Triazolyl donor/acceptor chromophore decorated unnatural nucleosides and oligonucleotides with duplex stability comparable to that of a natural adenine/thymine pair

Journal of Organic Chemistry

Volumn 78, Issue 2, 2013, Pages 278-291

  Bag, Subhendu Sekhar ^a   Talukdar, Sangita ^a   Matsumoto, Katsuhiko ^b   Kundu, Rajen ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY GUWAHATI   (India)

^b KYOTO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

CHARGE TRANSFER INTERACTION; CLICK CHEMISTRY; DUPLEX STABILITY; STATIC QUENCHING; UV-VIS SPECTRA;

BIOMOLECULES; CHARGE TRANSFER; NUCLEIC ACIDS; OLIGONUCLEOTIDES; STABILIZATION;

CHROMOPHORES;

ADENINE; NUCLEOSIDE; OLIGONUCLEOTIDE; THYMINE; TRIAZOLE DERIVATIVE;

ARTICLE; BASE PAIRING; CHEMICAL INTERACTION; CHROMATOPHORE; CLICK CHEMISTRY; COMPLEX FORMATION; DNA STRUCTURE; FLUORESCENCE; PROTON TRANSPORT; SYNTHESIS; ULTRAVIOLET RADIATION;

ADENINE; BASE PAIRING; CLICK CHEMISTRY; DNA; FLUORESCENCE; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOSIDES; OLIGONUCLEOTIDES; THYMINE; TRIAZOLES;

EID: 84872579497     PISSN: 00223263     EISSN: 15206904     Source Type: Journal    
DOI: 10.1021/jo302033f     Document Type: Article

References (121)

