.F., 3rd (2000) J. Am. Chem. Soc., 122(11), 2433-2439.
36. Faulhammer, D. and Famulok, M. (1996) Angew. Chem. Int. Ed. Engl., 35, 2809-2813.
37. Roth, A. and Breaker, R.R. (1998) Proc. Natl. Acad. Sci. USA, 95(11), 6027-6031.
38. Li, J., Zheng, W., Kwon, A.H. and Lu, Y. (2000) Nucleic Acids Res., 28(2), 481-488.
39. Geyer, C.R. and Sen, D. (1997) Chem. Biol., 4(8), 579-593.
40. Perrin, D.M., Garestier, T. and Helene, C. (2001) J. Am. Chem. Soc., 123(8), 1556-1563.
41. Feldman, A.R. and Sen, D. (2001) J. Mol. Biol., 313(2), 283-294.
42. Ordoukhanian, P. and Joyce, G.F. (2002) J. Am. Chem. Soc., 124(42), 12499-12506.
43. Liu, Z., Mei, S.H., Brennan, J.D. and Li, Y. (2003) J. Am. Chem. Soc., 125(25), 7539-7545.
44. Cruz, R.P.G., Withers, J.W. and Li, Y. (2003) Chem. Biol., 11(1), 57-67.
45. Faulhammer, D. and Famulok, M. (1997) J. Mol. Biol., 269(2), 188-202.
46. Cairns, M.J., King, A. and Sun, L.Q. (2003) Nucleic Acids Res., 31(11), 2883-2889.
47. Vester, B., Lundberg, L.B., Sorensen, M.D., Babu, B.R., Douthwaite, S. and Wengel, J. (2002) J. Am. Chem. Soc., 124(46), 13682-13683.
48. Peracchi, A. (2000) J. Biol. Chem., 275(16), 11693-11697.
49. Flynn-Charlebois, A., Wang, Y., Prior, T.K., Rashid, I., Hoadley, K.A., Coppins, R.L., Wolf, A.C. and Silverman, S. K. (2003) J. Am. Chem. Soc., 125(9), 2444-2454.
50. Flynn-Charlebois, A., Prior, T.K., Hoadley, K.A. and Silverman, S.K. (2003) J. Am. Chem. Soc., 125(18), 5346-5350.
51. Wang, Y. and Silverman, S.K. (2003) J. Am. Chem. Soc., 125(23), 6880-6881.
52. Li, Y. and Sen, D. (1998) Chem. Biol., 5(1), 1-12.
53. Li, Y. (1997) Ph. D. thesis, Simon Fraser University.
54. Travascio, P., Li, Y. and Sen, D. (1998) Chem. Biol., 5(9), 505-517.
55. Carmi, N., Shultz, L.A. and Breaker, R.R. (1996) Chem. Biol., 3(12), 1039-1046.
56. Carmi, N., Balkhi, S.R. and Breaker, R.R. (1998) Proc. Natl. Acad. Sci. USA, 95(5), 2233-2237.
57. Carmi, N. and Breaker, R.R. (2001) Bioorg. Med. Chem., 9(10), 2589-2600.
58. Burmeister, J., von Kiedrowski, G. and Ellington, A.D. (1997) Angew. Chem. Int. Ed. Engl., 36, 1321-1322.
59. Cuenoud, B. and Szostak, J.W. (1995) Nature, 375(6532), 611-614.
60. Levy, M. and Ellington, A.D. (2001) Bioorg. Med. Chem., 9(10), 2581-2587.
61. Levy, M. and Ellington, A.D. (2002) J. Mol. Evol., 54(2), 180-190.
62. Li, Y., Liu, Y. and Breaker, R.R. (2000) Biochemistry, 39(11), 3106-3114.
63. Breaker, R.R. (1999) Nat. Biotechnol., 17(5), 422-423.
64. Bruesehoff, P.J., Li, J., Augustine, A.J., 3rd and Lu, Y. (2002) Comb. Chem. High Throughput Screen, 5(4), 327-335.
65. Impey, H.L., Applegate, T.L., Haughton, M.A., Fuery, C.J., King, J.E. and Todd, A.V. (2000) Anal. Biochem., 286(2), 300-303.
