Oligonucleotide Conjugates of Nile Red

Nucleosides, Nucleotides and Nucleic Acids

Volumn 23, Issue 1-2, 2004, Pages 509-520

  Prokhorenko, Igor A ^a   Dioubankova, Natalia N ^a   Korshun, Vladimir A ^a  

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

Author keywords

Interaction with ds DNA; Modified oligonucleotides; Nile Red

Indexed keywords

AMINE; BENZOPHENOXAZINE; CARBAMIC ACID DERIVATIVE; DOUBLE STRANDED DNA; FLUORESCENT DYE; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG; URIDINE 2' CARBAMATE; URIDINE DERIVATIVE;

ARTICLE; CHEMICAL BINDING; COVALENT BOND; DENATURATION; FLUORESCENCE; HYDROPHOBICITY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; SPECTRAL SENSITIVITY;

CARBAMATES; DNA; KINETICS; OLIGONUCLEOTIDES; OXAZINES; SPECTROPHOTOMETRY, ULTRAVIOLET; STAINING AND LABELING; TEMPERATURE;

EID: 1542469386     PISSN: 15257770     EISSN: None     Source Type: Journal    
DOI: 10.1081/NCN-120028344     Document Type: Article

References (37)

1. Duggan, D.J.; Bittner, M.; Chen, Y.; Meltzer, P.; Trent, J.M. Expression profiling using cDNA microarrays. Nat. Genet. 1999, 21, 10-14.
2. Lichter, P.; Tang, C.J.; Call, K.; Hermanson, G.; Evans, G.A.; Housman, D.; Ward, D.C. High-resolution mapping of human chromosome 11 by in situ hybridization with cosmid clones. Science 1990, 247, 64-69.
3. McNeil, J.A.; Johnson, C.V.; Carter, K.C.; Singer, R.H.; Lawrence, J.B. Localizing DNA and RNA within nuclei and chromosomes by fluorescence in situ hybridization. Genet. Anal. Tech. Appl. 1991, 8, 41-58.
4. Chen, X.; Kwok, P.Y. Template-directed dye-terminator incorporation (TDI) assay: a homogeneous DNA diagnostic method based on fluorescence reonance energy transfer. Nucleic Acids Res. 1997, 25, 347-353.
5. Haugland, R.P. Handbook of Fluorescent Probes and Research Products; Molecular Probes: Eugene, OR, 2002.
6. Sackett, D.L.; Wolff, J. Nile red as a polarity-sensitive fluorescent probe of hydrophobic protein surfaces. Anal. Biochem. 1987, 167, 228-234.
7. Hou, Y.W.; Bardo, A.M.; Martinez, C.; Higgins, D.A. Characterization of molecular scale environments in polymer films by single molecule spectroscopy. J. Phys. Chem., B 2000, 104, 212-219.
8. Dutta, A.K.; Kamada, K.; Ohta, K. Spectroscopic studies of Nile Red in organic solvents and polymers. J. Photochem. Photobiol., A Chem. 1996, 93, 57-64.
9. Hendriks, J.; Gensch, T.; Hviid, L.; van Der Horst, M.A.; Hellingwerf, K.J.; van Thor, J.J. Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile Red. Biophys. J. 2002, 82, 1632-1643.
10. Epps, D.E.; Sarver, R.W.; Rogers, J.M.; Herberg, J.T.; Tomich, P.K. The ligand affinity of proteins measured by isothermal denaturation kinetics. Anal. Biochem. 2001, 292, 40-50.
11. Fukumoto, S.; Fujimoto, T. Deformation of lipid droplets in fixed samples. Histochem. Cell Biol. 2002, 118, 423-428.
12. Miura, S.; Gan, J.W.; Brzostowski, J.; Parisi, M.J.; Schultz, C.J.; Londos, C.; Oliver, B.; Kimmel, A.R. Functional conservation for lipid storage droplet association among perilipin, ADRP, and TIP47 (PAT)-related proteins in mammals, drosophila, and dictyostelium. J. Biol. Chem. 2002, 277, 32253-32257.
13. Nunnally, B.K.; He, H.; Li, L.-C.; Tucker, S.A.; McGrown, L.B. Cheracterization of visible dyes for four-decay fluorescence detection in DNA sequencing. Anal. Chem. 1997, 69, 2392-2397.
14. Simmonds, A.; Miler, J.N.; Moody, C.J.; Swann, E.; Briggs, M.S.J.; Bruce, I.E.; Benzophenoxazine dyes. US Patent 6,166,202, December 26, 2000.
15. Motohashi, N.; Mitscher, L.A.; Meyer, R. Potential antitumor phenoxazines. Med. Res. Rev. 1991, 11, 239-294.
16. Daban, J.-R. Fluorescent labeling of proteins with Nile Red and 2-methoxy-2,4-diphenyl-3(2H)-furanone: physicochemical basis and application to the rapid staining of sodium dodecyl sulfate polyacrylamide gels and western blots. Electrophoresis 2001, 22, 874-880.
17. Alba, F.J.; Bermudez, A.; Daban, J.-R. Green-light transilluminator for the detection without photodamage of proteins and DNA labeled with different fluorescent dyes. Electrophoresis 2001, 22, 399-403.
