Pyrene excimer for DNA sensors

Current Organic Chemistry

Volumn 15, Issue 4, 2011, Pages 465-476

  Wang, Chunming ^a   Wu, Cuichen ^a   Chen, Yan ^b   Song, Yanling ^a   Tan, Weihong ^b   Yang, Chaoyong James ^a  

^a XIAMEN UNIVERSITY   (China)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

Aptamers; Binary probes; DNA sensors; Fluorescence lifetime; Molecular beacons; Pyrene excimer; Stokes shift

Indexed keywords

BIOMOLECULES; DIMERS; DNA; EXCITED STATES; FLUORESCENCE; OPTICAL PROPERTIES; PROTEINS; QUANTUM THEORY; VIRUSES;

APTAMERS; BINARY PROBES; DNA SENSORS; EXCIMERS; FLUORESCENCE LIFETIMES; MOLECULAR BEACON; MOLECULAR RECOGNITION ELEMENT; PYRENE EXCIMER; SMALL MOLECULES; STOKES SHIFT;

PYRENE;

EID: 79551677926     PISSN: 13852728     EISSN: None     Source Type: Journal    
DOI: 10.2174/138527211794474465     Document Type: Review

References (73)

1. Wang, J. From DNA biosensors to gene chips. Nucleic Acids Res. 2000, 28, 3011-3016.
2. Tombelli, S.; Marrazza, G.; Mascini, M. Recent advances on DNA biosensors. Int. J. Environ. Anal. Chem. 2001, 80, 87-99.
3. Tao, L.; Lin, L.; Hong, Z.; Long, J. DNA and RNA sensor. Sci. China, Ser. B 2005, 48, 1-10.
4. Suman A.K. Recent advances in DNA biosensor. Sens. Transducers J. 2008, 92, 122-133.
5. Becker, R.S.; Singh, I.S.; Jackson, E.A. Comprehensive spectroscopic investigation of polynuclear aromatic hydrocarbons. I. Absorption spectra and state assignments for the tetracyclic hydrocarbons and their alkylsubstituted derivatives. J. Chem. Phys. 1963, 38, 2144-2171.
6. Marti, A.A.; Jockusch, S.; Stevens, N.; Ju, J.Y.; Turro, N.J. Fluorescent hybridization probes for sensitive and selective DNA and RNA detection. Acc. Chem. Res. 2007, 40, 402-409.
7. Yao, C.X.; Kraatz, H.B.; Steer, R.P. Photophysics of pyrene-labelled compounds of biophysical interest. Photochem. Photobiol. Sci. 2005, 4, 191-199.
8. Birks, J. B. Photophysics of aromatic molecules-a postscript. Org. Mol. Photophys. 1975, 2, 409-613.
9. Kalyanasundaram, K.; Thomas, J.K. Environmental effects on vibronic band intensities in pyrene monomer fluorescence and their application in studies of micellar systems. J. Am. Chem. Soc. 1977, 99, 2039-2044.
10. Birks, J. Excimers. Rep. Prog. Phys. 1975, 38, 903-974.
11. Lehrer, S.S. Intramolecular pyrene excimer fluorescence: A probe of proximity and protein conformational change. Fluoresc. Spectrosc. 1997, 278, 286-295.
12. Soutar, A.K.; Pownall, H.J.; Hu, A.S.; Smith, L.C. Phase transitions in bilamellar vesicles. Measurements by pyrene excimer fluorescence and effect on transacylation by lecithin-cholesterol acyltransferase. Biochemistry 1974, 13, 2828-2836.
13. Reynisson, J.; Vejby-Christensen, L.; Wilbrandt, R.; Harrit, N.; Berg, R.H. Structural properties of DNO investigated with pyrene excimer formation. J. Pept. Sci. 2000, 6, 603-611.
14. Ahn, T.; Kim, J.S.; Choi, H.I.; Yun, C.H. Development of peptide substrates for trypsin based on monomer/excimer fluorescence of pyrene. Anal. Biochem. 2002, 306, 247-251.
15. Yoshida, H.; Horita, K.; Todoroki, K.; Nohta, H.; Yamaguchi, M. Highly selective fluorimetric determination of acidic amino acids by highperformance liquid chromatography following intramolecular excimerforming derivatization with a pyrene-labeling reagent. Bunseki Kagaku 2003, 52, 1113-1119.
16. Sahoo, D.; Narayanaswami, V.; Kay, C.M.; Ryan, R.O. Pyrene excimer fluorescence: A spatially sensitive probe to monitor lipid-induced helical rearrangement of apolipophorin III. Biochemistry (Mosc). 2000, 39, 6594-6601.
