Duplex-quadruplex motifs in a peculiar structural organization cooperatively contribute to thrombin binding of a DNA aptamer

Acta Crystallographica Section D: Biological Crystallography

Volumn 69, Issue 12, 2013, Pages 2403-2411

  Krauss, Irene Russo ^a   Pica, Andrea ^a   Merlino, Antonello ^a,b   Mazzarella, Lelio ^a,b   Sica, Filomena ^a,b,c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b CNR   (Italy)

^c NATIONAL INSTITUTE OF BIOSTRUCTURES AND BIOSYSTEMS   (Italy)

Author keywords

Aptamers; Duplex quadruplex motifs; Thrombin

Indexed keywords

APTAMER; THROMBIN; THROMBIN APTAMER;

APTAMERS; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DUPLEX-QUADRUPLEX MOTIFS; HUMAN; METABOLISM; NUCLEOTIDE SEQUENCE; PROTEIN BINDING; X RAY CRYSTALLOGRAPHY;

APTAMERS; DUPLEX-QUADRUPLEX MOTIFS; THROMBIN;

APTAMERS, NUCLEOTIDE; BASE SEQUENCE; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN BINDING; THROMBIN;

EID: 84889634850     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444913022269     Document Type: Article

References (48)

1. Balasubramanian, S. & Neidle, S. (2009). Curr. Opin. Chem. Biol. 13, 345-353.
2. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
3. Chinnapen, D. J. & Sen, D. (2002). Biochemistry, 41, 5202-5212.
4. Chou, S.-H., Chin, K.-H. & Wang, A. H.-J. (2005). Trends Biochem. Sci. 30, 231-234.
5. Dolinnaya, N. G., Yuminova, A. V., Spiridonova, V. A., Arutyunyan, A. M. & Kopylov, A.M. (2012). J. Biomol. Struct. Dyn. 30, 524-531.
6. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
7. Fernando, H., Sewitz, S., Darot, J., Tavaré, S., Huppert, J. L. & Balasubramanian, S. (2009). Nucleic Acids Res. 37, 6716-6722.
8. Gatto, B., Palumbo, M. & Sissi, C. (2009). Curr. Med. Chem. 16, 1248-1265.
9. Hasegawa, H., Taira, K., Sode, K. & Ikebukuro, K. (2008). Sensors, 8, 1090-1098.
10. Hooft, R. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Nature (London), 381, 272.
11. Jayasena, S. D. (1999). Clin. Chem. 45, 1628-1650.
12. Keefe, A. D., Pai, S. & Ellington, A. (2010). Nature Rev. Drug Discov. 9, 537-550.
13. Kumari, S., Bugaut, A., Huppert, J. L. & Balasubramanian, S. (2007). Nature Chem. Biol. 3, 218-221.
14. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
15. Lawrence, M. C. & Colman, P. M. (1993). J. Mol. Biol. 234, 946-950.
16. Li, T., Wang, E. & Dong, S. (2009). PLoS One, 4, e5126.
17. Lin, P.-H., Chen, R.-H., Lee, C.-H., Chang, Y., Chen, C.-S. & Chen, W.-Y. (2011). Colloids Surf. B, 88, 552-558.
18. Lipps, H. J. & Rhodes, D. (2009). Trends Cell Biol. 19, 414-422.
19. Long, S. B., Long, M. B., White, R. R. & Sullenger, B. A. (2008). RNA, 14, 2504-2512.
20. Macaya, R. F., Schultze, P., Smith, F.W., Roe, J. A. & Feigon, J. (1993). Proc. Natl Acad. Sci. USA, 90, 3745-3749.
21. Macaya, R. F., Waldron, J. A., Beutel, B. A., Gao, H., Joesten, M. E., Yang, M., Patel, R., Bertelsen, A. H. & Cook, A. F. (1995). Biochemistry, 34, 4478-4492.
