Molecular beacons and related probes for intracellular RNA imaging

Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology

Volumn 2, Issue 1, 2010, Pages 11-19

  Santangelo, Philip J ^a  

^a Emory University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELLULAR COMPARTMENTS; CELLULAR RNA; DEGRADATION PATHWAYS; IMAGING PROBE; LIVE CELL; MOLECULAR BEACON;

NUCLEIC ACIDS; PROBES;

RNA;

NUCLEIC ACID BASE; RNA;

CELL PERMEABILIZATION; IMAGING; KINETICS; MEDICAL RESEARCH; MICROINJECTION; MOLECULAR BEACON; MOLECULAR PROBE; PRIORITY JOURNAL; REVIEW; RNA ANALYSIS; SENSITIVITY ANALYSIS;

ANIMALS; CELLS; HUMANS; MAMMALS; MOLECULAR IMAGING; NANOTECHNOLOGY; RNA; RNA PROBES;

EID: 77953658619     PISSN: 19395116     EISSN: 19390041     Source Type: Journal    
DOI: 10.1002/wnan.52     Document Type: Review

References (58)

1. Fusco D, et al. Single mRNA molecules demonstrate probabilisticmovement in livingmammalian cells. Curr Biol 2003, 13:161-167.
2. Daigle N, Ellenberg J. LambdaN-GFP: anRNAreporter system for live-cell imaging. Nat Methods 2007, 4:633-636.
3. Ozawa T, et al. Imaging dynamics of endogenous mitochondrial RNA in single living cells. NatMethods 2007, 4:413-419.
4. Politz JC, Taneja KL, Singer RH. Characterization of hybridization between synthetic oligodeoxynucleotides and RNA in living cells. Nucleic Acids Res 1995, 23:4946-4953.
5. Leonetti JP, et al. Intracellular distribution of microinjected antisense oligonucleotides. Proc Natl Acad Sci U S A 1991, 88:2702-2706.
6. Brodsky AS, Silver PA. Identifying proteins that affect mRNA localization in living cells. Methods 2002, 26:151-155.
7. Shav-Tal Y, et al. Dynamics of single mRNPs in nuclei of living cells. Science 2004, 304(5678): 1797-1800.
8. Giorgi C, Moore M. The nuclear nurture and cytoplasmic nature of localized mRNPs. Semin Cell Dev Biol 2007, 18:186-193.
9. de Silanes IL, Quesada MP, Esteller M. Aberrant regulation of messenger RNA 3′-untranslated region in human cancer. Cell Oncol 2007, 29:1-17.
10. Jambhekar A, Derisi JL. Cis-acting determinants of asymmetric, cytoplasmic RNA transport. RNA 2007, 13:625-642.
11. Simmonds P, Tuplin A, Evans DJ. Detection of genomescale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: implications for virus evolution and host persistence. RNA 2004, 10:1337-1351.
12. Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotechnol 1996, 14:303-308.
13. Sokol DL, et al. Real time detection of DNA.RNA hybridization in living cells. Proc Natl Acad Sci U S A 1998, 95:11538-11543.
14. Tsourkas A, et al. Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Res 2003, 31:1319-1330.
15. Tyagi S, Bratu DP, Kramer FR. Multicolor molecular beacons for allele discrimination. Nat Biotechnol 1998, 16(1):49-53.
16. Bratu DP, et al. Visualizing the distribution and transport of mRNAs in living cells. Proc Natl Acad Sci U S A 2003, 100:13308-13313.
17. Santangelo PJ, et al. Dual FRET molecular beacons for mRNA detection in living cells. Nucleic Acids Res 2004, 32(6):e57.
18. Tsuji A, et al. Direct observation of specific messenger RNA in a single living cell under a fluorescence microscope. Biophys J 2000, 78:3260-3274.
19. Tsuji A, et al. Development of a time-resolved fluorometric method for observing hybridization in living cells using fluorescence resonance energy transfer. Biophys J 2001, 81(1):501-515.
20. Abe H, Kool ET. Flow cytometric detection of specific RNAs in native human cells with quenched autoligating FRET probes. Proc Natl Acad Sci U S A 2006, 103:263-268.
21. Molenaar C, et al. Linear 2′ O-Methyl RNA probes for the visualization of RNA in living cells. Nucleic Acids Res 2001, 29(17):E89-E89.
22. Nitin N, et al. Peptide-linked molecular beacons for efficient delivery and rapid mRNA detection in living cells. Nucleic Acids Res 2004, 32(6):e58.
23. Rhee WJ, et al., Target accessibility and signal specificity in live-cell detection of BMP-4 mRNA using molecular beacons. Nucleic Acids Res, 2008, 36(5):e30.
24. Santangelo P, et al. Live-cell characterization and analysis of a clinical isolate of bovine respiratory syncytial virus, using molecular beacons. J Virol 2006, 80:682-688.
25. Santangelo PJ, Nitin N, Bao G. Direct visualization of mRNA colocalization with mitochondria in living cells using molecular beacons. J Biomed Opt 2005, 10(4):44025.
26. Mhlanga MM, et al. tRNA-linked molecular beacons for imaging mRNAs in the cytoplasm of living cells. Nucleic Acids Res 2005, 33:1902-1912.
27. Tyagi S, Alsmadi O. Imaging native beta-actin mRNA in motile fibroblasts. Biophys J 2004, 87:4153-4162.
28. Vargas DY, et al. Mechanism of mRNA transport in the nucleus. Proc Natl Acad Sci U S A 2005, 102:17008-17013.