1. McLaughlin, L. W.; Wilson, M.; Ha, S. B. Use of Nucleoside Analogues To Probe Biochemical Processes. In Comprehensive Natural Product Chemistry, Vol. 7, DNA and Aspects of Molecular Biology; Barton, D. H. R., Nakanishi, K., Meth-Cohn, O., Eds.; Elsevier: New York, 1999; pp 252-284.
2. Kool, E. T.; Morales, J. C.; Guckian, K. M. Angew. Chem., Int. Ed. 2000, 39, 990
3. Kool, E. T. Acc. Chem. Res. 2002, 35, 936
4. Geyer, C. R.; Battersby, T. R.; Benner, S. A. Structure 2003, 11, 1485
5. Benner, S. A. Nature 2003, 421, 118
6. Benner, S. A.; Sismour, A. M. Nat. Rev. Genet. 2005, 6, 533
7. Kimoto, M.; Cox, R. S., 3rd.; Hirao, I. Expert Rev. Mol. Diagn. 2011, 3, 321
8. Hirao, I.; Kimoto, M.; Yamashige, R. Acc. Chem. Res. [Online early access]. DOI: 10.1021/ar200257x. Published Online: Jan 20, 2012. http://pubs.acs.org/doi/abs/10.1021%2Far200257x, accessed 11/4/2012.
9. Piccirilli, J. A.; Krauch, T.; Moroney, S. E.; Benner, S. A. Nature 1990, 343, 33
10. Yang, Z.; Hutter, D.; Sheng, P.; Sismour, A. M.; Benner, S. A. Nucleic Acids Res. 2006, 34, 6095
11. Hirao, I.; Kimoto, M.; Mitsui, T.; Fujiwara, T.; Kawai, R.; Sato, A.; Harada, Y.; Yokoyama, S. Nat. Methods 2006, 3, 729
12. Doi, Y.; Chiba, J.; Morikawa, T.; Inouye, M. J. Am. Chem. Soc. 2008, 130, 8762
13. Delaney, J. C.; Gao, J.; Liu, H.; Shrivastav, N.; Essigmann, J. M.; Kool, E. T. Angew. Chem., Int. Ed. 2009, 48, 4524
14. Kim, H.-J.; Chen, F.; Benner, S. A. J. Org. Chem. 2012, 77, 3664
15. Smith, S. A.; Rajur, S. B.; McLaughlin, L. W. Nat. Struct. Biol. 1994, 1, 198
16. Lesser, D. R.; Kurpiewski, M. R.; Jen-Jacobson, L. Science 1990, 250, 776
17. Kornberg, A.; Baker, T. A. DNA Replication, 2 nd ed.; W. H. Freeman: New York, 1992.
18. Echols, H.; Goodman, M. F. Annu. Rev. Biochem. 1991, 60, 477
19. Strazewski, P.; Tamm, C. Angew. Chem., Int. Ed. Engl. 1990, 29, 36
20. Seo, Y. J.; Matsuda, S.; Romesberg, F. E. J. Am. Chem. Soc. 2009, 131, 5046
21. Teo, Y. N.; Wilson, J. N.; Kool, E. T. J. Am. Chem. Soc. 2009, 131, 3923
22. Kempe, T.; Sundquist, W. I.; Chow, F.; Hu, S. L. Nucleic Acids Res. 1985, 13, 45
23. Zischler, H.; Nanda, I.; Schafer, R.; Schmid, M.; Epplen, J. T. Hum. Genet. 1989, 82, 227
24. Hustedt, E. J.; Spaltenstein, A.; Kirchner, J. J.; Hopkins, P. B.; Robinson, B. H. Biochemistry 1993, 32, 1774
25. Haugland, R. P. The Handbook: A Guide to Fluorescent Probes and Labeling Technologies; Molecular Probes: Carlsbad, CA, 2005.
26. Okamoto, A.; Saito, Y.; Saito, I. J. Photochem. Photobiol., C 2005, 6, 108
27. Bag, S. S.; Kundu, R.; Matsumoto, K.; Saito, Y.; Saito, I. Bioorg. Med. Chem. Lett. 2010, 20, 3227
28. Teo, Y. N.; Kool, E. T. Chem. Rev. 2012, 112, 4221
29. Schweitzer, B. A.; Kool, E. T. J. Am. Chem. Soc. 1995, 117, 1863
30. Kool, E. T. Annu. Rev. Biochem. 2002, 71, 191
31. Seo, Y. J.; Matsuda, S.; Romesberg, F. E. J. Am. Chem. Soc. 2009, 131, 5046
32. Jarchow-Choy, S. K.; Sjuvarsson, E.; Sintim, H. O.; Eriksson, S.; Kool, E. T. J. Am. Chem. Soc. 2009, 131, 5488
33. Nakano, S.-i.; Fujii, M.; Sugimoto, N. J. Nucleic Acids [Online] 2011, Article 967098. DOI: 10.4061/2011/967098. http://www.hindawi.com/journals/jna/ 2011/967098/, accessed 11/4/2012.
34. Chen, F.; Yang, Z.; Yan, M.; Alvarado, J. B.; Wang, G.; Benner, S. A. Nucleic Acids Res. 2011, 39, 3949
35. Lavergne, T.; Malyshev, D. A.; Romesberg, F. E. Chem.-Eur. J. 2012, 18, 1231
36. Wojciechowski, F.; Leumann, C. J. Chem. Soc. Rev. 2011, 40, 5669
37. Grigorenko, N. A.; Leumann, C. J. Chem.-Eur. J. 2009, 15, 639
38. Wilson, J. N.; Teo, Y. N.; Kool, E. T. J. Am. Chem. Soc. 2007, 129, 15426
39. Robertson, N.; McGowan, C. A. Chem. Soc. Rev. 2003, 32, 96
