Conjugates of oligonucleotides with polyaromatic fluorophores as promising DNA probes

Biosensors and Bioelectronics

Volumn 13, Issue 7-8, 1998, Pages 771-778

  Balakin, K V ^a   Korshun, V A ^a   Mikhalev, I I ^a   Maleev, G V ^a   Malakhov, A D ^a   Prokhorenko, I A ^a   Berlin, Yu A ^a  

^a SHEMYAKIN OVCHINNIKOV INSTITUTE OF BIOORGANIC CHEMISTRY   (Russian Federation)

Author keywords

4,4' dimethoxytrityl; DMT; LCAA CPG; Long chain aminoalkyl controlled pore glass

Indexed keywords

HYBRIDIZATION; OLIGONUCLEOTIDES; PERYLENE; PERYLENEACETIC ACID; POLYAROMATIC FLUOROPHORES; PYRENE;

CARBOXYLIC ACIDS; DNA SEQUENCES; DYES; FLUORESCENCE; MOLECULAR STRUCTURE; MONOMERS; OLIGOMERS; SYNTHESIS (CHEMICAL);

BIOSENSORS;

DNA; OLIGODEOXYNUCLEOTIDE; PERYLENE; PYRENE;

BIOSENSOR; CHEMICAL STRUCTURE; CONFERENCE PAPER; DNA HYBRIDIZATION; DNA PROBE; DNA SEQUENCE; NUCLEOTIDE SEQUENCE; SPECTROFLUOROMETRY;

ANIMALS; DNA; DNA PROBES; FLUORESCENT DYES; HUMANS; OLIGONUCLEOTIDES;

EID: 0032191459     PISSN: 09565663     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0956-5663(98)00041-4     Document Type: Article

References (26)

1. Balakin K.V., Korshun V.A., Prokhorenko I.A., Maleev G.V., Kudelina I.A., Gontarev S.V., Berlin Yu.A. A new reagent for labeling macromolecules: an activated derivative of the pyrene bichromophore with excimer fluorescence (English translation in Russ. J. Bioorg. Chem., 23, 28-36). Bioorg. Khim. 23:1997;33-41.
2. Balakin K.V., Malakhov A.D., Korshun V.A., Berlin Yu.A. A method of synthesis of oligonucleotides labeled with pyrene (English translation in Russ. J. Bioorg. Chem. 24, 341-343). Bioorg. Khim. 24:1998;388-390.
3. Cardullo R.A., Agrawal S., Flores C., Zamecnik P.C., Wolf D.E. Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA. 85:1988;8790-8794.
4. Deck L.M., Daub G.H. Synthesis of 10-(chloromethyl)benzo[a]pyrene. J. Org. Chem. 48:1983;3577-3580.
5. Ebata K., Masuko M., Ohtani H., Kashiwasake-Jibu M. Nucleic acid hybridization accompanied with excimer formation from two pyrene-labeled probes. Photochem. Photobiol. 62:1995;836-839.
6. Frazer J.D., Horner S.M., Woski S.A. Synthesis of a novel pyrene-containing nucleoside and its incorporation into oligonucleotides. Tetrahedron Lett. 39:1998;1279-1282.
7. Haugland, R.P., 1996. Handbook of Fluorescent Probes and Research Chemicals, 6th ed. Molecular Probes, Inc., Eugene, OR.
8. Kierzek R., Li Y., Turner D.H., Bevilacqua P.C. 5′-Amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation. J. Am. Chem. Soc. 115:1993;4985-4992.
9. Korshun V.A., Prokhorenko I.A., Gontarev S.V., Skorobogatyi M.V., Balakin K.V., Manasova E.V., Malakhov A.D., Berlin Yu.A. New pyrene derivatives for fluorescent labeling of oligonucleotides. Nucleosides and Nucleotides. 16:1997;1461-1464.
10. Lee L.G., Connell C.R., Bloch W. Allelic discrimination by nick-translation PCR with fluorogenic probes. Nucleic Acids Res. 21:1993;3761-3766.
11. Letsinger R.L., Wu T. Control of excimer emission and photochemistry of stilbene units by oligonucleotide hybridization. J. Am. Chem. Soc. 116:1994;811-812.
12. Li Y., Bevilacqua C., Mathews D., Turner D.H. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry. 34:1995;14394-14399.
13. Mann J.S., Shibata Y., Meehan T. Synthesis and properties of an oligonucleotide modified with a pyrene derivative at the 5′-phosphate. Bioconjugate Chem. 3:1992;554-558.
14. Morrison L.E., Halder T.C., Stols L.M. Solution-phase detection of polynucleotides using interacting fluorescent labels and competitive hybridization. Anal. Biochem. 183:1989;231-244.
15. III complex in pure liquid phase. Angew. Chem. Int. Ed. 29:1990;1167-1169.
16. Prober J.M., Trainor G.L., Dam R.J., Hobbs F.W., Robertson C.W., Zagursky R.J., Cocuzza A.J., Jensen M.A., Baumeister K. A system for rapid DNA sequencing with fluorescent chain-terminating dideoxynucleotides. Science. 238:1987;336-341.
17. Rippe K., Fritsch V., Westhof E., Jovin T.M. Alternating d(G-A) sequences form a parallel-stranded DNA homoduplex. EMBO J. 11:1992;3777-3786.
18. Sixou S., Szoka F.C. Jr., Green G.A., Giusti B., Zon G., Chin D.J. Intracellular oligonucleotide hybridization detected by fluorescence resonance energy transfer (FRET). Nucleic Acids Res. 22:1994;662-668.
19. Tong G., Lawlor J.M., Tregear G.W., Haralambidis J. Oligonucleotide-polyamide hybrid molecules containing multiple pyrene residues exhibit significant excimer fluorescence. J. Am. Chem. Soc. 117:1995;12151-12158.
20. Tyagi S., Kramer F.R. Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnol. 14:1996;303-308.
21. Wachter L., Jablonski J.-A., Ramachandran L. A simple and efficient procedure for the synthesis of 5′ aminoalkyl oligodeoxynucleotides. Nucleic Acids Res. 14:1986;7985-7994.
22. Yamana K., Gokota T., Ozaki H., Nakano H., Sangen O., Shimidzu T. Enhanced fluorescence in the binding of oligonucleotides with a pyrene group in the sugar fragment to complementary polynucleotides. Nucleosides and Nucleotides. 11:1992;383-390.
23. Yamana K., Nunota K., Nakano H., Sangen O. A new method for introduction of a pyrene group into a terminal position of an oligonucleotide. Tetrahedron Lett. 35:1994;2555-2558.
24. Yamana K., Takei M., Nakano H. Synthesis of oligonucleotide derivatives containing pyrene labeled glycerol linkers: enhanced excimer fluorescence on binding to a complementary DNA sequence. Tetrahedron Lett. 38:1997;6051-6054.
25. Yguerabide J., Talavera E., Alvarez J.M., Afkir M. Pyrene-labeled DNA probes for homogeneous detection of complementary DNA sequences: poly(C) model system. Anal. Biochem. 241:1996;238-247.
26. Zieger H.E. Alkylperylenes. The isomeric ethylperylenes. J. Org. Chem. 31:1966;2977-2981.