DNA-catalyzed formation of nucleopeptide linkages

Angewandte Chemie - International Edition

Volumn 47, Issue 9, 2008, Pages 1753-1757

  Pradeepkumar, P I ^a   Höbartner, Claudia ^a   Baum, Dana A ^a   Silverman, Scott K ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

Amino acids; Deoxyribozymes; DNA; In vitro selection; Nucleopeptides

Indexed keywords

AMINES; AMINO ACIDS; CHEMICAL ATTACK; CHEMICAL REACTIONS; DNA; FORMING; FUNCTIONAL GROUPS; GENES; OLIGONUCLEOTIDES; ORGANIC ACIDS; RNA;

CHEMICAL EQUATIONS; DEOXYRIBOZYME; DEOXYRIBOZYMES; IN VITRO SELECTION; NUCLEOPEPTIDES; NUCLEOPHILIC ATTACKS; SIDE CHAINS; TRIPHOSPHATE;

NUCLEIC ACIDS;

AMINO ACID; DEOXYRIBOZYME; DNA; NUCLEOPROTEIN; PEPTIDE;

ARTICLE; CATALYSIS; CHEMISTRY;

AMINO ACIDS; CATALYSIS; DNA; DNA, CATALYTIC; NUCLEOPROTEINS; PEPTIDES;

EID: 41049088859     PISSN: 14337851     EISSN: None     Source Type: Journal    
DOI: 10.1002/anie.200703676     Document Type: Article

References (55)

