Site-directed spin-labeling of nucleic acids by click chemistry: Detection of abasic sites in duplex DNA by EPR spectroscopy

Journal of the American Chemical Society

Volumn 132, Issue 30, 2010, Pages 10424-10428

  Jakobsen, Ulla ^a   Shelke, Sandip A ^b   Vogel, Stefan ^a   Sigurdsson, Snorri Th ^b  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b UNIVERSITY OF ICELAND   (Iceland)

Author keywords

[No Author keywords available]

Indexed keywords

CLICK CHEMISTRY; CONFORMATIONAL CHANGE; DUPLEX DNA; EPR SPECTROSCOPY; EPR STUDIES; ETHYNYL; FUNCTIONALIZED; MODIFIED NUCLEOTIDES; NITROXIDES; QUANTITATIVE YIELDS; RIGID LINKERS; SOLID SUPPORTS; SPIN LABEL; STRUCTURAL DEFORMATION; SYNTHETIC ROUTES;

DEFORMATION; DNA; ELECTRON SPIN RESONANCE SPECTROSCOPY; GENES; LABELS; MERCURY (METAL); MERCURY COMPOUNDS; NUCLEIC ACIDS; OLIGONUCLEOTIDES; PARAMAGNETIC RESONANCE;

SPIN DYNAMICS;

5 ETHYNYLDEOXYURIDINE; AZIDE; DEOXYURIDINE DERIVATIVE; DOUBLE STRANDED DNA; MERCURY; NITROXIDE; OLIGOMER; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; CONFORMATIONAL TRANSITION; CONJUGATION; DNA STRUCTURE; ELECTRON SPIN RESONANCE; MACROMOLECULE; NUCLEIC ACID SYNTHESIS; PURIFICATION; QUANTITATIVE ANALYSIS; SPIN LABELING;

DNA; ELECTRON SPIN RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; SPIN LABELS;

EID: 77955025443     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja102797k     Document Type: Article

References (58)

