A folding-based approach for the luminescent detection of a short rna hairpin

Journal of the American Chemical Society

Volumn 135, Issue 10, 2013, Pages 3812-3814

  Penas, Cristina ^a   Pazos, Elena ^a   Mascareñas, José L ^a   Vázquez, M Eugenio ^a  

^a Universidade de Santiago de Compostela ^*  (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BASIC PEPTIDES; HELICAL CONFORMATION; LUMINESCENCE EMISSION; MACROCYCLIC COMPLEX; RATIONAL DESIGN; SHORT RNAS;

AMINO ACIDS; PEPTIDES; RNA;

LUMINESCENCE;

MACROCYCLIC COMPOUND; SHORT HAIRPIN RNA;

ALPHA HELIX; ARTICLE; BACTERIOPHAGE; LUMINESCENCE; PROTEIN CONFORMATION;

HETEROCYCLIC COMPOUNDS, 1-RING; LUMINESCENCE; LUMINESCENT MEASUREMENTS; MOLECULAR STRUCTURE; PEPTIDES; PROTEIN FOLDING; RNA, SMALL INTERFERING; TERBIUM;

EID: 84874966413     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja400270a     Document Type: Article

References (51)

1. Hobert, O. Science 2008, 319, 1785-1786
2. Mandal, M.; Breaker, R. R. Nat. Rev. Mol. Cell Biol. 2004, 5, 451-463
3. Lönnberg, T.; Lönnberg, H. Curr. Opin. Chem. Biol. 2005, 9, 665-673
4. Okamura, K.; Lai, E. C. Nat. Rev. Mol. Cell Biol. 2008, 9, 673-678
5. Armitage, B. A. Curr. Opin. Chem. Biol. 2011, 15, 806-812
6. Sivaraman, D.; Biswas, P.; Cella, L. N.; Yates, M. V.; Chen, W. Trends Biotechnol. 2011, 29, 307-313
7. Guo, J.; Ju, J.; Turro, N. J. Anal. Bioanal. Chem. 2011, 402, 3115-3125
8. Kummer, S.; Knoll, A.; Socher, E.; Bethge, L.; Herrmann, A.; Seitz, O. Angew. Chem., Int. Ed. 2011, 50, 1931-1934
9. Zengeya, T.; Gupta, P.; Rozners, E. Angew. Chem., Int. Ed. 2012, 51, 12593-12596
10. Qi, X.; Xia, T.; Roberts, R. W. Biochemistry 2010, 49, 5782-5789
11. Hagihara, M.; Fukuda, M.; Hasegawa, T.; Morii, T. J. Am. Chem. Soc. 2006, 128, 12932-12940
12. Schifferer, M.; Griesbeck, O. J. Am. Chem. Soc. 2012, 134, 15185-15188
13. Valencia-Burton, M.; McCullough, R. M.; Cantor, C. R.; Broude, N. E. Nat. Methods 2007, 4, 421-427
14. Gosser, Y.; Hermann, T.; Majumdar, A.; Hu, W.; Frederick, R.; Jiang, F.; Xu, W.; Patel, D. J. Nat. Struct. Biol. 2001, 8, 146-150
15. Schärpf, M.; Sticht, H.; Schweimer, K.; Boehm, M.; Hoffmann, S.; Rösch, P. FEBS J. 2000, 267, 2397-2408
16. Ye, X.; Gorin, A.; Frederick, R.; Hu, W.; Majumdar, A.; Xu, W.; McLendon, G.; Ellington, A.; Patel, D. J. Chem. Biol. 1999, 6, 657-669
17. Puglisi, J. D.; Chen, L.; Blanchard, S.; Frankel, A. D. Science 1995, 270, 1200-1203
18. Puglisi, J. D.; Tan, R.; Calnan, B. J.; Frankel, A. D.; Williamson, J. R. Science 1992, 257, 76-80
19. Pazos, E.; Jiménez, A.; Mascareñas, J. L.; Vazquez, M. E. Chem. Sci. 2011, 2, 1984-1987
20. Pazos, E.; Goličnik, M.; Mascareñas, J. L.; Eugenio Vázquez, M. Chem. Commun. 2012, 48, 9534-9536
21. Vazquez, O.; Sánchez, M. I.; Mascareñas, J. L.; Vazquez, M. E. Chem. Commun. 2010, 46, 5518-5520