1. Y.-C. Tse, K. Kirkegaard, J. C. Wang, J. Biol. Chem. 1980, 255, 5560-5565.
2. a) J. C. Connelly, D. R. Leach, Mol. Cell 2004, 13, 307-316;
3. b) K. C. Nitiss, M. Malik, X. He, S. W. White, J. L. Nitiss, Proc. Natl. Acad. Sci. USA 2006, 103, 8953-8958.
4. a) V. Ambros, D. Baltimore, J. Biol. Chem. 1978, 253, 5263-5266;
5. b) P. G. Rothberg, T. J. Harris, A. Nomoto, E. Wimmer, Proc. Natl. Acad. Sci. USA 1978, 75, 4868-4872.
6. A. Samad, R. B. Carroll, Mol. Cell. Biol. 1991, 11, 1598-1606.
7. a) C. M. Dreef-Tromp, H. van den Elst, J. E. van den Boogaart, G. A. van der Marel, J. H. van Boom, Nucleic Acids Res. 1992, 20, 2435-2439;
8. b) S. Flohr, V. Jungmann, H. Waldmann, Chem. Eur. J. 1999, 5, 669-681;
9. c) J. Robles, M. Beltrán, V. Marchán, Y. Pérez, I. Travesset, E. Pedroso, A. Grandas, Tetrahedron 1999, 55, 13251-13264;
10. d) L. Debéthune, G. Kohlhagen, A. Grandas, Y. Pommier, Nucleic Acids Res. 2002, 30, 1198-1204;
11. e) D. A. Jeyaraj, H. Prinz, H. Waldman, Chem. Eur. J. 2002, 8, 1879-1887.
12. a) G. M. Emilsson, R. R. Breaker, Cell. Mol. Life Sci. 2002, 59, 596-607;
13. b) S. K. Silverman, Org. Biomol. Chem. 2004, 2, 2701-2706;
14. c) J. C. Achenbach, W. Chiuman, R. P. Cruz, Y. Li, Curr. Pharm. Biotechnol. 2004, 5, 321-336;
15. d) A. Peracchi, ChemBioChem 2005, 6, 1316-1322.
16. C. Höbartner, S. K. Silverman, Biopolymers 2007, 87, 279-292.
17. R. R. Breaker, G. F. Joyce, Chem. Biol. 1994, 1, 223-229.
18. a) S. W. Santoro, G. F. Joyce, Proc. Natl. Acad. Sci. USA 1997, 94, 4262-4266;
19. b) S. K. Silverman, Nucleic Acids Res. 2005, 33, 6151-6163.
20. 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.
21. a) W. Wang, L. P. Billen, Y. Li, Chem. Biol. 2002, 9, 507-517;
22. b) Y. Li, Y. Liu, R. R. Breaker, Biochemistry 2000, 39, 3106-3114.
23. a) B. Cuenoud, J. W. Szostak, Nature 1995, 375, 611-614;
24. b) A. Sreedhara, Y. Li, R. R. Breaker, J. Am. Chem. Soc. 2004, 126, 3454-3460;
25. c) N. Carmi, L. A. Shultz, R. R. Breaker, Chem. Biol. 1996, 3, 1039-1046;
26. d) N. Carmi, S. R. Balkhi, R. R. Breaker, Proc. Natl. Acad. Sci. USA 1998, 95, 2233-2237;
27. e) T. L. Sheppard, P. Ordoukhanian, G. F. Joyce, Proc. Natl. Acad. Sci. USA 2000, 97, 7802-7807.
28. J. Burmeister, G. von Kiedrowski, A. D. Ellington, Angew. Chem. 1997, 109, 1379-1381;
29. Angew. Chem. Int. Ed. Engl. 1997, 36, 1321-1324.
30. a) D. J. Chinnapen, D. Sen, Proc. Natl. Acad. Sci. USA 2004, 101, 65-69;
31. b) D. J. Chinnapen, D. Sen, J. Mol. Biol. 2007, 365, 1326-1336.
32. a) Y. Li, D. Sen, Nat. Struct. Biol. 1996, 3, 743-747;
33. b) Y. Li, D. Sen, Biochemistry 1997, 36, 5589-5599.
34. R. L. Coppins, S. K. Silverman, Nat. Struct. Mol. Biol. 2004, 11, 270-274.
35. R. L. Coppins, S. K. Silverman, J. Am. Chem. Soc. 2005, 127, 2900-2907.
36. E. Zelin, Y. Wang, S. K. Silverman, Biochemistry 2006, 45, 2767-2771.
37. D. A. Baum, S. K. Silverman, Angew. Chem. 2007, 119, 3572-3574;
38. Angew. Chem. Int. Ed. 2007, 46, 3502-3504.
39. C. Höbartner, S. K. Silverman, Angew. Chem. 2007, 119, 7564-7568;
40. Angew. Chem. Int. Ed. 2007, 46, 7420-7424.
41. Preparation of the DNA-peptide-DNA conjugates by solid-phase synthesis is described in the Supporting Information.
42. Neither 7S11 nor any of its variants function with a DNA-rA-DNA-conjugate as the substrate that provides the 2′-OH group. Therefore, any deoxyribozymes from this positive control selection experiment should be different from those identified previously.
43. See the Supporting Information for procedures and data not shown in the figures.
44. E. Zelin, S. K. Silverman, ChemBioChem 2007, 8, 1907-1911.
45. [20] which is not the case for Tyr1.
46. a) S. P. Adler, D. Purich, E. R. Stadtman, J. Biol. Chem. 1975, 250, 6264-6272;
47. b) B. Juodka, M. Pfötz, D. Werner, Nucleic Acids Res. 1991, 19, 6391-6398.
48. Y. Wang, S. K. Silverman, J. Am. Chem. Soc. 2003, 125, 6880-6881.
49. R. L. Coppins, S. K. Silverman, J. Am. Chem. Soc. 2004, 126, 16426-16432.
50. a) M. Illangasekare, G. Sanchez, T. Nickles, M. Yarus, Science 1995, 267, 643-647;
51. b) R. K. Kumar, M. Yarus, Biochemistry 2001, 40, 6998-7004;
52. c) B. Zhang, T. R. Cech, Nature 1997, 390, 96-100;
53. d) B. Zhang, T. R. Cech, Chem. Biol. 1998, 5, 539-553;
54. e) L. Sun, Z. Cui, R. L. Gottlieb, B. Zhang, Chem. Biol. 2002, 9, 619-628.
55. S. Baskerville, D. P. Bartel, Proc. Natl. Acad. Sci. USA 2002, 99, 9154-9159.