17. Drury, J. Examination of lipid-bound conformation of apolipoprotein E4 by pyrene excimer fluorescence. J. Biol. Chem. 2005, 280, 14605-14610.
18. Basusarkar, P.; Chandra, S.; Bhattacharyya, B. The colchicine-binding and pyrene-excimer-formation activities of tubulin involve a common cysteine residue in the beta subunit. Eur. J. Biochem. 1997, 244, 378-383.
19. Li, Y.; Li, H.W.; Ma, L.J.; Dang, Y.Q.; Wu, Y.Q. A unique protein labeling system based on melittin and the non-covalent binding-induced pyrene excimer. Chem. Commun. 2010, 46, 3768-3770.
20. Han, M. K.; Lin, P.; Paek, D.; Harvey, J.J.; Fuior, E.; Knutson, J.R. Fluorescence studies of pyrene maleimide-labeled translin: Excimer fluorescence indicates subunits associate in a tail-to-tail configuration to form octamer. Biochemistry (Mosc). 2002, 41, 3468-3476.
21. Honda, K.; Fujishima, S.H.; Ojida, A.; Hamachi, I. Pyrene excimer-based dual-emission detection of a oligoaspartate tag-fused protein by using a Zn-11-DpaTyr probe. ChemBioChem 2007, 8, 1370-1372.
22. Santra, M.K.; Dasgupta, D.; Panda, D. Pyrene excimer fluorescence of yeast alcohol dehydrogenase: A sensitive probe to investigate ligand binding and unfolding pathway of the enzyme. Photochem. Photobiol. 2006, 82, 480-486.
23. Zhang, R.X.; Tang, D.; Lu, P.; Yang, X.Y.; Liao, D.L.; Zhang, Y.J.; Zhang, M.J.; Yu, C.; Yam, V.W.W. Nucleic Acid-Induced Aggregation and Pyrene Excimer Formation. Org. Lett. 2009, 11, 4302-4305.
24. Malakhov, A.D.; Skorobogatyi, M.V.; Prokhorenko, I.A.; Gontarev, S.V.; Kozhich, D.T.; Stetsenko, D.A.; Stepanova, I.A.; Shenkarev, Z.O.; Berlin, Y.A.; Korshun, V.A. 1-(phenylethynyl)pyrene and 9,10- bis(phenylethynyl)anthracene, useful fluorescent dyes for DNA labeling: Excimer formation and energy transfer. Eur. J. Org. Chem. 2004, 6, 1298-1307.
25. Masuko, M.; Ohtani, H.; Ebata, K.; Shimadzu, A. Optimization of excimerforming two-probe nucleic acid hybridization method with pyrene as a fluorophore. Nucleic Acids Res. 1998, 26, 5409-5416.
26. Christensen, U.B.; Pedersen, E.B. Intercalating nucleic acids with pyrene nucleotide analogues as next-nearest neighbors for excimer fluorescence detection of single-point mutations under nonstringent hybridization conditions. Helv. Chim. Acta 2003, 86, 2090-2097.
27. Conlon, P.; Yang, C.Y.J.; Wu, Y.R.; Chen, Y.; Martinez, K.; Kim, Y.M.; Stevens, N.; Marti, A.A.; Jockusch, S.; Turro, N.J.; Tan, W.H. Pyrene excimer signaling molecular beacons for probing nucleic acids. J. Am. Chem. Soc. 2008, 130, 336-342.
28. Wang, K.M.; Tang, Z. W.; Yang, C. Y. J.; Kim, Y. M.; Fang, X. H.; Li, W.; Wu, Y. R.; Medley, C. D.; Cao, Z. H.; Li, J.; Colon, P.; Lin, H.; Tan, W. H. Molecular engineering of DNA: Molecular beacons. Angew. Chem. Int. Ed. 2009, 48, 856-870.
29. 2+-induced blue shift of the pyrene excimer emission: A new signal transduction mode of pyrene probes. Org. Lett. 2001, 3, 889-892.
30. Strauss, J.; Daub, J. Optically active cyclic hexapeptides with covalently attached pyrene probes: Selective alkaline earth metal ion recognition using excimer emission. Org. Lett. 2002, 4, 683-686.
31. Schazmann, B.; Alhashimy, N.; Diamond, D. Chloride selective calix[4]arene optical sensor combining urea functionality with pyrene excimer transduction. J. Am. Chem. Soc. 2006, 128, 8607-8614.
32. Focsaneanu, K.S.; Scaiano, J.C. Potential analytical applications of differential fluorescence quenching: pyrene monomer and excimer emissions as sensors for electron deficient molecules. Photochem. Photobiol. Sci. 2005, 4, 817-821.
