Improved hydration-sensitive dual-fluorescence labels for monitoring peptide-nucleic acid interactions

Bioconjugate Chemistry

Volumn 22, Issue 1, 2011, Pages 101-107

  Zamotaiev, Oleksandr M ^a   Postupalenko, Viktoriia Y ^b   Shvadchak, Volodymyr V ^b   Pivovarenko, Vasyl G ^a   Klymchenko, Andrey S ^b   Mély, Yves ^b  

^a TARAS SHEVCHENKO NATIONAL UNIVERSITY OF KYIV   (Ukraine)

^b UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

2 FURANYL 3 HYDROXYCHROMONE; 3 HYDROXY 4' METHOXYFLAVONE; CHROMONE DERIVATIVE; DNA; FLAVONE DERIVATIVE; OLIGONUCLEOTIDE; TRANSACTIVATOR PROTEIN; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; COVALENT BOND; DNA HAIRPIN; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; NONHUMAN; NUCLEOTIDE BINDING SITE; NUCLEOTIDE SEQUENCE; PKA; PROTEIN DNA BINDING; QUANTUM YIELD;

HUMAN IMMUNODEFICIENCY VIRUS 1;

EID: 78751609924     PISSN: 10431802     EISSN: 15204812     Source Type: Journal    
DOI: 10.1021/bc100434d     Document Type: Article

References (36)

