Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation

ChemBioChem

Volumn 16, Issue 1, 2015, Pages 167-176

  Kanamori, Takashi ^a   Ohzeki, Hiroki ^a   Masaki, Yoshiaki ^a   Ohkubo, Akihiro ^a   Takahashi, Mari ^b   Tsuda, Kengo ^b   Ito, Takuhiro ^b   Shirouzu, Mikako ^b   Kuwasako, Kanako ^b,c   Muto, Yutaka ^b,c   Sekine, Mitsuo ^a   Seio, Kohji ^a  

^a TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^b RIKEN   (Japan)

^c MUSASHINO UNIVERSITY   (Japan)

Author keywords

DNA structures; Fluorescent probes; NMR spectroscopy; RNA; Sensors

Indexed keywords

5 (BENZOFURAN 2 YL)DEOXYURIDINE; ACETIC ACID ETHYL ESTER; ACETONITRILE; BENZOFURAN DERIVATIVE; METHANOL; OLIGONUCLEOTIDE; RNA; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; URACIL; WATER; BENZOFURAN; DEOXYURIDINE; DNA; FLUORESCENT DYE; TRIPLEX DNA;

ARTICLE; CHEMICAL MODIFICATION; CONFORMATIONAL TRANSITION; FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; PHOTOCHEMISTRY; SOLVENT EFFECT; SUZUKI REACTION; TRIPLE HELIX; VISCOSITY; ANALOGS AND DERIVATIVES; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SPECTROFLUOROMETRY;

BASE SEQUENCE; BENZOFURANS; DEOXYURIDINE; DNA; DNA, SINGLE-STRANDED; FLUORESCENT DYES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; RNA; SPECTROMETRY, FLUORESCENCE; URACIL;

EID: 84919779002     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.201402346     Document Type: Article

References (73)