18. Yan, X.; Miragila, S.; Yuan, P.M. Red-emitting [8,9]benzophenoxazine nucleic acid dyes and methods for their use. US Patent 6,140,500, October 31, 2000.
19. Waring, M.J. DNA modification and cancer. Ann. Rev. Biochem. 1981, 50, 159-192.
20. Chin, K.-H.; Chen, F.-M.; Chou, S.-H. Solution structure of the ActD-5′-CCGTT3GTGG-3′ complex: drug interaction with tandem G·T mismatches and hairpin loop backbone. Nucleic Acids Res. 2003, 31, 2622-2629.
21. 1H NMR spectroscopy. J. Mol. Biol. 1996, 262, 53-68.
22. Shinomiya, M.; Chu, W.; Carlson, R.G.; Weaver, R.F.; Takusagawa, F. Structural, physical, and biological characteristics of RNA·DNA binding agent N8-actinomycin D. Biochemistry 1995, 34, 8481-8491.
23. Kamitori, S.; Takusagawa, F. Crystal structure of the 2:1 complex between d(GAAGCTTC) and the anticancer drug actinomycin D. J. Mol. Biol. 1992, 225, 445-456.
24. Ren, J.; Chaires, J.B. Sequence and structural selectivity of nucleic acid binding ligands. Biochemistry 1999, 38, 16067-16075.
25. Savintsev, I.V.; Vekshin, N.L. Non stacking binding of 7-amino-actinomycin D and actinomycin D to DNA and model nucleotide systems in solutions. Mol. Biol. (Moscow) 2002, 36, 725-730.
26. Wadkins, R.M.; Vladu, B.; Tung, C.-S. Actinomycin D binds to metastable hairpins in single-stranded DNA. Biochemistry 1998, 37, 11915-11923.
27. Wadkins, R.M.; Tung, C.-S.; Vallone, P.M.; Benight, A.S. The role of the loop in binding of an actinomycin D analog to hairpins formed by single-stranded DNA. Arch. Biochem. Biophys. 2000, 384, 199-203.
28. Chou, S.-H.; Chin, K.-H.; Chen, F.-M. Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding. Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 6625-6630.
29. Alekseev, N.N.; Bezborodov, V.S.; Gorelenko, A.Y.; Novikov, L.S.; Shchors, N.P. Synthesis of 3-substituted 9-diethylaminobenzo[a]phenoxazin-5-ones, their luminescent characteristics, and the orientation ordering in the nematic phase. J. Org. Chem. USSR 1985, 21, 2047-2048.
30. Petrochenko, E.V.; Gorelenko, A.Y.; Alekseev, N.N. The synthesis and properties of a new fluorescent label-N-hydroxysuccinimide ester of 9-diethylaminobenzo[a]phenoxazine-5-on-3-oxyacetic acid. Doklady AN BSSR 1991, 35, 918-922 (Rus).
31. Bhansali, K.G.; Kook, A.M. Synthesis and characterization of a series of 5H-benzo[a]phenoxazin-5-one derivatives as potential antiviral/antitumor agents. Heterocycles 1993, 36, 1239-1251.
32. Briggs, M.S.J.; Bruce, I.; Miller, J.N.; Moody, C.J.; Simmonds, A.C.; Swann, E. Synthesis of functionalised dyes and their coupling to amines and amino acids. J. Chem. Soc., Perkin Trans., 1 1997, 1051-1058.
33. Brousmiche, D.W.; Serin, J.M.; Frechet, J.M.J.; He, G.S.; Lin, T.-C.; Chung, S.J.; Prasad, P.N. Fluorescence resonance energy transfer in a novel two-photon absorbing system. J. Am. Chem. Soc. 2003, 125, 1448-1449.
34. Korshun, V.A.; Stetsenko, D.A.; Gait, M.J. Novel uridin-2′-yl carbamates: synthesis, incorporation into oligodeoxyribonucleotides, and remarkable fluorescence properties of 2′-pyren-1-ylmethylcarbamate. J. Chem. Soc., Perkin Trans., 1 2002, 1092-1104.
35. Arzumanov, A.; Godde, F.; Moreau, S.; Toulmé, J.-J.; Weeds, A.; Gait, M.J. Use of the fluorescent nucleoside analogue benzo[g]quinazoline 2′-O-methylriboside to monitor the binding of the HIV-1 tat protein or antisense oligonucleotides to the TAR RNA stem-loop. Helv. Chim. Acta 2000, 83, 1424-1436.
36. Deye, J.F.; Berger, T.A. Nile Red as a solvatochromic dye for measuring solvent strength in normal liquids and mixtures of normal liquids with supercritical and near critical fluids. Anal. Chem. 1990, 62, 615-622.
37. Dioubankova, N.N.; Malakhov, A.D.; Stetsenko, D.A.; Gait, M.J.; Volynsky, P.E.; Efremov, R.G.; Korshun, V.A. Pyrenemethyl ara-uridine-2′-carbamate: a strong interstrand excimer in the major groove of DNA duplex. ChemBioChem 2003, 4, 841-847.