1. Cohen, B. E., McAnaney, T. B., Park, E. S., Jan, Y. N., Boxer, S. G., and Jan, L. Y. (2002) Probing protein electrostatics with a synthetic fluorescent amino acid Science 296, 1700-1703
2. Nitz, M., Mezo, A. R., Ali, M. H., and Imperiali, B. (2002) Enantioselective synthesis and application of the highly fluorescent and environment-sensitive amino acid 6-(2-dimethylaminonaphthoyl) alanine (DANA) Chem. Commun. 8, 1912-1913
3. Vazquez, M. E., Nitz, M., Stehn, J., Yaffe, M. B., and Imperiali, B. (2003) Fluorescent caged phosphoserine peptides as probes to investigate phosphorylation-dependent protein associations J. Am. Chem. Soc. 125, 10150-10151
4. Vazquez, M. E., Rothman, D. M., and Imperiali, B. (2004) A new environment-sensitive fluorescent amino acid for Fmoc-based solid phase peptide synthesis Org. Biomol. Chem. 2, 1965-1966
5. Vazquez, M. E., Blanco, J. B., and Imperiali, B. (2005) Photophysics and biological applications of the environment-sensitive fluorophore 6-N, N-dimethylamino-2,3-naphthalimide J. Am. Chem. Soc. 127, 1300-1306
6. Loving, G. and Imperiali, B. (2008) A versatile amino acid analogue of the solvatochromic fluorophore 4-N, N-dimethylamino-1,8-naphthalimide: A powerful tool for the study of dynamic protein interactions J. Am. Chem. Soc. 130, 13630-13638
7. Cohen, B. E., Pralle, A., Yao, X., Swaminath, G., Gandhi, C. S., Jan, Y. N., Kobilka, B. K., Isacoff, E. Y., and Jan, L. Y. (2005) A fluorescent probe designed for studying protein conformational change Proc. Natl. Acad. Sci. U.S.A. 102, 965-970
8. Venkatraman, P., Nguyen, T. T., Sainlos, M., Bilsel, O., Chitta, S., Imperiali, B., and Stern, L. J. (2007) Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells Nat. Chem. Biol. 3, 222-228
9. Harikumar, K. G., Pinon, D. I., Wessels, W. S., Prendergast, F. G., and Miller, L. J. (2002) Environment and mobility of a series of fluorescent reporters at the amino terminus of structurally related peptide agonists and antagonists bound to the cholecystokinin receptor J. Biol. Chem. 277, 18552-18560
10. Sen, S., Paraggio, N. A., Gearheart, L. A., Connor, E. E., Issa, A., Coleman, R. S., Wilson Iii, D. M., Wyatt, M. D., and Berg, M. A. (2005) Effect of protein binding on ultrafast DNA dynamics: Characterization of a DNA:APE1 complex Biophys. J. 89, 4129-4138
11. Yang, X., Liu, W. H., Jin, W. J., Shen, G. L., and Yu, R. Q. (1999) DNA binding studies of a solvatochromic fluorescence probe 3-methoxybenzanthrone Spectrochim. Acta, Part A 55, 2719-2727
12. Kumar, C. V. and Asuncion, E. H. (1993) DNA binding studies and site selective fluorescence sensitization of an anthryl probe J. Am. Chem. Soc. 115, 8547-8553
13. Klymchenko, A. S., Shvadchak, V. V., Yushchenko, D. A., Jain, N., and Mely, Y. (2008) Excited-state intramolecular proton transfer distinguishes microenvironments in single-and double-stranded DNA J. Phys. Chem. B 112, 12050-12055
14. Shvadchak, V. V., Klymchenko, A. S., De Rocquigny, H., and Mely, Y. (2009) Sensing peptide-Oligonucleotide interactions by a two-color fluorescence label: Application to the HIV-1 nucleocapsid protein Nucleic Acids Res. 37 e25
15. Sengupta, P. K. and Kasha, M. (1979) Excited state proton-transfer spectroscopy of 3-hytdroxyflavone and quercetin Chem. Phys. Lett. 68, 382-385
16. Das, R., Klymchenko, A. S., Duportail, G., and Mely, Y. (2009) Unusually slow proton transfer dynamics of a 3-hydroxychromone dye in protic solvents Photochem. Photobiol. Sci. 8, 1583-1589
17. Shynkar, V. V., Klymchenko, A. S., Piemont, E., Demchenko, A. P., and Mely, Y. (2004) Dynamics of intermolecular hydrogen bonds in the excited states of 4′-dialkylamino-3-hydroxyflavones. On the pathway to an ideal fluorescent hydrogen bonding sensor J. Phys. Chem. A 108, 8151-8159
18. Enander, K., Choulier, L., Olsson, A. L., Yushchenko, D. A., Kanmert, D., Klymchenko, A. S., Demchenko, A. P., Mely, Y., and Altschuh, D. (2008) A peptide-based, ratiometric biosensor construct for direct fluorescence detection of a protein analyte Bioconjugate Chem. 19, 1864-1870
19. Chou, P.-T., Martinez, M. L., and Clements, H. (1993) Reversal of excitation behavior of proton-transfer vs. charge-transfer by dielectric perturbation of electronic manifolds J. Phys. Chem. 97, 2618-2622
20. Ormson, S. M., Brown, R. G., Vollmer, F., and Rettig, W. (1994) Switching between charge- and proton-transfer emission in the excited state of a substituted 3-hydroxyflavone J. Photochem. Photobiol., A 81, 65-72
21. Swinney, T. C. and Kelley, D. F. (1993) Proton transfer dynamics in substituted 3-hydroxyflavones: Solvent polarization effects J. Chem. Phys. 99, 211-221
22. Klymchenko, A. S. and Demchenko, A. P. (2003) Multiparametric probing of intermolecular interactions with fluorescent dye exhibiting excited state intramolecular proton transfer Phys. Chem. Chem. Phys. 5, 461-468
23. Demchenko, A. P., Mely, Y., Duportail, G., and Klymchenko, A. S. (2009) Monitoring biophysical properties of lipid membranes by environment-sensitive fluorescent probes Biophys. J. 96, 3461-3470
24. Strandjord, A. J. G. and Barbara, P. F. (1985) Proton-transfer kinetics of 3-hydroxyflavone: Solvent effects J. Phys. Chem. 89, 2355-2361
25. McMorrow, D. and Kasha, M. (1984) Intramolecular excited-state proton transfer in 3-hydroxyflavone. Hydrogen-bonding solvent perturbations J. Phys. Chem. 88, 2235-2243
26. Klymchenko, A. S. and Demchenko, A. P. (2004) 3-Hydroxychromone dyes exhibiting excited-state intramolecular proton transfer in water with efficient two-band fluorescence New J. Chem. 28, 687-692
27. Kuciak, M., Gabus, C., Ivanyi-Nagy, R., Semrad, K., Storchak, R., Chaloin, O., Muller, S., Mely, Y., and Darlix, J. L. (2008) The HIV-1 transcriptional activator Tat has potent nucleic acid chaperoning activities in vitro Nucleic Acids Res. 36, 3389-3400
28. Boudier, C., Storchak, R., Sharma, K. K., Didier, P., Follenius-Wund, A., Muller, S., Darlix, J. L., and Mely, Y. (2010) The mechanism of HIV-1 Tat-directed nucleic acid annealing supports its role in reverse transcription J. Mol. Biol. 400, 487-501
29. Pfister, J. R., Wymann, W. E., Schuler, M. E., and Roszkowski, A. P. (1980) Inhibition of histamine-induced gastric secretion by flavone-6-carboxylic acids J. Med. Chem. 23, 335-338
30. Eastman, J. W. (1967) Quantitative spectrofluorimetry-the fluorescence quantum yield of quinine sulfate Photochem. Photobiol. 6, 55-72
31. Doroshenko, A. O., Sychevskaya, L. B., Grygorovych, A. V., and Pivovarenko, V. G. (2002) Fluorescence probing of cell membranes with azacrown substituted ketocyanine dyes J. Fluoresc. 12, 455-464
32. Reichardt, C. (1994) Solvatochromic dyes as solvent polarity indicators Chem. Rev. 94, 2319-2358
33. Egele, C., Barbier, P., Didier, P., Piemont, E., Allegro, D., Chaloin, O., Muller, S., Peyrot, V., and Mely, Y. (2008) Modulation of microtubule assembly by the HIV-1 Tat protein is strongly dependent on zinc binding to Tat Retrovirology 5, 62
34. De Rocquigny, H., Ficheux, D., Gabus, C., Fournie-Zaluski, M. C., Darlix, J. L., and Roques, B. P. (1991) First large scale chemical synthesis of the 72 amino acid HIV-1 nucleocapsid protein NCp7 in an active form Biochem. Biophys. Res. Commun. 180, 1010-1018
35. Godet, J., De Rocquigny, H., Raja, C., Glasser, N., Ficheux, D., Darlix, J. L., and Mely, Y. (2006) During the early phase of HIV-1 DNA synthesis, nucleocapsid protein directs hybridization of the TAR complementary sequences via the ends of their double-stranded stem J. Mol. Biol. 356, 1180-1192
36. Shojania, S. and ONeil, J. D. (2006) HIV-1 Tat is a natively unfolded protein: The solution conformation and dynamics of reduced HIV-1 Tat-(1-72) by NMR spectroscopy J. Biol. Chem. 281, 8347-8356