Fluorescent 5-alkynyl-2′-deoxyuridines: High emission efficiency of a conjugated perylene nucleoside in a DNA duplex

ChemBioChem

Volumn 7, Issue 5, 2006, Pages 810-816

  Skorobogatyi, Mikhail V ^a   Malakhov, Andrei D ^a   Pchelintseva, Anna A ^a   Turban, Alexander A ^b   Bondarev, Stanislav L ^b   Korshun, Vladimir A ^a  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

^b B I STEPANOV INSTITUTE OF PHYSICS   (Belarus)

Author keywords

Luminescence; Nucleic acid hybridization; Nucleosides; Perylene; Pyrene

Indexed keywords

BENZOXAZOLE DERIVATIVE; DEOXYURIDINE DERIVATIVE; DOUBLE STRANDED DNA; OLIGONUCLEOTIDE; PERYLENE; PHOSPHORAMIDIC ACID DERIVATIVE; PYRENE;

ARTICLE; CONJUGATION; FLUORESCENCE; HYBRIDIZATION; PRIORITY JOURNAL; SPECTROSCOPY; SYNTHESIS; THERMAL ANALYSIS;

DEOXYURIDINE; DNA; MODELS, MOLECULAR; MOLECULAR STRUCTURE; NUCLEOSIDES; ORGANOPHOSPHORUS COMPOUNDS; PERYLENE; SENSITIVITY AND SPECIFICITY; SPECTROMETRY, FLUORESCENCE; STEREOISOMERISM; TEMPERATURE;

EID: 33646805423     PISSN: 14394227     EISSN: 14397633     Source Type: Journal    
DOI: 10.1002/cbic.200600040     Document Type: Article

References (41)

