Slow non-specific accumulation of 2'-deoxy and 2'-O-methyl oligonucleotide probes at mitochondria in live cells

Nucleic Acids Research

Volumn 38, Issue 9, 2010, Pages

  Rhee, Won Jong ^a   Bao, Gang ^a  

^a Emory University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBONYL CYANIDE CHLOROPHENYLHYDRAZONE; CYANINE DYE; FLUORESCENT DYE; OLIGODEOXYNUCLEOTIDE; OLIGOMETHYLNUCLEOTIDE; OLIGONUCLEOTIDE; RNA; UNCLASSIFIED DRUG; CARBOCYANINE; CYANINE DYE 3;

ARTICLE; CHEMICAL INTERACTION; CONTROLLED STUDY; FLUORESCENCE IMAGING; HELA CELL; HUMAN; HUMAN CELL; MITOCHONDRIAL MEMBRANE POTENTIAL; MITOCHONDRION; MOLECULAR BEACON; OLIGONUCLEOTIDE PROBE; PRIORITY JOURNAL; RNA ANALYSIS; SIGNAL TRANSDUCTION; STIMULUS RESPONSE; CELL CULTURE; CHEMISTRY; MITOCHONDRIAL MEMBRANE;

ALEXA;

CARBOCYANINES; CELLS, CULTURED; FLUORESCENT DYES; HUMANS; MEMBRANE POTENTIAL, MITOCHONDRIAL; MITOCHONDRIA; MITOCHONDRIAL MEMBRANES; OLIGONUCLEOTIDE PROBES;

EID: 77953968712     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq050     Document Type: Article

References (35)

