Procesy przenoszenia energii (FRET) w badaniach czteroniciowych form DNA

• Autorzy: Juskowiak B. , Gałęzowska E. , Paczesny J.

Warianty tytułu

EN

Fluorescence resonance energy transfer (FRET) in the studies of tetraplex DNA structures

• Języki publikacji: PL

Abstrakty

EN

DNA sequences with stretches of multiple guanines can form four-stranded tetraplex DNA structures called guanine-quadruplexes or G4 DNA. They contain stacked arrays of planar guanine quartets linked by connecting loops. Evidence supports the occurrence of quadruplexes in the cell nucleus and a number of biological functions have been attributed to quadruplexes. In eukaryotic systems guanine-rich sequences are positioned at the ends of chromosomes and are called tclomcric DNA. The study of telomeric DNA has acquired importance through the discovery of the relationship between telomerase activity in most cancer cells and telomere folding into tetraplex structure. Coordination of certain metal cations stabilizes G-quadruplex as do some promising small organic molecules, which are regarded as potential anticancer drugs. Among many techniques employed to explore properties of G-quadrupIexes, fluorescence resonance energy transfer (FRET) has been recognized as a powerful tool to explore tetraplex formation due to extreme sensitivity and the distance dependency of the FRET process. This review shows how FRET contributes to G-quadruplex research and focuses on the FRET application, describing briefly also the underlying principles. Information about molecular structure, binding events, and motion are considered to be potentially available from FRET measurements. In a typical FRET experiment a guanine-rich oligonucleotide labeled with proper fluorophores (FRET donor and acceptor) undergoes structural transformations (folding or unfolding), which are monitored by spectral changes in the fluorescence spectra of FRET partners. We tried to summarize the current developments in the field of the various applications of FRET measurements for the fundamental structural and kinetic investigations of G-quadru-plexes and their complexes with metal cations and organic ligands. Fundamental applications include studies of quadruplex unfolding kinetics with the use of complementary DNA or PNA (Peptide Nucleic Acid) strands as a duplex trap or determination of thermodynamic parameters. Practical applications are illustrated by the FRET-based selection of quadruplex-binding ligands, construction of the quadruplex-based nanomotor, design of molecular probes for protein recognition, and development of sensors for the detection of potassium ions in aqueous media. The presented examples of FRET studies showed that FRET is particularly use ful in structural studies of oligonucleotides capable of folding into tetraplex structure.

Słowa kluczowe

PL

czteroniciowe DNA; fluorescencja; G-kwadrupleks; białka; ligandy oddziałujące z G-kwadrupleksami; procesy przenoszenia energii (FRET); telomerowe DNA; tetrapleks; trombinowy aptamer (TBA)

EN

fluorescence; Fluorescence Energy Transfer (FRET); G-quadruplex; proteins; quadruplex-binding ligands; telomeric DNA; tetraplex DNA structure; Thrombin Binding Aptamer (TBA)

• Wydawca: Polskie Towarzystwo Chemiczne
• Czasopismo: Wiadomości Chemiczne
• Rocznik: 2006
• Tom: [Z] 60, 7-8
• Strony: 547--566
• Opis fizyczny: rys., tab., bibliogr. 56 poz.

Twórcy

autor

Juskowiak B.

autor

Gałęzowska E.

autor

Paczesny J.

• Wydział Chemii, Uniwersytet im. A. Mickiewicza, ul. Grunwaldzka 6, 60-780 Poznań