22. Marson, G., Palumbo, M. & Sissi, C. (2012). Curr. Pharm. Des. 18, 2027-2035.
23. Mayer, G., Müller, J., Mack, T., Freitag, D. F., Hover, T., Pötzsch, B. & Heckel, A. (2009). ChemBioChem, 10, 654-657.
24. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. (2005). Acta Cryst. D61, 458-464.
25. Mori, T., Oguro, A., Ohtsu, T. & Nakamura, Y. (2004). Nucleic Acids Res. 32, 6120-6128.
26. Müller, J., Freitag, D., Mayer, G. & Pötzsch, B. (2008). J. Thromb. Haemost. 6, 2105-2112.
27. Müller, J., Wulffen, B., Pötzsch, B. & Mayer, G. (2007). ChemBio-Chem, 8, 2223-2226.
28. Murshudov, G. N., Skubák, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
29. Musumeci, D. & Montesarchio, D. (2012). Pharmacol. Ther. 136, 202-215.
30. Nagatoishi, S., Isono, N., Tsumoto, K. & Sugimoto, N. (2011). Biochimie, 93, 1231-1238.
31. Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.
32. Pasternak, A., Hernandez, F. J., Rasmussen, L. M., Vester, B. & Wengel, J. (2011). Nucleic Acids Res. 39, 1155-1164.
33. Patel, D. J., Phan, A. T. & Kuryavyi, V. (2007). Nucleic Acids Res. 35, 7429-7455.
34. Phan, A. T., Kuryavyi, V., Darnell, J. C., Serganov, A., Majumdar, A., Ilin, S., Raslin, T., Polonskaia, A., Chen, C., Clain, D., Darnell, R. B. & Patel, D. J. (2011). Nature Struct. Mol. Biol. 18, 796-804.
35. Pileur, F., Andreola, M. L., Dausse, E., Michel, J., Moreau, S., Yamada, H., Gaidamakov, S. A., Crouch, R. J., Toulmé, J. J. & Cazenave, C. (2003). Nucleic Acids Res. 31, 5776-5788.
36. Rangnekar, A., Zhang, A. M., Li, S. S., Bompiani, K. M., Hansen, M. N., Gothelf, K. V., Sullenger, B. A. & LaBean, T. H. (2012). Nanomedicine, 8, 673-681.
37. Russo Krauss, I., Merlino, A., Giancola, C., Randazzo, A., Mazzarella, L. & Sica, F. (2011). Nucleic Acids Res. 39, 7858-7867.
38. Russo Krauss, I., Merlino, A., Randazzo, A., Mazzarella, L. & Sica, F. (2010). Acta Cryst. F66, 961-963.
39. Russo Krauss, I., Merlino, A., Randazzo, A., Novellino, E., Mazzarella, L. & Sica, F. (2012). Nucleic Acids Res. 40, 8119-8128.
40. Russo Krauss, I., Merlino, A., Vergara, A. & Sica, F. (2013). Int. J. Mol. Sci. 14, 11643-11691.
41. Silverman, A. P., Bu, W., Cohen, S. M. & Lippard, S. J. (2002). J. Biol. Chem. 277, 49743-49749.
42. Spiridonova, V. A., Rog, E. V., Dugina, T. N., Strukova, S. M. & Kopylov, A. M. (2003). Russ. J. Bioorg. Chem. 29, 450-453.
43. Tan, W., Wang, H., Chen, Y., Zhang, X., Zhu, H., Yang, C., Yang, R. & Liu, C. (2011). Trends Biotechnol. 29, 634-640.
44. Tasset, D. M., Kubik, M. F. & Steiner, W. (1997). J. Mol. Biol. 272, 688-698.
45. Wang, K. Y., Krawczyk, S. H., Bischofberger, N., Swaminathan, S. & Bolton, P. H. (1993). Biochemistry, 32, 11285-11292.
46. Williamson, J. R. (1994). Annu. Rev. Biophys. Biomol. Struct. 23, 703-730.
47. Zavyalova, E., Golovin, A., Reshetnikov, R., Mudrik, N., Panteleyev, D., Pavlova, G. & Kopylov, A. (2011). Curr. Med. Chem. 18, 3343-3350.
48. Zhou, G., Huang, X. & Qu, Y. (2010). Biochem. Eng. J. 52, 117-122.