33. Fujimoto, K.; Shimizu, H.; Inouye, M. Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons. J. Org. Chem. 2004, 69, 3271-3275.
34. Yang, C.J.; Jockusch, S.; Vicens, M.; Turro, N.J.; Tan, W.H. Light-switching excimer probes for rapid protein monitoring in complex biological fluids. Proc. Natl. Acad. Sci. USA 2005, 102, 17278-17283.
35. Yamana, K.; Iwase, R.; Furutani, S.; Tsuchida, H.; Zako, H.; Yamaoka, T.; Murakami, A. 2'-Pyrene modified oligonucleotide provides a highly sensitive fluorescent probe of RNA. Nucleic Acids Res. 1999, 27, 2387-2392.
36. Mahara, A.; Iwase, R.; Sakamoto, T.; Yamana, K.; Yamaoka, T.; Murakami, A. Bispyrene-conjugated 2'-O-methyloligonucleotide as a highly specific RNA-recognition probe. Angew. Chem. Int. Ed. 2002, 41, 3648-3650.
37. Yamana, K.; Ohtani, Y.; Nakano, H.; Saito, I. Bis-pyrene labeled DNA aptamer as an intelligent fluorescent biosensor. Bioorg. Med. Chem. Lett. 2003, 13, 3429-3431.
38. Yamana, K.; Ohshita, Y.; Fukunaga, Y.; Nakamura, M.; Maruyama, A. Bispyrene- labeled molecular beacon: A monomer-excimer switching probe for the detection of DNA base alteration. Biorg. Med. Chem. 2008, 16, 78-83.
39. Yamana, K.; Iwai, T.; Ohtani, Y.; Sato, S.; Nakamura, M.; Nakano, H. Bispyrene- labeled oligonucleotides: Sequence specificity of excimer and monomer fluorescence changes upon hybridization with DNA. Bioconjug. Chem. 2002, 13, 1266-1273.
40. Wilson, J.N.; Kool, E.T. Fluorescent DNA base replacements: reporters and sensors for biological systems. Org. Biomol. Chem. 2006, 4, 4265-4274.
41. Paris, P.L.; Langenhan, J.M.; Kool, E.T. Probing DNA sequences in solution with a monomer-excimer fluorescence color change. Nucleic Acids Res. 1998, 26, 3789-3793.
42. Matray, T.J.; Kool, E.T. A specific partner for abasic damage in DNA. Nature 1999, 399, 704-708.
43. Cho, Y.J.; Kool, E.T. Enzymatic synthesis of fluorescent oligomers assembled on a DNA backbone. ChemBioChem 2006, 7, 669-672.
44. Tyagi, S.; Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 1996, 14, 303-308.
45. Drake, T.J.; Tan, W. Molecular beacon DNA probes and their bioanalytical applications. Appl. Spectrosc. 2004, 58, 269A-280A.
46. Li, J.; Cao, Z.C.; Tang, Z.; Wang, K.; Tan, W. Molecular beacons for protein-DNA interaction studies. Methods Mol. Biol. 2008, 429, 209-224.
47. Tan, W.; Wang, K.; Drake, T.J. Molecular beacons. Curr. Opin. Chem. Biol. 2004, 8, 547-553.
48. Tan, W.; Fang, X.; Li, J.; Liu, X. Molecular beacons: a novel DNA probe for nucleic acid and protein studies. Chemistry 2000, 6, 1107-1111.
49. Matsumoto, K.; Shinohara, Y.; Bag, S.S.; Takeuchi, Y.; Morii, T.; Saito, Y.; Saito, I. Pyrene-labeled deoxyguanosine as a fluorescence sensor to discriminate single and double stranded DNA structures: Design of ends free molecular beacons. Bioorg. Med. Chem. Lett. 2009, 19 (22), 6392-6395.
50. Marti, A.A.; Li, X.; Jockusch, S.; Stevens, N.; Li, Z.; Raveendra, B.; Kalachikov, S.; Morozova, I.; Russo, J.J.; Akins, D.L.; Ju, J.; Turro, N.J. Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection. Tetrahedron 2007, 63, 3591-3600.
51. Marti, A.A.; Li, X.; Jockusch, S.; Li, Z.; Raveendra, B.; Kalachikov, S.; Russo, J.J.; Morozova, I.; Puthanveettil, S.V.; Ju, J.; Turro, N.J. Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy. Nucleic Acids Res. 2006, 34, 3161-3168.
