Avoiding false-positive signals with nuclease-vulnerable molecular beacons in single living cells

Nucleic Acids Research

Volumn 35, Issue 16, 2007, Pages

  Chen, Antony K ^a   Behlke, Mark A ^b   Tsourkas, Andrew ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b INTEGRATED DNA TECHNOLOGIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MYC PROTEIN; NUCLEASE; TAMOXIFEN; ANTINEOPLASTIC HORMONE AGONISTS AND ANTAGONISTS; ENDONUCLEASE; EXONUCLEASE; FLUORESCENT DYE; MESSENGER RNA; PROTEIN; QUANTUM DOT;

ACCURACY; ARTICLE; BREAST CANCER; CALIBRATION; CANCER CELL; CELL COMPARTMENTALIZATION; CELL NUCLEUS; CONTROLLED STUDY; CYTOLOGY; CYTOPLASM; FLUORESCENCE ANALYSIS; GENE EXPRESSION; HUMAN; HUMAN CELL; MOLECULAR BIOLOGY; NUCLEOTIDE SEQUENCE; ONCOGENE C MYC; PRIORITY JOURNAL; QUANTUM MECHANICS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA ANALYSIS; SIGNAL TRANSDUCTION; ARTIFACT; CHEMISTRY; DRUG EFFECT; EVALUATION; FLUORESCENCE MICROSCOPY; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; OLIGONUCLEOTIDE PROBE; TUMOR CELL LINE;

ANTINEOPLASTIC AGENTS, HORMONAL; ARTIFACTS; CELL LINE, TUMOR; CELL NUCLEUS; CYTOPLASM; ENDONUCLEASES; EXONUCLEASES; FLUORESCENT DYES; HUMANS; MICROSCOPY, FLUORESCENCE; OLIGONUCLEOTIDE PROBES; PROTEINS; PROTO-ONCOGENE PROTEINS C-MYC; QUANTUM DOTS; RNA, MESSENGER; TAMOXIFEN; TRANSCRIPTION, GENETIC;

EID: 34548724424     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkm593     Document Type: Article

References (39)

