Tiny molecular beacons: LNA/2'-O-methyl RNA chimeric probes for imaging dynamic mRNA processes in living cells

ACS Chemical Biology

Volumn 7, Issue 9, 2012, Pages 1586-1595

  Catrina, Irina E ^a   Marras, Salvatore A E ^b   Bratu, Diana P ^a,c  

^a CITY UNIVERSITY OF NEW YORK   (United States)

^b PUBLIC HEALTH RESEARCH INSTITUTE   (United States)

^c CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2' O METHYL RNA OLIGONUCLEOTIDE; LOCKED NUCLEIC ACID; MESSENGER RNA; NUCLEOTIDE; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CONFOCAL MICROSCOPY; DROSOPHILA MELANOGASTER; FEMALE; MOLECULAR BEACON; NONHUMAN; OOCYTE; PRIORITY JOURNAL;

ANIMALS; BASE SEQUENCE; DROSOPHILA MELANOGASTER; MICROSCOPY, CONFOCAL; MOLECULAR IMAGING; OLIGONUCLEOTIDES; OOCYTES; RNA PROBES; RNA, MESSENGER;

DROSOPHILA MELANOGASTER;

EID: 84868135812     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb300178a     Document Type: Article

References (32)

1. Tautz, D., and Pfeifle, C. (1989) A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma 98, 81-85. (Pubitemid 19205971)
2. Ainger, K., Avossa, D., Morgan, F., Hill, S. J., Barry, C., Barbarese, E., and Carson, J. H. (1993) Transport and localization of exogenous myelin basic protein mRNA microinjected into oligodendrocytes. J. Cell Biol. 123, 431-441. (Pubitemid 23313966)
3. Cha, B. J., Koppetsch, B. S., and Theurkauf, W. E. (2001) In vivo analysis of Drosophila bicoid mRNA localization reveals a novel microtubule-dependent axis specification pathway. Cell 106, 35-46. (Pubitemid 32709956)
4. Glotzer, J. B., Saffrich, R., Glotzer, M., and Ephrussi, A. (1997) Cytoplasmic flows localize injected oskar RNA in Drosophila oocytes. Curr. Biol. 7, 326-337. (Pubitemid 27195609)
5. MacDougall, N., Clark, A., MacDougall, E., and Davis, I. (2003) Drosophila gurken (TGFalpha) mRNA localizes as particles that move within the oocyte in two dynein-dependent steps. Dev. Cell. 4, 307-319. (Pubitemid 36342357)
6. Hachet, O., and Ephrussi, A. (2004) Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization. Nature 428, 959-963. (Pubitemid 38560311)
7. Fusco, D., Accornero, N., Lavoie, B., Shenoy, S. M., Blanchard, J. M., Singer, R. H., and Bertrand, E. (2003) Single mRNA molecules demonstrate probabilistic movement in living mammalian cells. Curr. Biol. 13, 161-167. (Pubitemid 36154346)
8. Forrest, K. M., and Gavis, E. R. (2003) Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila. Curr. Biol. 13, 1159-1168. (Pubitemid 36872938)
9. Tyagi, S. (2009) Imaging intracellular RNA distribution and dynamics in living cells. Nat. Methods 6, 331-338.
10. Tyagi, S., and Kramer, F. R. (1996) Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303-308.
11. Kloc, M., Wilk, K., Vargas, D., Shirato, Y., Bilinski, S., and Etkin, L. D. (2005) Potential structural role of non-coding and coding RNAs in the organization of the cytoskeleton at the vegetal cortex of Xenopus oocytes. Development 132, 3445-3457. (Pubitemid 41246119)
12. Vargas, D. Y., Raj, A., Marras, S. A., Kramer, F. R., and Tyagi, S. (2005) Mechanism of mRNA transport in the nucleus. Proc. Natl. Acad. Sci. U.S.A. 102, 17008-17013. (Pubitemid 41692674)
