Antisense activity detection by inhibition of fluorescence resonance energy transfer

Luminescence

Volumn 19, Issue 2, 2004, Pages 85-93

  Benitez Hess M L ^a   DiPaolo, J A ^b   Alvarez Salas, L M ^a  

^a DEPARTAMENTO DE FÍSICA   (Mexico)

^b NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Antisense; Energy transfer; Fluorescence; Green fluorescent protein; Oligodeoxynucleotides

Indexed keywords

FORSTER RESONANCE ENERGY TRANSFER; GENE EXPRESSION; GENE THERAPY; NUCLEIC ACIDS; PROTEINS;

ANTISENSE; ANTISENSE ACTIVITY; ANTISENSE OLIGODEOXYNUCLEOTIDES; ENERGY TRANSFER EFFECTS; ENERGY-TRANSFER; FLUORESCENCE RESONANCE ENERGY TRANSFER; GREEN FLUORESCENT PROTEIN; HUMAN PAPILLOMA VIRUS; IN-VIVO; OLIGODEOXYNUCLEOTIDES;

ENERGY TRANSFER;

AMINO ACID; ANTISENSE OLIGODEOXYNUCLEOTIDE; GREEN FLUORESCENT PROTEIN; MESSENGER RNA; NUCLEIC ACID; RIBONUCLEASE H; YELLOW FLUORESCENT PROTEIN; BACTERIAL PROTEIN; PHOTOPROTEIN; RECOMBINANT PROTEIN; VIRUS RNA; YELLOW FLUORESCENT PROTEIN, BACTERIA;

ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; ENZYME ASSAY; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENE EXPRESSION; HUMAN PAPILLOMAVIRUS TYPE 16; HYBRIDIZATION; NONHUMAN; PROTEIN VARIANT; STATISTICAL SIGNIFICANCE; CHEMISTRY; DNA PROBE; DRUG ANTAGONISM; FLOW CYTOMETRY; FLUORESCENCE MICROSCOPY; GENETICS; HUMAN; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SYNTHESIS;

BACTERIAL PROTEINS; BASE SEQUENCE; DNA PROBES, HPV; FLOW CYTOMETRY; FLUORESCENCE RESONANCE ENERGY TRANSFER; GREEN FLUORESCENT PROTEINS; HUMANS; LUMINESCENT PROTEINS; MICROSCOPY, FLUORESCENCE; MOLECULAR SEQUENCE DATA; OLIGODEOXYRIBONUCLEOTIDES, ANTISENSE; RECOMBINANT PROTEINS; RNA, MESSENGER; RNA, VIRAL;

EID: 7544244886     PISSN: 15227235     EISSN: 10991271     Source Type: Journal    
DOI: 10.1002/bio.763     Document Type: Article

References (37)