1. McAdams,H.H. and Arkin A. (1997) Stochastic mechanisms in gene expression. Proc. Nad Acad. Sci. USA, 94, 814-819.
2. Blake,W.J., Kaern,M., Cantor,C.R. and Collins J.J. (2003) Noise in eukaryotic gene expression. Nature, 422, 633-637.
3. Hume,D.A. (2000) Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood, 96 2323-2328.
4. Ross,I.L., Browne,C.M. and Hume,D.A. (1994) Transcription of individual genes in eukaryotic cells occurs randomly and infrequently Immunol. Cell. Biol., 72, 177-185.
5. Kepler,T.B. and Elston,T.C. (2001) Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations. Biophys. J., 81, 3116-3136.
6. Swain,P.S., Elowitz,M.B. and Siggia,E.D. (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Nad Acad. Sci. USA, 99, 12795-12800.
7. Tyagi S. and Kramer,F.R. (1996) Molecular beacons: Probes that fluoresce upon hybridization. Nat. Biotechnol., 14, 303-308.
8. Tyagi,S. and Alsmadi,O. (2004) Imaging native beta-actin mRNA in motile fibroblasts. Biophys; J., 87, 4153-4162.
9. Bratu,D.P., Cha,B.J., Mhlanga,M.M., KramerF.R. and Tyagi,S. (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl Acad. Sci. USA, 100, 13308-13313.
10. Santangelo,PJ., Nix,B., Tsourkas,A. and Bao,G. (2004) Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res., 32, e57.
11. Perlette J. and Tan,W. (2001) Real-time monitoring of intracellular mRNA hybridization inside single living cells. Anal. Chem., 73, 5544-5550.
12. 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.
13. Mhlanga,M.M., Vargas,D.Y., Fung,C.W., Kramer,F.R. and Tyagi.S. (2005) tRNA-finked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res., 33, 1902-1912.
14. Vargas,D.Y., Raj,A., Marras,S.A., Krainer,F.R. and Tyagi S. (2005) Mechanism of mRNA transport in the nucleus. Proc. Natl Acad. Sci. USA 102, 17008-17013.
15. Santangelo,P., Nitin,N., LaConteL., Woolums,A. and Bao,G. (2006) Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus, using molecular beacons. J. Virol., 80, 682-688.
16. Peng,X.H., Cao,Z.H., Xia,J.T., Carlson,G.W., Lewis,M.M., Wood,W.C. and Yang,L. (2005) Real-time detection of gene expression in cancer cells using molecular beacon imaging: New strategies for cancer research. Cancer Res., 65, 1909-1917.
17. Medley,C.D., Drake,T.J., TomasiniJ.M., Rogers,R.J. and Tan W. (2005) Simultaneous monitoring of the expression of multiple genes inside of single breast carcinoma cells. Anal. Chem., 77, 4713-4718.
18. DrakeT.J., Medley,C.D., Sen,A., Rogers,R.J. and Tan,W. (2005) Stochasticity of manganese superoxide dismutase mRNA expression in breast carcinoma cells by molecular beacon imaging. Chembiochem. 6, 2041-2047.
19. Li J.J., Fang,X., Schuster S.M. and Tan,W. (2000) Molecular beacons: A novel approach to detect protein - DNA interactions. This work was partially supported by kt U.S. NSF Career Award (CHE-9733650) and by a U.S. Office of Naval Research Young Investigator Award (NO0014-98-1-0621). Angew. Chem. Int. Ed. Engl., 39, 1049-1052.
20. Li J.J., Geyer,R. and Tan,W. (2000) Using molecular beacons as a sensitive fluorescence assay for enzymatic cleavage of single stranded DNA. Nucleic Acids Res., 28, E52.
21. 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 2′ O-Methyl, RNA probes for the visualization of RNA in living cellt. Nucleic Acids Res., 29, E89-89.
22. Ben-Yosef T., Yanuka O., Halle,D. and Benvenisty,N. (1998) Involvement of Myc targets in c-myc and N-myc induced human tumors. Oncogene, 17, 165-171.
23. Dubik D. Shiu R.P. (1988) Transcriptional regulation of c-myc onpogene expression by estrogen in hormone-responsive human breast cancer cells. J. Biol. Chem., 263, 12705-12708.
24. Robanus-Maandag,E.C., Bosch C.A., Kristel P.M., Hart,A.A., Faneyte.I.F., Nederlof,P.M., Peterse J.L. and van de Vijver M.J. (2003) Association of C-MYC amplification with progression from the in situ to the invasive stage in-C-MYC-amplified breast carcinomas. J. Pathol., 201, 75-82.
25. Corzo,C., Corominas,J.M., Tusquets,I., Salido,M., Bellet M., Fabregat,X., Serrano,S. and Sole,F. (2006) The MYC oncogene in breast cancer progression: From benign epithelium to invasive carcinoma. Cancer Genet. Cytogenet., 165, 151-156.
26. Blancato J., Singh,B., Liu,A., Liao;D.J. and Dickson,R.B. (2004) Correlation of amplification and overexpression of the c-myc oncogene in high-grade breast cancer: FISH, in situ hybridisation and immunohistochemical analyses. Br. J. Cancer, 90, 1612-1619.
27. 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.
28. Berthois,Y., Katzenellenbogen.J.A. and Katzenellenbogen,B.S. (1986) Phenol red in tissue culture media is a weak estrogen: Implications concerning the study of estrogen-responsive cells in culture. Proc. Nod Acad. Sci. USA, 83, 2496-2500.
29. Chu,I., Blackwell,K., Chen,S. and Slingerland J. (2005) The dual ErbBI/ ErbB2 inhibitor, lapatinib (GW572016), cooperates with tamoxifen to inhibit both cell proliferation- and estrogen-dependent gene expression in antiestrogep-resistant breast cancer. Cancer Res., 65, 18-25.
30. WolfS.F., Haines,L., Fisch,J., Kremsky,J.N., Dougherty,J.P. and Jacobs,K. (1987) Rapid hybridization kinetics of DNA attached to submicron latex particles. Nucleic Acids Res., 15, 2911-2926.
31. Henry,M.R., Stevens,P.W., Sun, J. and Kelso,D.M. (1999) Real-time measurements of DNA hybridization on microparticles with fluorescence resonance energy transfer. Anal. Biochem., 276, 204-214.
32. Brown,D.A., Kang,S.H., Gryaznov,S.M., DeDionisio,L., Heidenreich,O., Sullivan,S., Xu,X. and Nerenberg,M.I. (1994) Effect of phosphorothioate modification of oligodeoxynucleotides on specific protein binding. J. Biol. Chem., 269, 26801-26805.
33. Fisher,T.L., Terhorst,T., Cao,X. and Wagner,R.W. (1993) Intracellular disposition and metabolism of fluorescently-labeled unmodified and modified oligonucleotides microinjected into ammalian cells. Nucleic Acids Res., 21, 3857-3865.
34. Shah,Y.M., Al-Dhaheri M., Dong,Y., Ip,C., Jones,F.E. and Rowan,B.G. (2005) Selenium disrupts estrogen receptor (alpha) signaling and potentiates tamoxifen antagonism in endometrial cancer cells and tamoxifen-resistant breast cancer cells. Mol. Cancer Ther., 4 1239-1249.
35. Doisneau-Sixou,S.F., Cestac,P., Faye,J.C., Favre,G. and Sutherland,R.L. (2003) Additive effects of tamoxifen and the farnesyl transferase inhibitor FTI-277 on inhibition of MCF-7 breast cancer cell-cycle progression. Int. J. Cancer, 106, 789-798.
36. Johnson,D.R., Lee,P.K., Holmes,V.F. and Alvarez-Cohen,L. (2005) An internal reference technique for accurately quantifying specific mRNAs by real-time PCR with application to the tceA reductive dehalogenase gene. Appl. Environ. Microbiol, 71, 3866-3871.
37. Mitsuhashi,M., Tomozawa,S., Endo,K. and Shinagawa A. (2006) Quantification of mRNA in whole blood by assessing recovery of RNA and efficiency of cDNA synthesis. Clin. Chem., 52, 634-642.
38. Tian,X., Aruva,M.R., Qin,W., Zhu W., Sauter,E.R., Thakur,M.L. and Wickstrom,E. (2005) Noninvasive molecular imaging of MYC mRNA expression in human breast cancer xenografts with a [99mTc]peptide-peptide nucleic acid-peptide chimera. Bioconjug. Chem., 16, 70-79.
39. Tian,X., Chakrabarti,A., Amirkhanov,N.V., Aruva M.R., Zhang,K., Mathew,B., Cardi,C., Qin W., Sauter,E.R. et al. (2005) External imaging of CCND1, MYC, and KRAS oncogene mRNAs with tumor-targeted radionuclide-PNA-peptide chimeras. Ann. N.Y. Acad. Sci. 1059 106-144.