1. M. J. Rist, J. P. Marino, Curr. Org. Chem. 2002, 6, 775-793.
2. A. Okamoto, Y Saito, I. Saito, J. Photochem. Photobiol. C 2005, 6, 108-122.
3. R. T. Ranasinghe, T. Brown, Chem. Commun. 2005, 5487-5502.
4. J. N. Wilson, E. T. Kool, Org. Biomol. Chem. 2006, 4, 4265-4274.
5. L. M. Wilhelmsson, Q. Rev. Biophys. 2010, 43, 159-183.
6. R. W. Sinkeldam, N.J. Greco, Y Tor, Chem. Rev. 2010, 110, 2579-2619.
7. A. S. Boutorine, D. S. Novopashina, O. A. Krasheninina, K. Nozeret, A. G. Venyaminova, Molecules 2013, 18, 15357-15397.
8. A.A. Tanpure, M. G. Pawar, S. G. Srivatsan, Isr. J. Chem. 2013, 53, 366-378.
9. S. Tyagi, F. R. Kramer, Nat. Biotechnol. 1996, 14, 303-308.
10. Y Hara, T. Fujii, H. Kashida, K. Sekiguchi, X. Liang, K. Niwa, T. Takase, Y Yoshida, H. Asanuma, Angew. Chem. Int. Ed. 2010, 49, 5502-5506
11. Angew. Chem. 2010, 122, 5634-5638.
12. A. Okamoto, Chem. Soc. Rev. 2011, 40, 5815-5828.
13. O. Seitz, F. Bergmann, D. Heindl, Angew. Chem. Int. Ed. 1999, 38, 2203-2206
14. Angew. Chem. 1999, 111, 2340-2343.
15. E. Socher, L. Bethge, A. Knoll, N. Jungnick, A. Herrmann, O. Seitz, Angew. Chem. Int. Ed. 2008, 47, 9555-9559
16. Angew. Chem. 2008, 120, 9697-9701.
17. S. Kummer, A. Knoll, E. Socher, L. Bethge, A. Herrmann, O. Seitz, Angew. Chem. Int. Ed. 2011, 50, 1931-1934
18. Angew. Chem. 2011, 123, 1972-1975.
19. F. Hövelmann, I. Gaspar, A. Ephrussi, O. Seitz, J. Am. Chem. Soc. 2013, 135, 19025-19032.
20. I. Géci, V. V. Filichev, E. B. Pedersen, Chem. Eur. J. 2007, 13, 6379-6386.
21. O. Doluca, T. K. Hale, P. J.B. Edwards, C. Gonzalez, V. V. Filichev, ChemPlusChem 2014, 79, 58-66.
22. L. M. Wilhelmsson, A. Holmen, P. Lincoln, P. E. Nielsen, B. Norden, J. Am. Chem. Soc. 2001, 123, 2434-2435.
23. L. M. Wilhelmsson, P. Sandin, A. Holmen, B. Albinsson, P. Lincoln, B. Norden, J. Phys. Chem. B 2003, 107, 9094-9101.
24. A. Okamoto, K. Tainaka, I. Saito, Tetrahedron Lett. 2003, 44, 6871-6874.
25. S. G. Srivatsan, Y Tor, J. Am. Chem. Soc. 2007, 129, 2044-2053.
26. K. Miyata, R. Mineo, R. Tamamushi, M. Mizuta, A. Ohkubo, H. Taguchi, K. Seio, T. Santa, M. Sekine, J. Org. Chem. 2007, 72, 102-108.
27. M. Mizuta, K. Seio, K. Miyata, M. Sekine, J. Org. Chem. 2007, 72, 5046-5055.
28. M. Mizuta, K. Seio, K. Miyata, A. Ohkubo, H. Taguchi, M. Sekine, Nucleosides Nucleotides Nucleic Acids 2007, 26, 1335-1338.
29. O. Nakagawa, S. Ono, Z. Li, A. Tsujimoto, S. Sasaki, Angew. Chem. Int. Ed. 2007, 46, 4500-4503
30. Angew. Chem. 2007, 119, 4584-4587.
31. P. Sandin, G. Stengel, T. Ljungdahl, K. Börjesson, B. Macao, L. M. Wilhelmsson, Nucleic Acids Res. 2009, 37, 3924-3933.
32. K. Börjesson, S. Preus, A. H. El-Sagheer, T. Brown, B. Albinsson, L. M. Wilhelmsson, J. Am. Chem. Soc. 2009, 131, 4288-4293.
33. M. Mizuta, K. Seio, A. Ohkubo, M. Sekine, J. Phys. Chem. B 2009, 113, 9562-9569.
34. R.W. Sinkeldam, A.J. Wheat, H. Boyaci, Y. Tor, ChemPhysChem 2011, 12, 567-570.
35. R.W. Sinkeldam, P. Marcus, D. Uchenik, Y Tor, ChemPhysChem 2011, 12, 2260-2265.
36. A. A. Tanpure, S. G. Srivatsan, Chem. Eur. J. 2011, 17, 12820-12827.
37. M. G. Pawar, S. G. Srivatsan, Org. Lett. 2011, 13, 1114-1117.
38. W. Hirose, K. Sato, A. Matsuda, Eur. J. Org. Chem. 2011, 6206-6217.
39. J. Riedl, R. Pohl, L. Rulíšek, M. Hocek, J. Org. Chem. 2012, 77, 1026-1044.
40. A. A. Tanpure, S. G. Srivatsan, ChemBioChem 2012, 13, 2392-2399.
41. R.W. Sinkeldam, P.A. Hopkins, Y Tor, ChemPhysChem 2012, 13, 3350-3356.
