Parallel vs. anti-parallel orientation in a curdlan/oligo(dA) complex as estimated by a FRET technique

Organic and Biomolecular Chemistry

Volumn 3, Issue 12, 2005, Pages 2255-2261

  Numata, Munenori ^a   Koumoto, Kazuya ^b   Mizu, Masami ^b   Sakurai, Kazuo ^b   Shinkal, Seiji ^a  

^a KYUSHU UNIVERSITY   (Japan)

^b UNIVERSITY OF KITAKYUSHU   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; DNA; ENERGY TRANSFER; ENZYME IMMOBILIZATION; FLUORESCENCE; MACROMOLECULES; OLIGOMERS; POLYSACCHARIDES; QUENCHING; STEREOCHEMISTRY; X RAY CRYSTALLOGRAPHY;

ANTI-PARALLEL ORIENTATION; BIOMACROMOLECULES; POLYMERIC COMPLEXES; POLYNUCLEOTIDE;

CRYSTAL ORIENTATION;

BETA GLUCAN; CURDLAN; FLUORESCEIN; OLIGODEOXYADENYLIC ACID; OLIGODEOXYRIBONUCLEOTIDE;

ARTICLE; CHEMISTRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; ULTRAVIOLET SPECTROPHOTOMETRY;

BETA-GLUCANS; FLUORESCEIN; FLUORESCENCE RESONANCE ENERGY TRANSFER; OLIGODEOXYRIBONUCLEOTIDES; SPECTROPHOTOMETRY, ULTRAVIOLET;

EID: 23344447638     PISSN: 14770520     EISSN: None     Source Type: Journal    
DOI: 10.1039/b500156k     Document Type: Article

References (27)

1. W. Saenger, Principles of Nucleic Acid Structure, Springer-Verlag, New York, 1984.
2. (a) E. D. T. Atkins and K. D. Parker, Nature, 1968, 220, 784;
3. (b) R. H. Marchessault, Y. Deslandes. K. Ogawa and P. R. Sundararajan, Can. J. Chem., 1977, 55, 300;
4. (c) C. T. Chuah, A. Sarko, Y. Deslandes and R. H. Marchessault, Macromolecules, 1983, 16, 1375.
5. Y. Deslandes. R. H. Marchessault and A. Sarko, Macromolecules, 1980, 13, 1466.
6. (a) T. M. Mclntire and D. A. Brant, J. Am. Chem. Soc., 1998, 120. 6909:
7. (b) S. H. Young, W. J. Dong and R. R. Jacobs. J. Biol Chem., 2000, 275, 11874;
8. (c) S. H. Young and R. R. Jacobs, Carbohydr. Res., 1998, 310, 91.
9. (a) K. Sakurai and S. Shinkai, J. Am. Chem. Soc., 2000, 122, 4520;
10. (b) K. Sakurai, M. Mizu and S. Shinkai, Biomacromolecules, 2001, 2, 641;
11. (c) T. Kimura, K. Koumoto, K. Sakurai and S. Shinkai, Chem. Lett., 2000, 1243.
12. K. Miyoshi, K. Uezu, K. Sakurai and S. Shinkai, Chem. Biodiversity, 2004, 1, 916.
13. FRET has been known as a spectroscopic ruler to estimate the precise distance between two fluorophores (donor and acceptor) on the nano-scale because effective energy transfer between two fluorophores occurs only when they exist at a distance of less than 10 nm. For example, see: (a) I. Horsey, W. S. Furey, J. G. Harrison, M. A. Osborne and S. Balasubramanian. Chem Commun., 2000, 1043;
14. (b) S.-H. Young. W.-J. Dong and R. R. Jacobs. J. Biol. Chem., 2000, 275, 11874;
15. (c) H. Takakusa, K. Kikuchi, Y. Urano, S. Sakamoto, K. Yamaguchi and T. Nagano, J. Am, Chem, Soc., 2002, 124, 1653.
16. 5a,b therefore, we used oligo(dA) with 45 deoxyadenylic acid units to match the curdlan chain length with the curdlan chain length.
17. We assumed that two curdlan chains take a parallel orientation in the complex. This assumption is basically reasonable because if two curdlan chains take an anti-parallel orientation in the complex. FRET should be observed from both 3′dA-CUR and 5′dA-CUR complexes, so that both systems should give the same fluorescence spectra.
18. After addition of 10 vol% of Tris-HCl buffer (10.0 mM, pH = 8, 10.0 μl). the resultant aqueous solutions were used for fluorescence measurements, Here, we used F-CUR and 3′ (or 5′) TAMRA-labeled oligo(dA) in H 2 : 1 molar ratio.
19. Optical and electronic properties of gold nanoparticles are useful for the detection of biological polymers, see: (a) D. J. Maxwell. J. R. Taylor and S. Nie. J. Am. Chem. Hot:, 2002, 124, 9606;
20. (b) M. Brust, D. Bethel, C. J. Kiely and D. J. Schiffrin, Langmuir, 1998,14, 5425;
21. (c) F. P. Zamborini. M. C., Leopold. J. F. Hicks. P. J. Kulesza. M. A. Malik and R. W, Murray, J. Am. Chem. Soc., 2002, 124, 8958;
22. (d) T. Niazov, V. Pavlov, Y. Xiao. R. Gill and I. Willner, Nano Lett., 2004, 4, 1683.
23. K. Miyoshi, K. Sakurai, S. Shinkai and K. Uezu, Chem. Biodiversity, to be submitted.
24. The geometry-optimized structures obtained from MOPAC indicate that in a parallel orientation, the adenine residues perfectly fit the groove constructed by two curdlan chains, whereas in an anti-parallel orientation, the adenine residues cannot access the groove due to steric hindrance between the deoxyribose moiety and the curdlan double helix.
25. T. Yanaki, T. Norisue and M. Fujita, Macromolecules, 1980, 13, 1466.
26. M. Mizu, K. Koumoto, T. Anada, T. Matsumoto, M. Numata, S. Shinkai, T. Nagasaki and K. Sakurai, J. Am. Chem, Soc., 2004, 126, 8372.
27. T. Kimura. K. Koumoto, M. Mizu. K. Sakurai and S. Shinkai, Chem. Lett., 2002, 1240.