Bibliografia

• [1] M. Gellert, M.N. Lipsett, D.R. Davies, Proc. Natl. Acad. Sci. USA, 1962, 48, 2013.
• [2] W. Guschlbauer, J.F. Chantotand, D. Thiele, J. Biomol. Struct. Dyn., 1990, 8, 491.
• [3] A.M. Zahler, J.R. Williamson, T.R. Cech, D.M. Prescott, Nature, 1991, 350, 718.
• [4] S. Neidle, G. Parkinson, Nat. Rev. Drug Des., 2002, 1, 383.
• [5] J.L. Mergny, J.F. Riou, P. Mailliet, M.P. Teulade-Fichou, E. Gilson, Nucleic Acids Res., 2002, 30, 839.
• [6] T. Simonsson, Biol. Chem., 2001, 382, 621.
• [7] Y. Wang, D.J Patel, J. Mol. Biol., 1995, 251, 76.
• [8] M.A. Keniry, G.D. Strahan, E.A. Owen, R.H. Shafer, Eur. J. Biochem., 1995, 233, 631.
• [9] G. Laughlan, A.I. Murchie, D.G. Norman, M.H. Moore, P.C. Moody, D.M. Lilley, B. Luisi, Science, 1994, 265, 520.
• [10] S. Neidle, G. Parkinson, Curr. Opin. Struct. Biol., 2003, 13, 275.
• [11] Y. Wang, D.J. Patel, Structure, 1993, 1, 263.
• [12] G.N. Parkinson, M.H.P. Lee, S. Neidle, Nature, 2002, 417, 876.
• [13] P. Schultze, N.V. Hud, F.W. Smith, J. Feigon, Nucleic Acids Res., 1999, 27, 3018.
• [14] S.M. Haider, G.N. Parkinson, S. Neidle, J. Mol. Biol., 2002, 320, 189.
• [15] D. Sun, B. Thompson, B. E. Cathers, M. Salazar, S.M. Kerwin, J. O. Trent, T.C. Jenkins, S. Neidle, L.H. Hurley, J. Med. Chem., 1997, 40, 2113.
• [16] D. F. Shi, R. T. Wheelhouse, D. Sun, L. H. Hurley, J. Med. Chem., 2001, 44, 4509.
• [17] J.-L. Mergny, L. Lacroix, M.-P. Teulade-Fichou, C. Hounsou, L. Guittal, M. Hoarau, P.B. Arimondo, J.-P. Vigneron, J.-M. Lehn, J.-F. Riou, T. Garestier, C. Helene, Proc. Natl Acad. Sci. USA, 2001, 98, 3062.
• [18] S.M. Kerwin, Curr. Pharm. Des., 2000, 6, 441.
• [19] B. Juskowiak, E. Galezowska, N. Kaczorowska, T.W. Hermann, Bioorg. Med. Chem. Lett., 2004, 14, 3627.
• [20] L. Stryer, R.P. Haugland, Proc. Natl. Acad. Sci. USA, 1967, 58, 719.
• [21] R.M. Clegg, Methods Enzymol., 1992, 211, 353.
• [22] T. Förster, Ann. Phys., 1948, 2, 55.
• [23] E.A. Jares-Erijman, T.M. Jovin, J. Mol. Biol., 1996, 257, 597.
• [24] R.M. Clegg, A.I.H. Murchie, A. Zechel, D.M.J. Lilley, Proc. Natl. Acad Sci. USA, 1993, 90, 2994.
• [25] R.A. Cardullo, S. Agrawal, C. Flores, P.C. Zamecnik, D.E.Wolf, Proc. Natl. Acad. Sci. USA, 1988, 85, 8790.
• [26] J.L. Mergny, T. Garestier, M. Rougee, A.V. Lebedev, M. Chassignol, N.T. Thuong, C. Helene, Biochemistry, 1994, 33, 15321.
• [27] R.M. Clegg, A.I.H. Murchie, A. Zechel, C. Carlberg, S. Diekmann, D.M.J. Lilley, Biochemistry, 1992, 31, 4846.
• [28] S. Tyagi, D.P. Bratu, F.R. Kramer, Nat. Biotechnol., 1998, 16, 49.
• [29] D.G. Ginzinder, Exp. Hematol., 2002, 30, 503.