1. Wu, Y., Yang, C.J., Moroz, L.L. and Tan, W. (2008) Nucleic acid beacons for long-term real-time intracellular monitoring. Anal. Chem., 80, 3025-3028.
2. McCormick, S.M., Eskin, S.G., McIntire, L.V., Teng, C.L., Lu, C.M., Russel, C.G. and Chittur, K.K. (2001) DNA microarray reveals changes in gene expression of shear stressed human umbilical vein endothelial cells. Proc. Natl Acad. Sci. USA, 98, 8955-8960.
3. Sen-Banerjee, S., Mir, S., Lin, Z., Hamik, A., Atkins, G.B., Das, H., Banerjee, P., Kumar, A. and Jain, M.K. (2005) Kruppel-like factor 2 as a novel mediator of statin effects in endothelial cells. Circulation, 112, 720-726.
4. Sorescu, G.P., Song, H., Tressel, S.L., Hwang, J., Dikalov, S., Smith, D.A., Boyd, N.L., Platt, M.O., Lassegue, B., Griendling, K.K. et al. (2004) Bone morphogenic protein 4 produced in endothelial cells by oscillatory shear stress induces monocyte adhesion by stimulating reactive oxygen species production from a nox1-based NADPH oxidase. Circ. Res., 95, 773-779.
5. Barry, M.A. and Eastman, A. (1993) Identification of deoxyribonuclease II as an endonuclease involved in apoptosis. Arch. Biochem. Biophys., 300, 440-450.
6. Crouch, R.J. and Dirksen, M.L. (1982) In Linn, S.M. and Roberts, R.J. (eds), Nucleases, Vol. 14. Cold Spring Harbor Press, Plainview, NY, pp. 211-241.
7. Cummins, L.L., Owens, S.R., Risen, L.M., Lesnik, E.A., Freier, S.M., McGee, D., Guinosso, C.J. and Cook, P.D. (1995) Characterization of fully 2'-modified oligoribonucleotide hetero-and homoduplex hybridization and nuclease sensitivity. Nucleic Acids Res., 23, 2019-2024.
8. Baker, B.F., Lot, S.S., Condon, T.P., Cheng-Flournoy, S., Lesnik, E.A., Sasmor, H.M. and Bennett, C.F. (1997) 2'-O-(2-Methoxy)ethyl-modified anti-intercellular adhesion molecular 1 (ICAM-1) oligonucleotides selectively increase the ICAM-1 mRNA level and inhibit formation of the ICAM-1 translation initiation complex in human umbilical vein endothelial cells. J. Biol. Chem., 272, 11994-12000.
9. Molenaar, C., Marras, S.A., Slats, J.C., Truffert, J.C., Lemaitre, M., Raap, A.K., Dirks, R.W. and Tanke, H.J. (2001) Linear 20 O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res., 29, E89.
10. Prakash, T.P., Johnston, J.F., Graham, M.J., Condon, T.P. and Manoharan, M. (2004) 2'-O-[2-[(N, N-dimethylamino)oxy]ethyl]modified oligonucleotides inhibit expression of mRNA in vitro and in vivo. Nucleic Acids Res., 32, 828-833.
11. Sheth, U. and Parker, R. (2003) Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science, 300, 805-808.
12. Tyagi, S. and Kramer, F.R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
13. Tyagi, S., Bratu, D.P. and Kramer, F.R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol., 16, 49-53.
14. Bao, G., Rhee, W.J. and Tsourkas, A. (2009) Fluorescent Probes for Live-Cell RNA Detection. Annu. Rev. Biomed. Eng., 11, 25-47.
15. Yang, C.J., Lin, H. and Tan, W. (2005) Molecular assembly of superquenchers in signaling molecular interactions. J. Am. Chem. Soc., 127, 12772-12773.
16. Tsourkas, A., Behlke, M.A. and Bao, G. (2002) Structure-function relationships of shared-stem and conventional molecular beacons. Nucleic Acids Res., 30, 4208-4215.
17. Tsourkas, A., Behlke, M.A., Rose, S.D. and Bao, G. (2003) Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res., 31, 1319-1330.
18. Santangelo, P.J., Nix, B., Tsourkas, A. and Bao, G. (2004) Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res., 32, e57.
19. Rhee, W.J., Santangelo, P.J., Jo, H. and Bao, G. (2008) Target accessibility and signal specificity in live-cell detection of BMP-4 mRNA using molecular beacons. Nucleic Acids Res., 36, e30.
20. Nitin, N., Rhee, W.J. and Bao, G. (2009) Translation inhibition reveals interaction of 2'-deoxy and 2'-O-methyl molecular beacons with mRNA targets in living cells. Nucleic Acids Res., 37, 4977-4986.
21. Sokol, D.L., Zhang, X., Lu, P. and Gewirtz, A.M. (1998) Real time detection of DNA.RNA hybridization in living cells. Proc. Natl Acad. Sci. USA, 95, 11538-11543.
22. Marras, S.A., Kramer, F.R. and Tyagi, S. (2002) Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Res., 30, e122.
23. Marras, S.A.E., Kramer, F.R. and Tyagi, S. (1999) Multiplex detection of single-nucleotide variations using molecular beacons. Genetic Analysis: Biomol. Eng., 14, 151-156.
24. Zhang, P., Beck, T. and Tan, W. (2001) Design of a molecular beacon DNA probe with two fluorophores. Angew. Chem. Int. Ed. Engl., 40, 402-405.
25. Heytler, P.G. (1979) Uncouplers of oxidative phosphorylation. Methods Enzymol., 55, 462-472.
26. Finucane, D.M., Waterhouse, N.J., Amarante-Mendes, G.P., Cotter, T.G. and Green, D.R. (1999) Collapse of the inner mitochondrial transmembrane potential is not required for apoptosis of HL60 cells. Exp. Cell. Res., 251, 166-174.
27. Facompre, M., Wattez, N., Kluza, J., Lansiaux, A. and Bailly, C. (2000) Relationship between cell cycle changes and variations of the mitochondrial membrane potential induced by etoposide. Mol. Cell Biol. Res. Commun., 4, 37-42.
28. Armstrong, J.S., Steinauer, K.K., French, J., Killoran, P.L., Walleczek, J., Kochanski, J. and Knox, S.J. (2001) Bcl-2 inhibits apoptosis induced by mitochondrial uncoupling but does not prevent mitochondrial transmembrane depolarization. Exp. Cell. Res., 262, 170-179.
29. Castedo, M., Ferri, K., Roumier, T., Metivier, D., Zamzami, N. and Kroemer, G. (2002) Quantitation of mitochondrial alterations associated with apoptosis. J. Immunol. Methods, 265, 39-47.
30. Santangelo, P.J., Nitin, N. and Bao, G. (2005) Direct visualization of mRNA colocalization with mitochondria in living cells using molecular beacons. J. Biomed. Opt., 10, 044025.
31. Henze, K. and Martin, W. (2003) Evolutionary biology: essence of mitochondria. Nature, 426, 127-128.
32. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K. and Watson, J.D. (1994) Molecular Biology of the Cell, 3rd edn. Garland Publishing, New York, NY.
33. Johnson, L.V., Walsh, M.L., Bockus, B.J. and Chen, L.B. (1981) Monitoring of relative mitochondrial membrane potential in living cells by fluorescence microscopy. J. Cell. Biol., 88, 526-535.
34. Cady, N.C., Strickland, A.D. and Batt, C.A. (2007) Optimized linkage and quenching strategies for quantum dot molecular beacons. Mol. Cell Probes, 21, 116-124.
35. Nitin, N., Santangelo, P.J., Kim, G., Nie, S. and Bao, G. (2004) Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells. Nucleic Acids Res., 32, e58