C2′-pyrene-functionalized triazole-linked DNA: Universal DNA/RNA hybridization probes

Journal of Organic Chemistry

Volumn 77, Issue 1, 2012, Pages 5-16

  Sau, Sujay P ^a   Hrdlicka, Patrick J ^a  

^a UNIVERSITY OF IDAHO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION AND FLUORESCENCE SPECTROSCOPY; AVERAGE DIFFERENCE; CLICK REACTION; DEOXYURIDINE; DNA TARGETS; HYBRIDIZATION PROBE; HYDROGEN BONDINGS; MISMATCHED DNA; NUCLEIC ACID CHEMISTRY; PCR PRIMERS; PHOSPHORAMIDITES; POTENTIAL APPLICATIONS; PURINE DERIVATIVES; THERMAL DENATURATIONS;

DNA; FLUORESCENCE SPECTROSCOPY; HYDROGEN; MONOMERS; NITROGEN COMPOUNDS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; PYROLYSIS;

PROBES;

NUCLEOTIDE; OLIGODEOXYRIBONUCLEOTIDE; PHOSPHORAMIDIC ACID DERIVATIVE; PYRENE; TRIAZOLE; DNA; OLIGONUCLEOTIDE; PYRENE DERIVATIVE; RNA; TRIAZOLE DERIVATIVE;

ABSORPTION; ARTICLE; CHEMICAL MODIFICATION; CHEMICAL REACTION; DNA DENATURATION; DNA RNA HYBRIDIZATION; FLUORESCENCE SPECTROSCOPY; HYBRIDIZATION; SYNTHESIS; TEMPERATURE; BASE PAIRING; CHEMISTRY; CONFORMATION; DNA PROBE; METHODOLOGY; NUCLEIC ACID HYBRIDIZATION; RNA PROBE; SPECTROFLUOROMETRY;

BASE PAIRING; DNA; DNA PROBES; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDES; PYRENES; RNA; RNA PROBES; SPECTROMETRY, FLUORESCENCE; TRIAZOLES;

EID: 84855566199     PISSN: 00223263     EISSN: 15206904     Source Type: Journal    
DOI: 10.1021/jo201845z     Document Type: Article

References (74)

1. Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. Angew. Chem., Int. Ed. 2002, 41, 2596-2599
2. Tornøe, C. W.; Christensen, C.; Meldal, M. J. Org. Chem. 2002, 67, 3057-3064
3. Amblard, F.; Cho, J. H.; Schinazi, R. F. Chem. Rev. 2009, 109, 4207-4220
4. Ustinov, A. V.; Stepanova, I. A.; Dubnyakova, V. V.; Zatsepin, T. S.; Nozhevnikova, E. V.; Korshun, V. A. Russ. J. Bioorg. Chem. 2010, 36, 437-481
5. El-Sagheer, A. H.; Brown, T. Chem. Soc. Rev. 2010, 39, 1388-1405
6. Seo, T. S.; Li, Z.; Ruparel, H.; Ju, J. J. Org. Chem. 2003, 68, 609-612
7. Gierlich, J.; Burley, G. A.; Gramlich, P. M. E.; Hammond, D. M.; Carell, T. Org. Lett. 2006, 8, 3339-3342
8. Seela, F.; Sirivolu, V. R.; Chittepu, P. Bioconjugate Chem. 2008, 19, 211-224
9. Seela, F.; Ming, X. Helv. Chim. Acta 2008, 91, 1181-1200
10. Berndl, S.; Herzig, N.; Kele, P.; Lachmann, D.; Li, X.; Wolfbeis, O. S.; Wagenknecht, H.-A. Bioconjugate Chem. 2009, 20, 558-564
11. Seela, F.; Ingale, S. A. J. Org. Chem. 2010, 75, 284-295
12. Ding, P.; Wunnicke, D.; Steinhoff, H.-J.; Seela, F. Chem.-Eur. J. 2010, 16, 14385-14396
13. Jakobsen, U.; Shelke, S. A; Vogel, S.; Sigurdsson, S. T. J. Am. Chem. Soc. 2010, 132, 10424-10428
14. Onizuka, K.; Shibata, A.; Taniguchi, Y.; Sasaki, S. Chem. Commun. 2011, 47, 5004-5006
15. Kuboyama, T.; Nakahara, M.; Yoshino, M.; Cui, Y.; Sako, T.; Wada, Y.; Imanishi, T.; Obika, S.; Watanabe, Y.; Suzuki, M.; Doi, H. Bioorg. Med. Chem. 2011, 19, 249-255
16. Mercier, F.; Paris, J.; Kaisin, G.; Thonon, D.; Flagothier, J.; Teller, N.; Lemaire, C.; Luxen, A. Bioconjugate Chem. 2011, 22, 108-114
17. Burley, G. A.; Gierlich, J.; Mofid, M. R.; Nir, H.; Tal, S.; Eichen, Y.; Carell, T. J. Am. Chem. Soc. 2006, 128, 1398-1399
18. Kumar, R.; El-Sagheer, A.; Tumpane, J.; Lincoln, P.; Wilhelmsson, L. M.; Brown, T. J. Am. Chem. Soc. 2007, 129, 6859-6864
19. Xiong, H.; Seela, F. J. Org. Chem. 2011, 76, 5584-5597
20. Isobe, H.; Fujino, T.; Yamazaki, N.; Guillot-Nieckowski, M.; Nakamura, E. Org. Lett. 2008, 10, 3729-3732
21. Mutisya, D.; Selvam, C.; Kennedy, S. D.; Rozners, E. Bioorg. Med. Chem. Lett. 2011, 21, 3420-3422
22. El-Sagheer, A. H.; Brown, T. Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 15329-15334
23. Chittepu, P.; Sirivolu, V. R.; Seela, F. Bioorg. Med. Chem. 2008, 16, 8427-8439
24. Nakahara, M.; Kuboyama, T.; Izawa, A.; Hari, Y.; Imanishi, T.; Obika, S. Bioorg. Med. Chem. Lett. 2009, 19, 3316-3319
25. Østergaard, M. E.; Guenther, D. C.; Kumar, P.; Baral, B.; Deobald, L.; Paszczynski, A. J.; Sharma, P. K.; Hrdlicka, P. J. Chem. Commun. 2010, 46, 4929-4931
26. Kumar, T. S.; Wengel, J.; Hrdlicka, P. J. ChemBioChem 2007, 8, 1122-1125
27. Østergaard, M. E.; Kumar, P.; Baral, B.; Guenther, D. C.; Anderson, B. A; Ytreberg, F. M.; Deobald, L.; Paszczynski, A. J.; Sharma, P. K.; Hrdlicka, P. J. Chem.-Eur. J. 2011, 17, 3157-3165
28. Østergaard, M. E.; Hrdlicka, P. J. Chem. Soc. Rev. 2011, DOI: 10.1039/C1CS15014F.
29. Østergaard, M. E.; Cheguru, P.; Papasani, M. R.; Hill, R. A.; Hrdlicka, P. J. J. Am. Chem. Soc. 2010, 132, 14221-14228
30. Kumar, T. S.; Madsen, A. S.; Østergaard, M. E.; Wengel, J.; Hrdlicka, P. J. J. Org. Chem. 2008, 73, 7060-7066
31. Kumar, T. S.; Madsen, A. S.; Østergaard, M. E.; Sau, S. P.; Wengel, J.; Hrdlicka, P. J. J. Org. Chem. 2009, 74, 1070-1081
32. Sau, S. P.; Kumar, T. S.; Hrdlicka, P. J. Org. Biomol. Chem. 2010, 8, 2028-2036
33. Karmakar, S.; Anderson, B. A.; Rathje, R. L.; Andersen, S.; Jensen, T.; Nielsen, P.; Hrdlicka, P. J. J. Org. Chem. 2011, 76, 7119-7131
34. Yamana, K.; Iwase, R.; Furutani, S.; Tsuchida, H.; Zako, H.; Yamaoka, T.; Murakami, A. Nucleic Acids Res. 1999, 27, 2387-2392
35. Nakamura, M.; Fukunaga, Y.; Sasa, K.; Ohtoshi, Y.; Kanaori, K.; Hayashi, H.; Nakano, H.; Yamana, K. Nucleic Acids Res. 2005, 33, 5887-5895