40. Keren, K.; Krueger, M.; Gilad, R.; Ben-Yoseph, G.; Sivan, U.; Braun, E. Science 2002, 297, 72
41. Hall, D. B.; Holmlin, R. E.; Barton, J. K. Nature 1996, 382, 731
42. Liu, J.; Cao, Z.; Lu, Y. Chem. Rev. 2009, 109, 1948
43. Drummond, T. G.; Hill, M. G.; Barton, J. K. Nat. Biotechnol. 2003, 21, 1192
44. Kolpashchikov, D. M.; Gerasimova, Y. V.; Khan, M. S. ChemBioChem 2011, 12, 2564
45. Liu, L.; Li, Y.; Liotta, D.; Lutz, S. Nucleic Acids Res. 2009, 37, 4472
46. Stambasky, J.; Hocek, M.; Kouovsky, P. Chem. Rev. 2009, 109, 6729 and references therein
47. Kool, E. T. Acc. Chem. Res. 2002, 35, 936
48. Tor, Y.; Dervan, P. B. J. Am. Chem. Soc. 1993, 115, 4461
49. Clever, G. H.; Kaul, C.; Carell, T. Angew. Chem., Int. Ed. 2007, 46, 6226
50. Rostovtsev, V. V.; Green, L. G.; Fokin, V. V.; Sharpless, K. B. Angew. Chem., Int. Ed. 2002, 41, 2596
51. El-Sagheer, A. H.; Brown, T. Chem. Soc. Rev. 2010, 39, 1388
52. Marks, I. S.; Kang, J. S.; Jones, B. T.; Landmark, K. J.; Cleland, A. J.; Taton, T. A. Bioconjugate Chem. 2011, 22, 1259
53. Xiong, H.; Seela, F. J. Org. Chem. 2011, 76, 5584
54. Xiong, H.; Leonard, P.; Seela, F. Bioconjugate Chem. 2012, 23, 856
55. Sau, S. P.; Hrdlicka, P. J. J. Org. Chem. 2012, 77, 5
56. Ren, R. X.-F.; Chaudhuri, N. C.; Paris, P. L.; Rumney, S., IV; Eric T. Kool, E. T. J. Am. Chem. Soc. 1996, 118, 7671
57. Cahová, H.; Havran, L.; Brázdilová, P.; Pivoňková, H.; Pohl, R.; Fojta, M.; Hocek, M. Angew. Chem., Int. Ed. 2008, 47, 2059
58. Amblard, F.; Cho, J. H.; Schinazi, R. F. Chem. Rev. 2009, 109, 4207
59. Bag, S. S.; Kundu, R. J. Org. Chem. 2011, 76, 3348
60. Angell, Y. L.; Burgess, K. Chem. Soc. Rev. 2007, 36, 1674
61. Moses, J. E.; Moorhouse, A. D. Chem. Soc. Rev. 2007, 36, 1249
62. Tron, G. C.; Pirali, T.; Billington, R. A.; Canonico, P. L.; Sorba, G.; Genazzani, A. A. Med. Res. Rev. 2008, 28, 278
63. Hein, C. D.; Liu, X.-M.; Wang, D. Pharm. Res. 2008, 25, 2216
64. New, K.; Brechbiel, M. W. Cancer Biother. Radiopharm. 2009, 24, 289
65. Frisch, B.; Hassane, F. S.; Schuber, F. Methods Mol. Biol. 2010, 605, 267
66. Agalave, S. G.; Maujan, S. R.; Pore, V. S. Chem.-Asian. J. 2011, 6, 2696
67. Mulliken, R. S. J. Am. Chem. Soc. 1952, 74, 811
68. Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem. 1996, 100, 5541
69. Poulin, K. W.; Smirnov, A. V.; Hawkins, M. E.; Balis, F. M.; Knutson, J. R. Biochemistry 2009, 48, 8861
70. Wierzbinski, E.; de Leon, A.; Davis, K. L.; Bezer, S.; Wolak, M. A.; Kofke, M. J.; Schlaf, R.; Achim, C.; Waldeck, D. H. Langmuir 2012, 28, 1971
71. Hervas, M.; Navarro, J. A.; De la Rosa, M. A. Acc. Chem. Res. 2003, 36, 798
72. Berlin, Y. A.; Grozema, F. C.; Siebbeles, L. D. A.; Ratner, M. A. J. Phys. Chem. C 2008, 112, 10988
73. Morrison, L. E.; Stols, L. M. Biochemistry 1993, 32, 3095
74. Marras, S. A. E.; Kramer, F. R.; Tyagi, S. Nucleic Acids Res. 2002, 30, e122
75. Li, Q.; Luan, G.; Guo, Q.; Liang, J. Nucleic Acids Res. 2002, 30, e5
76. Nazarenko, I.; Pires, R.; Lowe, B.; Obaldy, M.; Rashtchian, A. Nucleic Acids Res. 2002, 30, 2089
77. Johansson, M. K.; Fidder, H.; Dick, D.; Cook, R. M. J. Am. Chem. Soc. 2002, 124, 6950
78. Eftink, M. R. Fluorescence Quenching: Theory and Applications. In Topics in Fluorescence Spectroscopy; Lakowicz, J. R., Ed.; Plenum Press: New York, 2002; Vol. 2, pp 53-126.
79. You, Y.; Tataurov, A. V.; Owczarzy, R. Biopolymers 2011, 95, 472
80. Moreira, B. G.; You, Y.; Behlke, M. A.; Owczarzy, R. Biochem. Biophys. Res. Commun. 2005, 327, 473
81. Kimoto, M.; Mitsui, T.; Yamashige, R.; Sato, A.; Yokoyama, S.; Hirao, I. J. Am. Chem. Soc. 2010, 132, 15418
82. Bag, S. S.; Kundu, R.; Matsumoto, K.; Saito, Y.; Saito, I. Bioorg. Med. Chem. Lett. 2010, 20, 3227