29. Santangelo PJ, Bao G. Dynamics of filamentous viral RNPs prior to egress. Nucleic Acids Res 2007, 35:3602-3611.
30. Wu Y, et al. Nucleic acid beacons for long-term real-time intracellular monitoring. Anal Chem 2008, 80:3025-3028.
31. Suzuki T, et al. Imaging endogenous gene expression in brain cancer in vivo with 111In-peptide nucleic acid antisense radiopharmaceuticals and brain drug-targeting technology. J Nucl Med 2004, 45:1766-1775.
32. Shi N, Boado RJ, Pardridge WM. Antisense imaging of gene expression in the brain in vivo. Proc Natl Acad Sci U S A 2000, 97:14709-14714.
33. Vester B, Wengel J. LNA (locked nucleic acid): highaffinity targeting of complementary RNA and DNA. Biochemistry 2004, 43:13233-13241.
34. Kurreck J, et al. Design of antisense oligonucleotides stabilized by locked nucleic acids. Nucleic Acids Res 2002, 30:1911-1918.
35. Aartsma-Rus A, et al. Comparative analysis of antisense oligonucleotide analogs for targeted DMD exon 46 skipping in muscle cells. Gene Ther 2004, 11:1391-1398.
36. Tsourkas A, Behlke MA, Bao G. Hybridization of 2′-O-methyl and 2′-deoxy molecular beacons to RNA and DNA targets. Nucleic Acids Res 2002, 30:5168-5174.
37. Romani A. Regulation of magnesium homeostasis and transport in mammalian cells. Arch Biochem Biophys 2007, 458(1):90-102.
38. FabaniMM, GaitMJ. miR-122 targeting with LNA/2′-O-methyl oligonucleotide mixmers, peptide nucleic acids (PNA), and PNA-peptide conjugates. RNA 2008, 14:336-346.
39. Politz JC, et al. Intranuclear diffusion and hybridization state of oligonucleotides measured by fluorescence correlation spectroscopy in living cells. Proc Natl Acad Sci U S A 1998, 95:6043-6048.
40. Politz JC, et al. Movement of nuclear poly(A) RNA throughout the interchromatin space in living cells. Curr Biol 1999, 9:285-291.
41. Sixou S, et al. Intracellular oligonucleotide hybridization detected by fluorescence resonance energy transfer (FRET). Nucleic Acids Res 1994, 22:662-668.
42. Perlette J, Tan W. Real-time monitoring of intracellular mRNA hybridization inside single living cells. Anal Chem 2001, 73:5544-5550.
43. Chen AK, Behlke MA, Tsourkas A. Avoiding falsepositive signals with nuclease-vulnerable molecular beacons in single living cells. Nucleic Acids Res 2007, 35:e105.
44. Clark RE, et al. Clinical use of streptolysin-O to facilitate antisense oligodeoxyribonucleotide delivery for purging autografts in chronic myeloid leukaemia. Bone Marrow Transplant 1999, 23:1303-1308.
45. GilesRV, et al. Single base discrimination for ribonuclease H-dependent antisense effects within intact human leukaemia cells. Nucleic Acids Res 1995, 23:954-961.
46. Giles RV, et al. Identification of a good c-myc antisense oligodeoxynucleotide target site and the inactivity at this site of novel NCH triplet - targeting ribozymes. Nucleosides Nucleotides 1999, 18:1935-1944.
47. Giles RV, et al. Selecting optimal oligonucleotide composition for maximal antisense effect following streptolysin O-mediated delivery into human leukaemia cells. Nucleic Acids Res 1998, 26:1567-1575.
48. Spiller DG, et al. Improving the intracellular delivery and molecular efficacy of antisense oligonucleotides in chronic myeloid leukemia cells: a comparison of streptolysin-O permeabilization, electroporation, and lipophilic conjugation. Blood 1998, 91:4738-4746.
49. Barry EL, Gesek FA, Friedman PA. Introduction of antisense oligonucleotides into cells by permeabilization with streptolysin O. Biotechniques 1993, 15:1016-1018 1020.
50. Walev I, et al. Delivery of proteins into living cells by reversible membrane permeabilization with streptolysin-O. Proc Natl Acad Sci U S A 2001, 98:3185-3190.
51. Paillasson S, et al. In situ hybridization in living cells: detection of RNA molecules. Exp Cell Res 1997, 231:226-233.
52. Sohail M. Antisense technology: inaccessibility and non-specificity. Drug Discov Today 2001, 6:1260-1261.
53. Sohail M, et al. Antisense oligonucleotides selected by hybridisation to scanning arrays are effective reagents in vivo. Nucleic Acids Res 2001, 29:2041-2051.
54. Sohail M, Southern EM. Hybridization of antisense reagents to RNA. Curr Opin Mol Ther 2000, 2:264-271.
55. Sohail M, Southern EM. Selecting optimal antisense reagents. Adv Drug Deliv Rev 2000, 44(1):23-34.
56. Sohail M, Southern EM. Using oligonucleotide scanning arrays to find effective antisense reagents. Methods Mol Biol 2001, 170:181-199.
57. Raj A, et al. Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 2008, 5:877-879.
58. Femino AM, et al. Visualization of single RNA transcripts in situ. Science 1998, 280(5363):585-590.