36. Kalra, N.; Babu, B. R.; Parmar, V. S.; Wengel, J. Org. Biomol. Chem. 2004, 2, 2885-2887
37. Jawalekar, A. M.; Meeuwenoord, N.; Cremers, J. S. G. O.; Overkleeft, H. S.; Marel, G. A. V. D.; Rutjes, F. P. J. T.; Delft, F. L. V. J. Org. Chem. 2008, 73, 287-290
38. Jørgensen, A. S.; Shaikh, K. I.; Enderlin, G.; Ivarsen, E.; Kumar, S.; Nielsen, P. Org. Biomol. Chem. 2011, 9, 1381-1388
39. Kiviniemi, A.; Virta, P.; Drenichev, M. S.; Mikhailov, S. N.; Lönnberg, H. Bioconjugate Chem. 2011, 22, 1249-1255
40. Patil, R. V.; Dekker, E. E. Nucleic Acids Res. 1990, 18, 3080-3080
41. Nichols, R.; Andrews, P. C.; Zhang, P.; Bergstrom, D. E. Nature 1994, 369, 492-493
42. Loakes, D.; Brown, D. M.; Linde, S.; Hill, F. Nucleic Acids Res. 1995, 23, 2361-2366
43. Chizhikov, V.; Wagner, M.; Ivshina, A.; Hoshino, Y.; Kapikian, A. Z.; Chumakov, K. J. Clin. Microbiol. 2002, 40, 2398-2407
44. Too, K.; Loakes, D. Universal Base Analogues and their Application to Biotechnology. In Modified Nucleosides: In Biochemistry, Biotechnology and Medicine, Herdewijn, P., Ed.; Wiley-VCH: Weinheim, Germany, 2008; pp 277-303.
45. Loakes, D.; Brown, D. M. Nucleic Acids Res. 1994, 22, 4039-4043
46. Berger, M.; Wu, Y.; Ogawa, A. K.; McMinn, D. L.; Schultz, P. G.; Romesberg, F. E. Nucleic Acids Res. 2000, 28, 2911-2914
47. Matray, T. J.; Kool, E. T. J. Am. Chem. Soc. 1998, 120, 6191-6192
48. Babu, B. R.; Wengel, J. Chem. Commun. 2001, 2114-2115
49. Raunak; Babu, B. R.; Parmar, V. S.; Harrit, N. H.; Wengel, J. Org. Biomol. Chem. 2004, 2, 80-89
50. MacKinnon, K. F.; Qualley, D. F.; Woski, S. A. Tetrahedron Lett. 2007, 48, 8074-8077
51. Seela, F.; Chen, Y. Nucleic Acids Res. 1995, 23, 2499-2505
52. Acedo, M.; De Clercq, E.; Eritja, R. J. Org. Chem. 1995, 60, 6262-6269
53. Cubero, E.; Güimil-García, R.; Luque, F. J.; Eritja, R.; Orozco, M. Nucleic Acids Res. 2001, 29, 2522-2534
54. Seela, F.; Debelak, H. Nucleic Acids Res. 2000, 28, 3224-3232
55. Koller, A. N.; Bozilovic, J.; Engels, J. W.; Gohlke, H. Nucleic Acids Res. 2010, 38, 3133-3146
56. For a successful example, see: Köhler, O.; Jarikote, D. V.; Seitz, O. ChemBioChem 2005, 6, 69-77
57. Patra, A.; Richert, C. J. Am. Chem. Soc. 2009, 131, 12671-12681
58. Trybulski, E. J.; Zhang, J.; Kramss, R. H.; Mangano, R. M. J. Med. Chem. 1993, 36, 3533-3541
59. Liu, F.; Tang, C.; Chen, Q.-Q.; Li, S.-Z.; Wu, H.-B.; Xie, L.-H.; Peng, B.; Wei, W.; Cao, Y.; Huang, W. Org. Electron. 2009, 10, 256-265
60. Okamoto, A.; Kanatani, K.; Saito, I. J. Am. Chem. Soc. 2004, 126, 4820-4827
61. Sanghvi, Y. S.; Hoke, G. D.; Freier, S. M.; Zounes, M. C.; Gonzalez, C.; Cummins, L.; Sasmor, H.; Cook, P. D. Nucleic Acids Res. 1993, 21, 3197-3203
62. Oliver, J. S.; Parker, K. A.; Suggs, J. W. Org. Lett. 2001, 3, 1977-1980
63. Millican, T. A.; Mock, G. A.; Chauncey, M. A.; Patel, T. P.; Eaton, M. A. W.; Gunning, J.; Cutbush, S. D.; Neidle, S.; Mann, J. Nucleic Acids Res. 1984, 12, 7435-7453
64. Langenegger, S. M.; Häner, R. ChemBioChem 2005, 6, 848-851
65. Nakano, S.; Uotani, Y.; Uenishi, K.; Fujii, M.; Sugimoto, N. Nucleic Acids Res. 2005, 33, 7111-7119
66. Verhagen, C.; Bryld, T.; Raunkjær, M.; Vogel, S.; Buchalová, K.; Wengel, J. Eur. J. Org. Chem. 2006, 2538-2548
67. Dougherty, G.; Pilbrow, J. R. Int. J. Biochem. 1984, 16, 1179-1192
68. Manoharan, M.; Tivel, K. L.; Zhao, M.; Nafisi, K.; Netzel, T. L. J. Phys. Chem. 1995, 99, 17461-1747
69. Seo, Y. J.; Ryu, J. H.; Kim, B. H. Org. Lett. 2005, 7, 4931-4933
70. Jiang, Y. L.; Kwon, K.; Stivers, J. T. J. Biol. Chem. 2001, 276, 42347-42354
71. Beuck, C.; Singh, I.; Bhattacharya, A.; Hecker, W.; Parmar, V. S.; Seitz, O.; Weinhold, E. Angew. Chem., Int. Ed. 2003, 42, 3958-3960
72. Fleming, D. A.; Thode, C. J.; Williams, M. E. Chem. Mater. 2006, 18, 2327-2334
73. Morris, J. V.; Mahaney, M. A.; Huber, J. R. J. Phys. Chem. 1976, 80, 969-974
74. Melhuish, W. H. J. Phys. Chem. 1961, 65, 229-235