1. Qin, P. Z. and Dieckmann, T. Curr. Opin. Struc. Biol. 2004, 14, 350-359
2. Schiemann, O. and Prisner, T. F. Q. Rev. Biophys. 2007, 40, 1-53
3. Sowa, G. Z. and Qin, P. Z. Prog. Nucleic Acid Res. 2008, 82, 147-197
4. Zhang, X., Cekan, P., Sigurdsson, S. T., and Qin, P. Methods Enzymol. 2009, 469, 303-328
5. Gannet, P. M., Darian, E., Powell, J., Johnson, E. M., Mundoma, C., Greenbaum, N. L., Ramsey, C. M., Dalal, N. S., and Budil, D. E. Nucleic Acids Res. 2002, 30, 5328-5337
6. Spaltenstein, A., Robinson, B. H., and Hopkins, P. B. J. Am. Chem. Soc. 1988, 110, 1299-1301
7. Barhate, N., Cekan, P., Massey, A. P., and Sigurdsson, S. T. Angew. Chem. 2007, 119, 2709-2712
8. Angew. Chem., Int. Ed. 2007, 46, 2655-2658.
9. Cekan, P., Smith, A. L., Barhate, N., Robinson, B. H., and Sigurdsson, S. T. Nucleic Acids Res. 2008, 36, 5946-5954
10. Obeid, S., Yulikov, M., Jeschke, G., and Marx, A. Angew. Chem. 2008, 120, 6886-6890
11. Angew. Chem., Int. Ed. 2008, 47, 6782-6785.
12. Edwards, T. E., Okonogi, T. M., Robinson, B. H., and Sigurdsson, S. T. J. Am. Chem. Soc. 2001, 123, 1527-1528
13. Kim, N.-K., Murali, A., and DeRose, V. J. Chem. Biol. 2004, 11, 939-948
14. Edwards, T. E., Okonogi, T. M., and Sigurdsson, S. T. Chem. Biol. 2002, 9, 699-706
15. Nagahara, S., Murakami, A., and Makino, K. Nucleosides Nucleotides 1992, 11, 889-901
16. Qin, P. Z., Butcher, S. E., Feigon, J., and Hubbell, W. L. Biochemistry 2001, 40, 6929-6936
17. Qin, P. Z., Hideg, K., Feigon, J., and Hubbell, W. L. Biochemistry 2003, 42, 6772-6783
18. Ramos, A. and Varani, G. J. Am. Chem. Soc. 1998, 120, 10992-10993
19. Rostovtsev, V. V., Green, L. G., Fokin, V. V., and Sharpless, K. B. Angew. Chem. 2002, 114, 4812-4825
20. Angew. Chem., Int. Ed. 2002, 41, 2596-2599.
21. Tornøe, C. W., Christensen, C., and Meldal, M. J. Org. Chem. 2002, 67, 3057-3064
22. Kolb, H. C., Finn, M. G., and Sharpless, K. B. Angew. Chem. 2001, 113, 2056-2075
23. Angew. Chem., Int. Ed. 2001, 40, 2004-2021.
24. Koèolka, P., Andersen, N. K., Jensen, F., and Nielsen, P. ChemBioChem 2007, 8, 2106-2116
25. Seela, F. and Sirivolu, V. R. Helv. Chim. Acta 2007, 90, 535-552
26. Park, S. M., Shen, Y., and Kim, B. H. Org. Biomol. Chem. 2007, 5, 610-612
27. Gierlich, J., Burley, G. A., Philipp, M. E. G., Hammond, D. E., and Carell, T. Org. Lett. 2006, 8, 3639-3642
28. Burley, G. A., Gierlich, J., Mofid, M. R., Nir, H., Tal, S., Eichem, Y., and Carell, T. J. Am. Chem. Soc. 2006, 128, 1398-1399
29. Lietard, J., Meyer, A., Vasseur, J.-J., and Morvan, F. Tetrahedron Lett. 2007, 48, 8795-8798
30. Miller, T. R. and Hopkins, P. B. Bioorg. Med. Chem. Lett. 1994, 4, 981-986
31. Liu, Q. and Tor, Y. Org. Lett. 2003, 5, 2571-2572
32. Chiou, S.-H. J. Biochem. 1983, 94, 1259-1267
33. Oikawa, S. and Kawanishi, S. Biochemistry 1996, 35, 4584-4590
34. Kumar, R., El-Sagheer, A., Tumpane, J., Lincoln, P., Wilhelmsson, L. M., and Brown, T. J. Am. Chem. Soc. 2007, 129, 6859-6864
35. Yu, Z., Kotake, Y., and Janzen, E. G. Redox Rep. 1996, 2, 133-139
36. Lee, B. Y., Park, S. R., Jeon, H. B., and Kim, K. S. Tetrahedron Lett. 2006, 47, 5105-5109
37. Schiemann, O., Piton, N., Plackmeyer, J., Bode, B. E., Prisner, T. F., and Engels, J. W. Nat. Protoc. 2007, 2 (4) 904-923
38. Piton, N., Mu, Y. G., Stock, G., Prisner, T. F., Schiemann, O., and Engels, J. W. Nucleic Acids Res. 2007, 35, 3128-3143
39. Lindahl, T. Nature 1993, 362, 709-715
40. Lhomme, J., Constant, J.-F., and Demeunynck, M. Biopolymers 1999, 52, 65-83
41. Greco, N. J. and Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784-10785
42. Valis, L., Amann, N., and Wagenknecht, H.-A. Org. Biomol. Chem. 2005, 3, 36-38
43. Rajendar, B., Nishizawa, S., and Teramae, N. Org. Biomol. Chem. 2008, 6, 670-673
44. Zhang, L.-K. and Gross, M. L. J. Am. Soc. Mass Spectrom. 2002, 13, 1418-1426
45. Hianik, T., Wang, X., Andreev, S., Dolinnaya, N., Oretskaya, T., and Thompson, M. Analyst 2006, 131, 1161-1166
46. Bartosík, M., Gajdo, V., Kosteèka, P., Fojta, M., Paleèek, E., Volkov, E., Ooretskaya, T., and Hianik, T. Electroanalysis 2009, 21, 295-302
47. Dolinnaya, N. G., Jan, M. R., Kawde, A. N., Oretskaya, T. S., and Tashlitsky, V. N. Electroanalysis 2006, 4, 399-404
48. Buzzeo, M. C. and Barton, J. K. Bioconjugate Chem. 2008, 19, 2110-2112
49. Sicoli, G., Mathis, G., Aci-Seche, S., Saint-Pierre, C., Boulard, Y., Gasparutto, D., and Gambarelli, S. Nucleic Acids Res. 2009, 37, 3165-3176
50. Coppel, Y., Berthet, N., Coulombeau, C., Coulombeau, C., Garcia, J., and Lhomme, J. Biochemistry 1997, 36, 4817-4830
51. Cekan, P. and Sigurdsson, S. T. J. Am. Chem. Soc. 2009, 131, 18054-18056
52. Torigoe, H., Kawahashi, K., Takamori, A., and Ono, A. Nucleosides, Nucleotides Nucleic Acids 2005, 24, 915-917
53. Miyake, Y., Togashi, H., Tashiro, M., Yamaguchi, H., Oda, S., Kudo, M., Tanaka, Y., Kondo, Y., Sawa, R., Fujimoto, T., Machinami, T., and Ono, A. J. Am. Chem. Soc. 2006, 128, 2172-2173
54. Ono, A. and Togashi, H. Angew. Chem. 2004, 116, 4400-4402
55. Angew. Chem., Int. Ed. 2004, 43, 4300-4302.
56. Kozasa, T., Miyakawa, Y., Ono, A., and Torigoe, H. Nucleic Acids Symp. Ser. 2008, 52, 197-198
57. Tanaka, Y., Oda, S., Yamaguchi, H., Kudo, M., Kondo, Y., Kijima, C., and Ono, A. Nucleic Acids Symp. Ser. 2006, 50, 47-48
58. Tanaka, Y., Oda, S., Yamaguchi, H., Kondo, Y., Kojima, C., and Ono, A. J. Am. Chem. Soc. 2007, 129, 244-245