1. R. T. Ranasinghe, T. Brown, Chem. Commun. 2005, 5487-5502.
2. F. Sanger, S. Nicklen, A. R. Coulson, Proc. Natl. Acad. Sci. USA 1977, 74, 5463-5467.
3. J. M. Prober, G. L. Trainor, R. J. Dam, R. W. Hobbs, C. W. Robertson, R. J. Zagursky, A. J. Cocuzza, M. A. Jensen, K. Baumeister, Science 1987, 238, 336-341.
4. P. N. Confalone, J. Heterocycl. Chem. 1990, 27, 31-46.
5. B. B. Rosenblum, L. G. Lee, S. L. Spurgeon, S. H. Khan, S. M. Menchen, C. R. Heiner, S. M. Chen, Nucleic Acids Res. 1997, 25, 4500-4504.
6. L. H. Thoresen, G.-S. Jiao, W. C. Haaland, M. L. Metzker, K. Burgess, Chem. Eur. J. 2003, 9, 4603-4610.
7. a) W. C. Furey, C. M. Joyce, M. A. Osborne, D. Klenerman, J. A. Peliska, S. Balasubramanian, Biochemistry 1998, 37, 2979-2990;
8. b) A. Okamoto, K. Kanatani, I. Saito, J. Am. Chem. Soc. 2004, 126, 4820-4827;
9. c) C. M. McKeen, L. J. Brown, J. T. G. Nicol, J. M. Mellor, T. Brown, Org. Biomol. Chem. 2003, 1, 2267-2275;
10. d) Y. Saito, K. Hanawa, K. Motegi, K. Omoto, A. Okamoto, I. Saito, Tetrahedron Lett. 2005, 46, 7605-7608;
11. e) A. Okamoto, K. Tainaka, K. Nishiza, I. Saito, J. Am. Chem. Soc. 2005, 127, 13128-13129;
12. f) A. Okamoto, Y. Ochi, I. Saito, Bioorg. Med. Chem. Lett. 2005, 15, 4279-4281.
13. V. A. Korshun, E. V. Manasova, K. V. Balakin, I. A. Prokhorenko, A. G. Buchatskii, Y. A. Berlin, Russ. J. Bioorg. Chem. 1996, 22, 807-809.
14. a) A. D. Malakhov, E. V. Malakhova, S. V. Kuznitsova, I. V. Grechishnikova, I. A. Prokhorenko, M. V. Skorobogatyi, V. A. Korshun, Y. A. Berlin, Russ. J. Bioorg. Chem. 2000, 26, 34-44;
15. b) G. T. Hwang, Y. J. Seo, B. H. Kim, J. Am. Chem. Soc. 2004, 126, 6528-6529;
16. c) G. T. Hwang, Y. J. Seo, S. J. Kim, B. H. Kim, Tetrahedron Lett. 2004, 45, 3543-3546;
17. d) G. T. Hwang, Y. J. Seo, B. H. Kim, Tetrahedron Lett. 2005, 46, 1475-1477;
18. e) Y. J. Seo, J. H. Ryu, B. H. Kim, Org. Lett. 2005, 7, 4931-4933;
19. f) Y. J. Seo, B. H. Kim, Chem. Commun. 2006, 150-152;
20. g) A. Okamoto, Y. Ochi, I. Saito, Chem. Commun. 2005, 1128-1130;
21. h) M. Rist, N. Amann, H.-A. Wagenknecht, Eur. J. Org. Chem. 2003, 2498-2504;
22. i) E. Mayer, L. Valis, C. Wagner, M. Rist, N. Amann, H.-A. Wagenknecht, ChemBioChem 2004, 5, 865-868;
23. j) C. Wagner, M. Rist, E. Mayer-Enthart, H.-A. Wagenknecht, Org. Biomol. Chem. 2005, 3, 2062-2063;
24. k) A. Trifonov, M. Raytchev, I. Buchvarov, M. Rist, J. Barbaric, H.-A. Wagenknecht, T. Fiebig, J. Phys. Chem. B 2005, 109, 19490-19495;
25. l) S. T. Gaballah, G. Collier, T. L. Netzel, J. Phys. Chem. B 2005, 109, 12175-12181;
26. m) S. T. Gaballah, Y. H. A. Hussein, N. Anderson, T. T. Lian, T. L. Netzel, J. Phys. Chem. A 2005, 109, 10832-10845.
27. Preliminary results were reported in: M. V. Skorobogatyj, A. A. Pchelintseva, A. V. Ustinov, V. A. Korshun, A. D. Malakhov, Nucleosides Nucleotides Nucleic Acids 2005, 24, 931-934.
28. M. Ahmadian, P. Zhang, D. E. Bergstrom, Nucleic Acids Res. 1998, 26, 3127-3135.
29. E. V. Malakhova, A. D. Malakhov, S. V. Kuznitsova, O. P. Varnavskii, A. P. Kadutskii, D. T. Kozhich, V. A. Korshun, Y. A. Berlin, Russ. J. Bioorg. Chem. 1998, 24, 611-617.
30. V. L. Andronova, M. V. Skorobogatyi, E. V. Manasova, Y. A. Berlin, V. A. Korshun, G. A. Galegov, Russ. J. Bioorg. Chem. 2003, 29, 262-266.
31. M. V. Skorobogatyi, A. A. Pchelintseva, A. L. Petrunina, I. A. Stepanova, V. L. Andronova, G. A. Galegov, A. D. Malakhov, V. A. Korshun, Tetrahedron 2006, 62, 1279-1287.
32. a) K. Sonogashira, Y. Tohda, N. Hagihara, Tetrahedron Lett. 1975, 16, 4467-4470;
33. b) K. Sonogashira in Comprehensive Organic Synthesis, Vol. 3 (Eds.: B. M. Trost, I. Fleming), Pergamon, Oxford, 1991, pp. 521-549;
34. c) R. Rossi, A. Carpita, F. Bellina, Org. Prep. Proc. Int. 1995, 27, 127-160;
35. d) K. Sonogashira in Handbook of Orgonopalladium Chemistry for Organic Synthesis, Vol. 1 (Eds.: E. Negishi, A. de Meijere), Wiley-Interscience, New York, 2002, pp. 493-529.
36. a) F. W. Hobbs, Jr., J. Org. Chem. 1989, 54, 3420-3422;
37. b) M. J. Robins, R. S. Vinayak, S. G. Wood, Tetrahedron Lett. 1990, 31, 3731-3734.
38. A part of the promoter region of a gene encoding a homologue of NG-dimethylarginine dimethyl amino hydrolase (a component of human major histocompatibility complex III; GenBank (http://www.ncbi.nlm.-nih.gov), AF129756, locus DJ01G24 (within MHC III, chr 6, 6p21)).
39. The name of each modified oligonucleotide derived from M contains the position number(s) and the type of modification (a-d).
40. ex = 430-480 nm).
41. D. R. Coulson, Inorg. Synth. 1972, 13, 121-124.