42. M.S. Noé, R. W. Sinkeldam, Y Tor, J. Org. Chem. 2013, 78, 8123-8128.
43. M. Mizuta, J.-i. Banba, T. Kanamori, R. Tawarada, A. Ohkubo, M. Sekine, K. Seio, J. Am. Chem. Soc. 2008, 130, 9622-9623.
44. T. Kanamori, Y Masaki, M. Mizuta, H. Tsunoda, A. Ohkubo, M. Sekine, K. Seio, Org. Biomol. Chem. 2012, 10, 1007-1013.
45. G. Barbarella, M. Zambianchi, L. Antolini, P. Ostoja, P. Maccagnani, A. Bongini, E. A. Marseglia, E. Tedesco, G. Gigli, R. Cingolani, J. Am. Chem. Soc. 1999, 121, 8920-8926.
46. S. S. Zade, M. Bendikov, Chem. Eur. J. 2007, 13, 3688-3700.
47. N. Amdursky, Y Erez, D. Huppert, Acc. Chem. Res. 2012, 45, 1548-1557.
48. Gaussian 09, Revision A.1, M.J. Frisch, G.W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G. A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H. P. Hratchian, A. F. Izmaylov, J. Bloino, G. Zheng, J. L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, Jr., J. E. Peralta, F. Ogliaro, M. Bearpark, J. J. Heyd, E. Brothers, K. N. Kudin, V. N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J. C. Burant, S. S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J. M. Millam, M. Klene, J. E. Knox, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, R. L. Martin, K. Morokuma, V. G. Zakrzewski, G. A. Voth, P. Salvador, J. J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.
49. J. Tomasi, B. Mennucci, R. Cammi, Chem. Rev. 2005, 105, 2999-3093.
50. E. C. Western, J. R. Daft, E. M. Johnson II, P. M. Gannett, K. H. Shaughnessy, J. Org. Chem. 2003, 68, 6767-6774.
51. T. Ishiyama, J. Takagi, J. F. Hartwig, N. Miyaura, Angew. Chem. Int. Ed. 2002, 41, 3056-3058
52. Angew. Chem. 2002, 114, 3182-3184.
53. C. Reichardt, Chem. Rev. 1994, 94, 2319-2358.
54. S. Hildbrand, A. Blaser, S. P. Parel, C.J. Leumann, J. Am. Chem. Soc. 1997, 119, 5499-5511.
55. S. A. Cassidy, P. Slickers, J. O. Trent, D. C. Capaldi, P. D. Roselt, C. B. Reese, S. Neidle, K. R. Fox, Nucleic Acids Res. 1997, 25, 4891-4898.
56. T. Searls, D. L Chen, T. Lan, L.W. McLaughlin, Biochemistry 2000, 39, 4375-4382.
57. M. Tarköy, A. K. Phipps, P. Schultze, J. Feigon, Biochemistry 1998, 37, 5810-5819.
58. A. K. Phipps, M. Tarköy, P. Schultze, J. Feigon, Biochemistry 1998, 37, 5820-5830.
59. I. K. Astakhova, J. Wengel, Acc. Chem. Res. 2014, 47, 1768-1777.
60. S. P. Jonstrup, J. Koch, J. Kjems, RNA 2006, 12, 1747-1752.
61. W. C. S. Cho, Mol. Cancer 2007, 6, 25.
62. C. Peyron, R. Benhida, C. Bories, P. M. Loiseau, Bioorg. Chem. 2005, 33, 439-447.
63. W. Hirose, K. Sato, A. Matsuda, Angew. Chem. Int. Ed. 2010, 49, 8392-8394
64. Angew. Chem. 2010, 122, 8570-8572.
65. P. Guo, X. Xu, X. Qiu, Y. Zhou, S. Yan, C. Wang, C. Lu, W. Ma, X. Weng, X. Zhang, X. Zhou, Org. Biomol. Chem. 2013, 11, 1610-1613.
66. J. Van Ness, L. K. Van Ness, D. J. Galas, Proc. Natl. Acad. Sci. USA 2003, 100, 4504-4509.
67. B.-C. Yin, Y-Q. Liu, B.-C. Ye, J. Am. Chem. Soc. 2012, 134, 5064-5067.
68. D. C. Ward, E. Reich, L. Stryer, J. Biol. Chem. 1969, 244, 1228-1237.
69. M.J. Adams, J. G. Highfield, G. F. Kirkbright, Anal. Chem. 1977, 49, 1850-1852.
70. J. R. Lakowicz, Principles of Fluorescence Spectroscopy, 3rd ed., Springer, New York, 2006.
71. F. Delaglio, S. Grzesiek, G.W. Vuister, G. Zhu, J. Pfeifer, A. Bax, J. Biomol. NMR 1995, 6, 277-293.
72. P. Güntert, Methods Mol. Biol. 2004, 278, 353-378.
73. R. Koradi, M. Billeter, K. Wüthrich, J. Mol. Graphics 1996, 14, 51-55.