22. Pazos, E.; Torrecilla, D.; Vázquez López, M.; Castedo, L.; Mascareñas, J. L.; Vidal, A.; Vazquez, M. E. J. Am. Chem. Soc. 2008, 130, 9652-9653
23. Pazos, E.; Vazquez, O.; Mascareñas, J. L.; Vazquez, M. E. Chem. Soc. Rev. 2009, 38, 3348-3359
24. Gunnlaugsson, T.; Leonard, J. P. Chem. Commun. 2005, 3114-3131
25. Pandya, S.; Yu, J.; Parker, D. Dalton Trans. 2006, 2757-2766
26. Gunnlaugsson, T.; Harte, A. J.; Leonard, J. P.; Nieuwenhuyzen, M. Chem. Commun. 2002, 2134-2135
27. Eliseeva, S. V.; Bunzli, J.-C. G. Chem. Soc. Rev. 2010, 39, 189-227
28. Xia, T.; Frankel, A.; Takahashi, T. T.; Ren, J.; Roberts, R. W. Nat. Struct. Biol. 2003, 10, 812-819
29. Greenblatt, J.; Nodwell, J. R.; Mason, S. W. Nature 1993, 364, 401-406
30. Prasch, S.; Schwarz, S.; Eisenmann, A.; Wöhrl, B. M.; Schweimer, K.; Rösch, P. Biochemistry 2006, 45, 4542-4549
31. Bunzli, J.-C. G.; Piguet, C. Chem. Soc. Rev. 2005, 34, 1048-1077
32. Nitz, M.; Sherawat, M.; Franz, K. J.; Peisach, E.; Allen, K. N.; Imperiali, B. Angew. Chem., Int. Ed. 2004, 43, 3682-3685
33. Parker, D.; Williams, J. A. G. J. Chem. Soc., Dalton Trans. 1996, 3613-3628
34. Santos, dos, C. M. G.; Harte, A. J.; Quinn, S. J.; Gunnlaugsson, T. Coord. Chem. Rev. 2008, 252, 2512-2527
35. Cocozaki, A. I.; Ghattas, I. R.; Smith, C. A. J. Bacteriol. 2008, 190, 7699-7708
36. Cai, Z.; Gorin, A.; Frederick, R.; Ye, X.; Hu, W.; Majumdar, A.; Kettani, A.; Patel, D. J. Nat. Struct. Biol. 1998, 5, 203-212
37. Coin, I.; Beyermann, M.; Bienert, M. Nat. Protoc. 2007, 2, 3247-3256
38. Thieriet, N.; Alsina, J.; Giralt, E.; Guibe, F.; Albericio, F. Tetrahedron Lett. 1997, 38, 7275-7278
39. Gomez-Martinez, P.; Dessolin, M.; Guibe, F.; Albericio, F. J. Chem. Soc., Perkin Trans. 1 1999, 2871-2874
40. Dadabhoy, A.; Faulkner, S.; Sammes, P. J. Chem. Soc., Perkin Trans. 2 2002, 348-357
41. Aarons, R. J.; Notta, J. K.; Meloni, M. M.; Feng, J.; Vidyasagar, R.; Narvainen, J.; Allan, S.; Spencer, N.; Kauppinen, R. A.; Snaith, J. S.; Faulkner, S. Chem. Commun. 2006, 909-911
42. Sainlos, M.; Imperiali, B. Nat. Protoc. 2007, 2, 3201-3209
43. Du, H.; Fuh, R. C. A.; Li, J.; Corkan, L. A.; Lindsey, J. S. Photochem. Photobiol. 1998, 68, 141-142
44. Dixon, J. M.; Taniguchi, M.; Lindsey, J. S. Photochem. Photobiol. 2005, 81, 212-213
45. Curve-fitting was made using the Levenberg-Marquardt algorithm for nonlinear least-squares regression as implemented in the DynaFit program. Kuzmic, P. Anal. Biochem. 1996, 237, 260-273
46. Cilley, C. D.; Williamson, J. R. RNA 1997, 3, 57-67
47. Calculated as described in: Armbruster, D. A.; Pry, T. Clin. Biochem. Rev. 2008, 29, S49-S52
48. Draper, D. E. J. Mol. Biol. 1999, 293, 255-270
49. Chen, Y. H.; Yang, J. S.; Chau, K. H. Biochemistry 1974, 13, 3350-3359
50. Greenfield, N. J.; Fasman, G. D. Biochemistry 1969, 8, 4108-4116
51. Rohl, C. A.; Chakrabartty, A.; Baldwin, R. L. Protein Sci. 1996, 5, 2623-2637