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Table 1
Saito, I. Photochem. Photobiol. C: Photochem. Rev. 2005, 6, 108; (d) Ranasinghe, R.
Fluorescence lifetimes of single stranded ODN I (X = 1d) and duplex ODN I/ODN IIa
T.; Brown, T. Chem. Commun. 2005, 5487; (e) Tor, Y. Ed.; Tetrahedron
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Soc. Rev. 2008, 37, 648; (g) Sinkeldam, R. W.; Greco, N. J.; Tor, Y. Chem. Rev.
2010, 110, 2579.
Sample
sf (ns)
ODN I (X = 1d)
0.90 (420 nm)
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A.; Cristalli, G. Bioorg. Med. Chem. Lett. 1931, 2001, 11; (b) Costanzi, S.;
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ODN I (X = 1d)/ODN II (X = A)
1.1 (420 nm), 2.2 (470 nm)
a
Experimental conditions: [ssODN or duplex ODN] = 3.0
sodium phosphate buffer, pH 7.0, 100 mM NaCl, kex = 365 nm.
lM in deaerated 50 mM
lifetime component (s = 1.1 ns) was resulted from the naphthalene
chromophore of 1d. The study of fluorescence lifetime clearly indi-
cated the existence of two excited species that are responsible for
fluorescence emission and strongly suggests that the longer life-
time component with a strong emission at 470 nm is from the exci-
plex between 1d and A. Actually, molecular modeling study of
duplex ODN I (X = 1d)/ODN II (N = A) by using MacroModel ver.
9.0 indicated a strong
p-stacking between methoxynaphthalene
6. (a) Okamoto, A.; Tainaka, K.; Saito, I. J. Am. Chem. Soc. 2003, 125, 4972; (b)
Okamoto, A.; Tanaka, K.; Fukuda, T.; Saito, I. J. Am. Chem. Soc. 2003, 125, 4972;
(c) Okamoto, A.; Kanatani, K.; Saito, I. J. Am. Chem. Soc. 2004, 126, 4820; (d)
Saito, Y.; Hanawa, K.; Motegi, K.; Omoto, K.; Okamoto, A.; Saito, I. Tetrahedron
Lett. 2005, 46, 7605; (e) Saito, Y.; Bag, S. S.; Kusakabe, Y.; Nagai, C.; Matsumoto,
K.; Kodate, S.; Suzuka, I.; Saito, I. Chem. Commun. 2007, 2133; (f) Saito, Y.;
Motegi, K.; Bag, S. S.; Saito, I. Bioorg. Med. Chem. 2008, 16, 107.
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Bioorg. Med. Chem. Lett. 2010, 20, 2817; (b) Matsumoto, K.; Takahashi, N.;
Suzuki, A.; Morii, T.; Saito, Y.; Saito, I. Bioorg. Med. Chem. Lett. 2011, 21, 1275; (c)
Saito, Y.; Shinohara, Y.; Ishioroshi, S.; Suzuki, A.; Tanaka, M.; Saito, I.
Tetrahedron Lett. 2011, 52, 2359.
moiety and adenine (Supplementary data, Fig. S2).
In conclusion, we have devised an unprecedented type of fluo-
rescent probe containing highly electron donating fluorescent
deoxyguanosine analogs which gave rise to the appearance of a
strong new emission at longer wavelength via exciplex formation
with adenine in hybridization with target DNA. Such electron
donating deoxyguanosine analogs 1b,c,d capable of forming ex-
cited state complexes specifically with adenine may be widely
used as a fluoresce probe for structural study of DNA and RNA
and for the fluorometric analysis of nucleic acids and fluorescent
imaging.
8. While many examples for fluorometric assay of DNA using pyrene eximer
emission are known,9 there has been no example, to our knowledge, for the
fluorometric analysis of nucleic acids using exciplex emission.
9. For examples, see: (a) Tong, G.; Lawlor, J. M.; Tregear, G. W.; Haralambidis, J. J.
Am. Chem. Soc. 1995, 117, 12151; (b) Yamana, K.; Iwai, T.; Ohtani, Y.; Sato, S.;
Nakamura, M.; Nakano, H. Bioconjugate Chem. 2002, 13, 1266; (c) Okamoto, A.;
Ichiba, T.; Saito, I. J. Am. Chem. Soc. 2004, 126, 8364; (d) Yamana, K.; Ohshita, Y.;
Fukunaga, Y.; Nakamura, M.; Maruyama, A. Bioorg. Med. Chem. 2008, 16, 78; (e)
Conlon, P.; Yang, C. J.; Wu, Y.; Chen, Y.; Martinez, K.; Kim, Y.; Stevens, N.; Marti,
A. A.; Jockusch, S.; Turro, N. J.; Tan, W. J. Am. Chem. Soc. 2008, 130, 336. and
references therein; (f) Matsumoto, K.; Shinohara, Y.; Bag, S. S.; Takeuchi, Y.;
Morii, T.; Saito, Y.; Saito, I. Bioorg. Med. Chem. Lett. 2009, 19, 6392.
10. It should be noted that such adenine specific exciplex formation is sequence
dependent. When the flanking base pair of fluorescent deoxyguanosine 1b was
G–C base pair, such A specific exciplex emission was not observed.
Supplementary data
Supplementary data associated with this article can be found, in
References and notes
1. For reviews, see: (a) Hawkins, M. E. Cell Biochem. Biophys. 2001, 34, 257; (b)
Rist, M. J.; Marino, J. P. Curr. Org. Chem. 2002, 6, 775; (c) Okamoto, A.; Saito, Y.;