13. Tyagi, S., and Alsmadi, O. (2004) Imaging native beta-actin mRNA in motile fibroblasts. Biophys. J. 87, 4153-4162. (Pubitemid 39602919)
14. Bratu, D. P. (2003) Imaging native mRNAs in living Drosophila oocytes using molecular beacons, in UMI Dissertation Services, #3105839, Doctoral Thesis, New York University, New York.
15. Mhlanga, M. M., Bratu, D. P., Genovesio, A., Rybarska, A., Chenouard, N., Nehrbass, U., and Olivo-Marin, J. C. (2009) In vivo colocalisation of oskar mRNA and trans-acting proteins revealed by quantitative imaging of the Drosophila oocyte. PLoS One 4, e6241.
16. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415. (Pubitemid 37442169)
17. Mathews, D. H., Sabina, J., Zuker, M., and Turner, D. H. (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940. (Pubitemid 29248642)
18. 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'-Omethyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res. 29, e89.
19. Wang, L., Yang, C. J., Medley, C. D., Benner, S. A., and Tan, W. (2005) Locked nucleic acid molecular beacons. J. Am. Chem. Soc. 127, 15664-15665. (Pubitemid 41643250)
20. Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination. Nat. Biotechnol. 16, 49-53. (Pubitemid 28035948)
21. Bratu, D. P. (2006) Molecular beacons: Fluorescent probes for detection of endogenous mRNAs in living cells. Methods Mol. Biol. 319, 1-14.
22. Koshkin, A. A., Fensholdt, J., Pfundheller, H. M., and Lomholt, C. (2001) A simplified and efficient route to 2'-O, 4'-C-methylenelinked bicyclic ribonucleosides (locked nucleic acid). J. Org. Chem. 66, 8504-8512. (Pubitemid 34000651)
23. Kierzek, E., Ciesielska, A., Pasternak, K., Mathews, D. H., Turner, D. H., and Kierzek, R. (2005) The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res. 33, 5082-5093. (Pubitemid 41487816)
24. Mathews, D. H., Turner, D. H., and Zuker, M. (2007) RNA secondary structure prediction. Curr. Protoc. Nucleic Acid Chem. 28, 11.2.1-11.2.17.
25. St Johnston, D. (2005) Moving messages: The intracellular localization of mRNAs. Nat. Rev. Mol. Cell. Biol. 6, 363-375. (Pubitemid 40637854)
26. Bratu, D. P., Cha, B. J., Mhlanga, M. M., Kramer, F. R., and Tyagi, S. (2003) Visualizing the distribution and transport of mRNAs in living cells. Proc. Natl. Acad. Sci. U.S.A. 100, 13308-13313. (Pubitemid 37444738)
27. Bonnet, G., Tyagi, S., Libchaber, A., and Kramer, F. R. (1999) Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. U.S.A. 96, 6171-6176. (Pubitemid 29256638)
28. Zimyanin, V. L., Belaya, K., Pecreaux, J., Gilchrist, M. J., Clark, A., Davis, I., and St Johnston, D. (2008) In vivo imaging of oskar mRNA transport reveals the mechanism of posterior localization. Cell 134, 843-853.
29. Farazi, T. A., Juranek, S. A., and Tuschl, T. (2008) The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members. Development 135, 1201-1214. (Pubitemid 351622465)
30. Bratu, D. P., Catrina, I. E., and Marras, S. A. (2011) Tiny molecular beacons for in vivo mRNA detection. Methods Mol. Biol. 714, 141-157.
31. Mullah, B., and Livak, K. (1999) Efficient automated synthesis of molecular beacons. Nucleosides, Nucleotides Nucleic Acids 18, 1311-1312. (Pubitemid 29362242)
32. Rasband, W. S. (1997-2011) ImageJ, U.S. National Institute of Health, Bethesda, MD, USA, http://imagej.nih.gov/ij/.