• [30] Simonsson, R. Sjöback, J. Biol. Chem., 1999, 274, 17379.
• [31] J.-L. Mergny, J.C. Maurizot, ChemBioChem, 2001, 2, 124.
• [32] P. Alberti, J. Ren, M.P. Teulade-Fichou, L. Guittat, J.F. Riou, J.B. Chaires, C. Hélene, J.P. Vigneron, J.M. Lehn, J.L. Mergny, J. Biomol. Struct. Dyn., 2001, 19, 505.
• [33] A. Yamauchi, T. Hayashita, A. Kato, S. Nishizawa, M.Watanabe, N. Teramae, Anal. Chem., 2000, 72, 5841.
• [34] T. Nojima, H. Ueyama, M. Takagi, S. Takenaka, Nucleic Acids Res. Suppl., 2002, 2, 125.
• [35] H. Ueyama, M. Takagi, S. Takenaka, J. Am. Chem. Soc., 2002, 124, 1428.
• [36] S. Takenaka, H. Ueyama, T. Nojima, M. Takagi, Anal. Bioanal. Chem., 2003, 375, 1006.
• [37] B. Juskowiak, E. Galezowska, A. Zawadzka, A. Gluszynska, S. Takenaka, Spectrochim. Acta P.A., 2006, 64, 835.
• [38] N. Kumar, S. Maiti, Nucleic Acids Res., 2005, 33, 6723.
• [39] N. Kumar, S. Maiti, Biochem. Biophys. Res. Commun., 2004, 319, 759.
• [40] A. Risitano, K.R. Fox, Nucleic Acids Res., 2004, 32, 2598.
• [41] R.A.J. Darby, M. Sollogoub, C. McKeen, L. Brown, A. Risitano, N. Brown, C. Barton, T. Brown, K.R. Fox, Nucleic Acid Res., 2002, 30, e39.
• [42] J.J. Li, X. Fang, W. Tan, Biochem. Biophys. Res. Commun., 2002, 292, 31.
• [43] R. Nutiu, Y. Li, J. Am. Chem. Soc., 2003, 125, 4771.
• [44] L. Ying, J.J. Green, H. Li, D. Klenerman, S. Balasubramanian, Proc. Natl. Acad. Sci. USA, 2003,100, 14629.
• [45] J.J. Green, L. Ying, D. Klenerman, S. Balasubramanian, J. Am. Chem. Soc., 2003, 125, 3763.
• [46] B. Datta, C. Schmitt, B.A. Armitage, J. Am. Chem. Soc., 2003, 125, 4111.
• [47] P. Alberti, J.L. Mergny, Proc. Natl. Acad. Sci. USA, 2003, 100, 1569.
• [48] A.A. Deniz, M. Dahan, J.R. Grunwell, T. Ha, A.E. Faulhaber, D.S. Chemla, S.Weiss, P.G. Schultz, Proc. Natl. Acad. Sci. USA, 1999, 96, 3670.
• [49] M.P. Teulade-Fichou, C. Carrasco, L. Guittat, C. Bailly, P. Alberti, J.L. Mergny, A. David, J.M. Lehn, W.D. Wilson, J. Am. Chem. Soc., 2003, 125, 4732.
• [50] L.C. Bock, L.C. Griffin, J.A. Latham, E.H. Vermaas, J.J. Toole, Nature, 1992, 355, 564.
• [51] N. Hamaguchi, A. Ellington, M. Stanton, Anal. Biochem., 2001, 294, 126.
• [52] A. Yamauchi, T. Hayashita, S. Nishizawa, M. Watanabe, N. Teramae, J. Am. Chem. Soc., 1999, 121, 2319.
• [53] W. Xia, R. H. Schmehl, C. Li, Eur. J. Org. Chem., 2000, 3, 387.
• [54] C. Li, G. Law,W. Wong, Org. Lett., 2004, 6, 4841.
• [55] S. Nagatoishi, T. Nojima, B. Juskowiak, S. Takenaka, Angew. Chem. Int. Ed. Engl., 2005, 44, 5067.
• [56] F. He, Y. Tang, S.Wang, Y. Li, D. Zhu, J. Am. Chem. Soc., 2005, 127, 12343.