52. Tyagi, S.; Landegren, U.; Tazi, M.; Lizardi, P.M.; Kramer, F.R. Extremely sensitive, background-free gene detection using binary probes and Q-beta replicase. Proc. Natl. Acad. Sci. USA 1996, 93, 5395-5400.
53. Marti, A.A.; Puckett, C.A.; Dyer, J.; Stevens, N.; Jockusch, S.; Ju, J.; Barton, J.K.; Turro, N.J. Inorganic-organic hybrid luminescent binary probe for DNA detection based on spin-forbidden resonance energy transfer. J. Am. Chem. Soc. 2007, 129, 8680-8681.
54. Tong, G.; Lawlor, J.M.; Tregear, G.W.; Haralambidis, J. Oligonucleotidepolyamide hybrid molecules containing multiple pyrene residues exhibit significant excimer fluorescence. J. Am. Chem. Soc. 1995, 117, 12151-12158.
55. Okamoto, A.; Kanatani, K.; Saito, I. Pyrene-labeled base-discriminating fluorescent DNA probes for homogeneous SNP typing. J. Am. Chem. Soc. 2004, 126, 4820-4827.
56. Okamoto, A.; Ichiba, T.; Saito, I. Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. J. Am. Chem. Soc. 2004, 126, 8364-8365.
57. Lee, I.J.; Yi, J.W.; Kim, B.H. Probe for i-motif structure and G-rich strands using end-stacking ability. Chem. Commun. 2009, 36, 5383-5385.
58. Chen, Y.; Yang, C.Y.J.; Wu, Y.R.; Conlon, P.; Kim, Y.; Lin, H.; Tan, W.H. Light-switching excimer beacon assays for ribonuclease H kinetic study. ChemBioChem 2008, 9, 355-359.
59. Liu, J.W.; Cao, Z.H.; Lu, Y. Functional nucleic acid sensors. Chem. Rev. 2009, 109, 1948-1998.
60. Bock, L.C.; Griffin, L.C.; Latham, J.A.; Vermaas, E.H.; Toole, J.J. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 1992, 355, 564-566.
61. Famulok, M.; Mayer, G.; Blind, M. Nucleic acid aptamers - From selection in vitro to applications in vivo. Acc. Chem. Res. 2000, 33, 591-599.
62. Robertson, D.L.; Joyce, G.F. Selection in vitro of an RNA enzyme that specifically cleaves single-stranded-DNA. Nature 1990, 344, 467-468.
63. Tuerk, C.; Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990, 249, 505-510.
64. Ellington, A.D.; Szostak, J. In vitro selection of RNA molecules that bind specific ligands. Nature 1990, 346, 818-822.
65. Fischer, N.; Tarasow, T.M.; Tok, J.B.H. Aptasensors for biosecurity applications. Curr. Opin. Chem. Biol. 2007, 11, 316-328.
66. Cho, E.J.; Lee, J.W.; Ellington, A.D. Applications of aptamers as sensors. Annu. Rev. Anal. Chem. 2009, 2, 241-264.
67. Mok, W.; Li, Y.F. Recent progress in nucleic acid aptamer-based biosensors and bioassays. Sensors 2008, 8, 7050-7084.
68. Navani, N.K.; Li, Y.F. Nucleic acid aptamers and enzymes as sensors. Curr. Opin. Chem. Biol. 2006, 10, 272-281.
69. Nagatoishi, S.; Nojima, T.; Juskowiak, B.; Takenaka, S. A pyrene-labeled Gquadruplex oligonucleotide as a fluorescent probe for potassium ion detection in biological applications. Angew. Chem. Int. Ed. 2005, 44, 5067-5070.
70. Wu, C.C.; Yan, L.; Wang, C.M.; Wang, C., Yang, C.Y.J. Target induced light-switching complementary aptamer fragment probes for direct detection of molecules in complex biological fluids. Biosens. Bioelectron. 2010, 25(10), 2232-2237.
71. Forster, T.; Kasper, K. Concentration reversal of the fluorescence of pyrene. Z. Elektrochem. Angew. Phys. Chem. 1955, 59, 976-980.
72. Yamana, K.; Ohashi, Y.; Nunota, K.; Kitamura, M.; Nakano, H.; Sangen, O.; Shimidzu, T. Synthesis of oligonucleotide derivatives with pyrene group at sugar fragment. Tetrahedron Lett. 1991, 32, 6347-6350.
73. Yang, Y.B.; Ji, S.M.; Zhou, F.K.; Zhao, J.Z. Synthesis of novel bispyrene diamines and their application as ratiometric fluorescent probes for detection of DNA. Biosens. Bioelectron. 2009, 24, 3442-3447.