66. Arnold, M.A. (1990) J. Biotechnol., 15(3), 219-228.
67. Wolfbeis, O.S. (2002) Anal. Chem., 74(12), 2663-2677.
68. Tyagi, S. and Kramer, F.R. (1996) Nat. Biotechnol., 14(3), 303-308.
69. Tan, W., Fang, X., Li, J. and Liu, X. (2000) Chemistry, 6(7), 1107-1111.
70. Nutiu, R. and Li, Y. (2002) Nucleic Acids Res., 30(18), e94.
71. Singh, K.K., Parwaresch, R. and Krupp, G. (1999) RNA, 5(10), 1348-1356.
72. Jenne, A., Hartig, J.S., Piganeau, N., Tauer, A., Samarsky, D.A., Green, M.R., Davies, J. and Famulok, M. (2001) Nat. Biotechnol., 19(1), 56-61.
73. Hartig, J.S. and Famulok, M. (2002) Angew. Chem. Int. Ed. Engl., 41(22), 4263-4266.
74. Stojanovic, M.N., de Prada, P. and Landry, D.W. (2001) Chem. Bio. Chem., 2(6), 411-415.
75. Todd, A.V., Fuery, C.J., Impey, H.L., Applegate, T.L. and Haughton, M.A. (2000) Clin. Chem., 46(5), 625-630.
76. Li, J. and Lu, Y. (2000) J. Am. Chem. Soc., 122, 10466-10467.
77. Lu, Y., Liu, J., Li, J., Bruesehoff, P.J., Pavot, C.M. and Brown, A.K. (2003) Biosens. Bioelectron., 18(5-6), 529-540.
78. Liu, J. and Lu, Y. (2003) J. Am. Chem. Soc.,125, 6642-6643.
79. Wang, D.Y. and Sen, D. (2001) J. Mol. Biol., 310(4), 723-734.
80. Levy, M. and Ellington, A.D. (2002) Chem. Biol., 9(4), 417-426.
81. Porta, H. and Lizardi, P.M. (1995) Biotechnology, (NY) 13(2), 161-164.
82. Thompson, K.M., Syrett, H.A., Knudsen, S.M. and Ellington, A.D. (2002) BMC Biotechnol., 2(1), 21.
83. Tang, J. and Breaker, R.R. (1997) Chem. Biol., 4(6), 453-459.
84. Araki, M., Okuno, Y., Hara, Y. and Sugiura, Y. (1998) Nucleic Acids Res., 26(14), 3379-3384.
85. Soukup, G.A. and Breaker, R.R. (1999) Structure Fold. Des., 7(7), 783-791.
86. Hermann, T. and Patel, D.J. (2000) Science, 287(5454), 820-825.
87. Patel, D.J., Suri, A.K., Jiang, F., Jiang, L., Fan, P., Kumar, R.A. and Nonin, S. (1997) J. Mol. Biol., 272(5), 645-664.
88. Wang, D.Y., Lai, B.H., Feldman, A.R. and Sen, D. (2002) Nucleic Acids Res., 30(8), 1735-1742.
89. Wang, D.Y., Lai, B.H. and Sen, D. (2002) J. Mol. Biol., 318(1), 33-43.
90. Soukup, G.A. and Breaker, R.R. (2000) Curr. Opin. Struct. Biol., 10(3), 318-325.
91. Braich, R.S., Chelyapov, N., Johnson, C., Rothemund, P.W. and Adleman, L. (2002) Science, 296(5567), 499-502.
92. Stojanovic, M.N., Mitchell, T.E. and Stefanovic, D. (2002) J. Am. Chem. Soc., 124(14), 3555-3561.
93. Stojanovic, M.N. and Stefanovic, D. (2003) J. Am. Chem. Soc., 125(22), 6673-6676.
94. Stojanovic, M.N. and Stefanovic, D. (2003) Nat. Biotechnol., 21(9), 1069-1074.
95. Lowe, H.C. and Khachigian, L.M. (2002) Circulation., 105(4), E29.
96. Cairns, M.J., Hopkins, T.M., Witherington, C., Wang, L, and Sun, L.Q. (1999) Nat. Biotechnol., 17(5), 480-486.
97. Sugimoto, N., Nakano, S., Katoh, M., Matsumura, A., Nakamuta, H., Ohmichi, T., Yoneyama, M. and Sasaki, M. (1995) Biochemistry, 34(35), 11211-11216.
98. Sriram, B. and Banerjea, A.C. (2000) Biochem. J., 352, 667-673.
99. Kurreck, J., Bieber, B., Jahnel, R. and Erdmann, V.A. (2002) J. Biol. Chem., 277(9), 7099-7107.
100. Zhang, X., Xu, Y., Ling, H. and Hattori, T. (1999) FEBS Lett., 458(2), 151-156.
101. Unwalla, H. and Banerjea, A.C. (2001) Biochem. J., 357(Pt. 1), 147-155.
102. Sun, L.Q., Cairns, M.J., Gerlach, W.L., Witherington, C., Wang, L. and King, A. (1999) J. Biol. Chem., 274(24), 17236-17241.