83. Sinkeldam, R. W.; Greco, N. J.; Tor, Y. Chem. Rev. 2010, 110, 2579
84. Chen, D.-W.; Beuscher, A. E., IV; Stevens, R. C.; Wirsching, P.; Lerner, R. A.; Janda, K. D. J. Org. Chem. 2001, 66, 1725
85. Štimac, A.; Leban, I.; Kobe, J. Synlett 1999, 1069
86. Štimac, A.; Kobe, J. Carbohydr. Res. 2000, 329, 317
87. Guezguez, R.; Bougrin, K.; Akri, K. E.; Benhida, R. Tetrahedron Lett. 2006, 47, 4807
88. Chittepu, P.; Sirivolu, V. R.; Seela, F. Bioorg. Med. Chem. 2008, 16, 8427
89. Malnuit, V.; Duca, M.; Manout, A.; Bougrin, K.; Benhida, R. Synlett 2009, 2123
90. Kolganova, N. A.; Florentiev, V. L.; Chudinov, A. V.; Zasedatelev, A. S.; Timofeev, E. N. Chem. Biodiversity 2011, 8, 568
91. te Velde, G.; Bickelhaupt, F. M.; van Gisbergen, S. J. A.; Guerra, C. F.; Baerends, E. J.; Snijders, J. G.; Ziegler, T. J. Comput. Chem. 2001, 22, 931
92. Guerra, C. F.; Snijders, J. G.; te Velde, G.; Baerends, E. J. Theor. Chem. Acc. 1998, 99, 391
93. ADF2010, Scientific Computing and Modelling, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands, http://www.scm.com, accessed 7/6/2011.
94. Grimme, S. J. Comput. Chem. 2004, 25, 1463-1473
95. Grimme, S. J. Comput. Chem. 2006, 27, 1787
96. van der Wijst, T.; Lippert, B.; Swart, M.; Guerra, C. F.; Bickelhaupt, F. M. J. Biol. Inorg. Chem. 2010, 15, 387
97. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 09, revision A.1; Gaussian, Inc.: Wallingford, CT, 2009.
98. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 364
99. Zhao, Y.; Truhlar, D. G. Acc. Chem. Res. 2008, 41, 157
100. Zhao, Y.; Truhlar, D. G. J. Chem. Phys. 2006, 125, 194101
101. Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 289
102. Boys, S. F.; Bernardi, F. Mol. Phys. 1970, 19, 553
103. Biegler König, F. W.; Schöbohm, J.; Bayles, D. J. Comput. Chem. 2001, 22, 545
104. Robertazzi, A.; Platts, J. A. J. Phys. Chem. A 2006, 110, 3992
105. Swart, M.; van der Wijst, T.; Guerra, C. F.; Bickelhaupt, F. M. J. Mol. Model. 2007, 13, 1245
106. Gao, J. Acc. Chem. Res. 1996, 29, 298
107. Monard, G.; Merz, K. M., Jr. Acc. Chem. Res. 1999, 32, 904
108. Svensson, M.; Humbel, S.; Froese, R. D. J.; Matsubara, T.; Sieber, S.; Morokuma, K. J. Phys. Chem. 1996, 100, 19357
109. Kosugi, T.; Hayashi, S. J. Chem. Theory Comput. 2012, 8, 322
110. Zimmermann, N.; Meggers, E.; Schultz, P. G. J. Am. Chem. Soc. 2002, 124, 13684
111. Atwell, S.; Meggers, E.; Spraggon, G.; Schultz, P. G. J. Am. Chem. Soc. 2001, 123, 12364
112. Takezawa, Y.; Shionoya, M. Acc. Chem. Res. [Online early access]. DOI: 10.1021/ar200313h. Published Online: March 27, 2012. http://pubs.acs.org/doi/ abs/10.1021%2Far200313h, accessed 11/4/2012.
113. Matsuda, S.; Fillo, J. D.; Henry, A. A.; Rai, P.; Wilkens, S. J.; Dwyer, T. J.; Geierstanger, B. H.; Wemmer, D. E.; Schultz, P. G.; Spraggon, G.; Romesberg, F. E. J. Am. Chem. Soc. 2007, 129, 10466
114. Malyshev, D. A.; Pfaff, D. A.; Ippoliti, S. I.; Hwang, G. T.; Dwyer, T. J.; Romesberg, F. E. Chemistry 2010, 16, 12650
115. Bugg, C. E. In Solid-State Packing Patterns of Purine Bases; Bergmann, E. D.; Pullman, B., Eds.; The Israel Academy of Sciences and Humanities: Jerusalem, 1971; pp 178-204.
116. Loeb, L. A.; Preston, B. D. Annu. Rev. Genet. 1986, 20, 201
117. Valis, L.; Amann, N.; Wagenknecht, H.-A. Org. Biomol. Chem. 2005, 3, 36
118. Greco, N. J.; Tor, Y. J. Am. Chem. Soc. 2005, 127, 10784
119. Berthet, N.; Constant, J. F.; Demeunynck, M.; Michon, P.; Lhomme, J. J. Med. Chem. 1997, 40, 3346
120. Lhomme, J.; Constant, J. F.; Demeunynck, M. Biopolymers 1999, 52, 65
121. Yoshimoto, K.; Nishizawa, S.; Minagawa, M.; Teramae, N. J. Am. Chem. Soc. 2003, 125, 8982