1. Bonham MA, Brown S, Boyd AL et al. An assessment of the antisense properties of RNase H-competent and steric-blocking oligomers. Nucleic Acids Res. 1995; 23: 1197-1203.
2. Vickers TA, Wyatt JR, Freier SM. Effects of RNA secondary structure on cellular antisense activity. Nucleic Acids Res. 2000; 28: 1340-1347.
3. Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H. Positional effects of short interfering RNAs targeting the human coagulation trigger tissue factor. Nucleic Acids Res. 2002; 30: 1757-1766.
4. Miyagishi M, Hayashi M, Taira K. Comparison of the suppressive effects of antisense oligonucleotides and siRNAs directed against the same targets in mammalian cells. Antisense Nucleic Acid Drug Dev. 2003; 13: 1-7.
5. Pan WH, Devlin HF, Kelley C, Isom HC, Clawson GA. A selection system for identifying accessible sites in target RNAs. RNA 2001; 7: 610-621.
6. Scherr M, Rossi JJ, Sczakiel G, Patzel V. RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts. Nucleic Acids Res. 2000; 28: 2455-2461.
7. Mathews DH, Turner DH. Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J. Mol. Biol. 2002; 317: 191-203.
8. Misteli T, Spector DL. Applications of the green fluorescent protein in cell biology and biotechnology. Nature Biotechnol. 1997; 15: 961-964.
9. Heim R, Tsien RY. Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr. Biol. 1996; 6: 178-182.
10. 2+ based on green fluorescent proteins and calmodulin. Nature 1997; 388: 882-887.
11. Harpur AG, Wouters FS, Bastiaens PI. Imaging FRET between spectrally similar GFP molecules in single cells. Nature Biotechnol. 2001; 19: 167-169.
12. dos Remedios C, Moens PD. Fluorescence resonance energy transfer spectroscopy is a reliable 'ruler' for measuring structural changes in proteins. Dispelling the problem of the unknown orientation factor. J. Struct. Biol. 1995; 115: 175-185.
13. Jensen KK, Martini L, Schwartz TW. Enhanced fluorescence resonance energy transfer between spectral variants of green fluorescent protein through zinc-site engineering. Biochemistry 2001; 40: 938-945.
14. Xu X, Gerard AL, Huang BC et al. Detection of programmed cell death using fluorescence energy transfer. Nucleic Acids Res. 1998; 26: 2034-2035.
15. 2+ imaging by a new calmodulin-GFP fusion molecule. Nature Struct. Biol. 2001; 8: 1069-1073.
16. Young DC, Kingsley SD, Ryan KA, Dutko FJ. Selective inactivation of eukaryotic β-galactosidase in assays for inhibitors of HIV-1 TAT using bacterial β-galactosidase as a reporter enzyme. Anal. Biochem. 1993; 215: 24-30.
17. Gorman CM, Moffat LF, Howard BH. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol. Cell Biol. 1982; 2: 1044-1051.
18. Berger J, Hauber J, Hauber R, Geiger R, Cullen BR. Secreted placental alkaline phosphatase: a powerful new quantitative indicator of gene expression in eukaryotic cells. Gene 1988; 66: 1-10.
19. Nordeen SK. Luciferase reporter gene vectors for analysis of promoters and enhancers. Biotechniques 1988; 6: 454-458.
20. Chalfie M, Tu Y, Euskirchen G, Ward WW, Prasher DC. Green fluorescent protein as a marker for gene expression. Science 1994; 263: 802-805.
21. Sambrook J, Fritsch EF, Maniatis T. Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press: New York, 1989.
22. Alvarez-Salas LM, Arpawong TE, DiPaolo JA. Growth inhibition of cervical tumor cells by antisense oligodeoxynucleotides directed to the human papillomavirus type 16 E6 gene. Antisense Nucleic Acid Drug Dev. 1999; 9: 441-450 (US Patents 6 084 090 and 6 277 980).
23. Van Der Meer BW, Coker GI, Chen S-Y. Resonance Energy Transfer, Theory and Data. CSH Publishers: New York, 1994.
24. Tyas L, Brophy VA, Pope A, Rivett AJ, Tavare JM. Rapid caspase-3 activation during apoptosis revealed using fluorescence-resonance energy transfer. EMBO Rep. 2000; 1: 266-270.
25. Mitra RD, Silva CM, Youvan DC. Fluorescence resonance energy transfer between blue-emitting and red-shifted excitation derivatives of the green fluorescent protein. Gene 1996; 173: 13-17.
26. Zuker M, Jacobson AB. Using reliability information to annotate RNA secondary structures. RNA 1998; 4: 669-679.
27. Agrawal S, Zhao Q. Antisense therapeutics. Curr. Opin. Chem. Biol. 1998; 2: 519-528.
28. Alvarez-Salas LM, Benitez-Hess ML, DiPaolo JA. Advances in the development of ribozymes and antisense oligodeoxynucleotides as antiviral agents for human papillomaviruses. Antivir. Ther. 2003; 8: 265-278.
29. Baker BF, Condon TP, Koller E et al. Discovery and analysis of antisense oligonucleotide activity in cell culture. Methods 2001; 23: 191-198.
30. Jaschke A. Artificial ribozymes and deoxyribozymes. Curr. Opin. Struct. Biol. 2001; 11: 321-326.
31. Patzel V, Steidl U, Kronenwett R, Haas R, Sczakiel G. A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability. Nucleic Acids Res. 1999; 27: 4328-4334.
32. Miyawaki A, Tsien RY. Monitoring protein conformations and interactions by fluorescence resonance energy transfer between mutants of green fluorescent protein. Methods Enzymol. 2000; 327: 472-500.
33. Venturini F, Braspenning J, Homann M, Gissmann L, Sczakiel G. Kinetic selection of HPV 16 E6/E7-directed antisense nucleic acids: anti-proliferative effects on HPV 16-transformed cells. Nucleic Acids Res. 1999; 27: 1585-1592.
34. Zhou Q, Xiao J, Liu Y. 2000. Participation of syntaxin 1A in membrane trafficking involving neurite elongation and membrane expansion. J. Neurosci. Res. 61: 321-328.
35. Tertoolen LG, Blanchetot C et al. Dimerization of receptor protein-tyrosine phosphatase α in living cells. BMC. Cell Biol. 2001; 2: 8-22.
36. Li HY, Ng EK, Lee SM et al. Protein-protein interaction of FHL3 with FHL2 and visualization of their interaction by green fluorescent proteins (GFP) two-fusion fluorescence resonance energy transfer (FRET). J. Cell Biochem. 2001; 80: 293-303.
37. Sourjik V, Berg HC. Binding of the Escherichia coli response regulator CheY to its target measured in vivo by fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 2002; 99: 12669-12674.