103. Yen, L., Strittmatter, S.M. and Kalb, R.G. (1999) Ann. Neurol., 46(3), 366-373.
104. Sioud, M. and Leirdal, M. (2000) J. Mol. Biol., 296(3), 937-947.
105. Cieslak, M., Niewiarowska, J., Nawrot, M., Koziolkiewicz, M., Stec, W.J. and Cierniewski, C.S. (2002) J. Biol. Chem., 277(9), 6779-6787.
106. Grimpe, B., Dong, S., Doller, C., Temple, K., Malouf, A.T. and Silver, J. (2002) J. Neurosci., 22(8), 3144-3160.
107. Zhang, L., Gasper, W.J., Stass, S.A., Ioffe, O.B., Davis, M.A. and Mixson, A.J. (2002) Cancer Res., 62(19), 5463-5469.
108. Sun, L.Q., Cairns, M.J., Saravolac, E.G., Baker, A. and Gerlach, W. L. (2000) Pharmacol. Rev., 52(3), 325-347.
109. Khachigian, L.M. (2000) J. Clin. Invest., 106(10), 1189-1195.
110. Sioud, M. and Leirdal, M. (2000) Biochem. Pharmacol., 60(8), 1023-1026.
111. Sioud, M. (2001) Curr. Mol. Med, 1(5), 575-588.
112. Santiago, F.S. and Khachigian, L.M. (2001) J. Mol. Med., 79(12), 695-706.
113. Opalinska, J.B. and Gewirtz, A.M. (2002) Nat. Rev. Drug Discov., 1(7), 503-514.
114. Warashina, M., Kuwabara, T., Nakamatsu, Y. and Taira, K. (1999) Chem. Biol., 6(4), 237-250.
115. Kuwabara, T., Warashina, M., Tanabe, T., Tani, K., Asano, S. and Taira, K. (1997) Nucleic Acids Res., 25(15), 3074-3081.
116. Wu, Y., Yu, L., McMahon, R., Rossi, J.J., Forman, S.J. and Snyder, D.S. (1999) Hum. Gene Ther., 10(17), 2847-2857.
117. Liu, C., Cheng, R., Sun, L.Q. and Tien, P. (2001) Biochem. Biophys. Res. Commun., 284(4), 1077-1082.
118. Hjiantoniou, E., Iseki, S., Uney, J. and Phylactou, L. (2003) Biochem. Biophys. Res. Commun., 300(1), 178-181.
119. Santiago, F.S., Lowe, H.C., Kavurma, M.M., Chesterman, C.N., Baker, A., Atkins, D.G. and Khachigian, L.M. (1999) Nat. Med., 5(11), 1264-1269.
120. Lowe, H.C., Fahmy, R.G., Kavurma, M.M., Baker, A., Chesterman, C.N. and Khachigian, L.M. (2001) Circ. Res., 89(8), 670-677.
121. Khachigian, L.M., Fahmy, R.G., Zhang, G., Bobryshev, Y.V. and Kaniaros, A. (2002) J. Biol. Chem., 277(25), 22985-22991.
122. Koizumi, M., Soukup, G.A., Kerr, J.N. and Breaker, R.R. (1999) Nat. Struct. Biol., 6(11), 1062-1071.
123. Cox, J.C., Hayhurst, A., Hesselberth, J., Bayer, T.S., Georgiou, G. and Ellington, A.D. (2002) Nucleic Acids Res., 30(20), e108.
124. Soukup, G.A. and Breaker, R.R. (1999) Proc. Natl. Acad. Sci. USA, 96(7), 3584-3589.
125. Robertson, M.P. and Ellington, A.D. (1999) Nat. Biotechnol., 17(1), 62-66.
126. Piganeau, N., Thuillier, V. and Famulok, M. (2001) J. Mol. Biol., 312(5), 1177-1190.
127. Vaish, N.K., Dong, F., Andrews, L., Schweppe, R.E., Ahn, N.G., Blatt, L. and Seiwert, S.D. (2002) Nat. Biotechnol., 20(8), 810-815.
128. Hartig, J.S., Najafi-Shoushtari, S.H., Grune, I., Yan, A., Ellington, A.D. and Famulok, M. (2002) Nat. Biotechnol., 20(7), 717-722.