Rapid miRNA imaging in cells using fluorogenic templated staudinger reaction between PNA-based probes

Methods in Molecular Biology

Volumn 1050, Issue , 2014, Pages 179-192

  Gorska, Katarzyna ^a   Winssinger, Nicolas ^a  

^a UNIVERSITÉ LOUIS PASTEUR   (France)

Author keywords

Imaging; miRNA; Peptide nucleic acid (PNA); Pro fluorophore; Rhodamine; Staudinger reaction; Templated reaction

Indexed keywords

AZIDE; MICRORNA; NUCLEIC ACID; PEPTIDE NUCLEIC ACID; PHOSPHINE; RNA; FLUORESCENT DYE; PHOSPHINE DERIVATIVE; RHODAMINE; TRIS(2 CARBOXYETHYL)PHOSPHINE; TRIS(2-CARBOXYETHYL)PHOSPHINE; SYNTHETIC DNA;

ARTICLE; CONJUGATION; HUMAN; HUMAN CELL; HYBRIDIZATION; IMAGING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAPID MIRNA IMAGING; STAUDINGER REACTION; SYNTHESIS; TURNOVER TIME; CELL ADHESION; CHEMISTRY; FLUORESCENCE IMAGING; FLUORESCENCE MICROSCOPY; METABOLISM; METHODOLOGY; TIME; ADHERENT CELL; CONTROLLED STUDY; DNA TEMPLATE; FLOW CYTOMETRY; IN VITRO STUDY; NUCLEIC ACID SYNTHESIS; RNA ANALYSIS; VALIDATION STUDY;

CELL ADHESION; FLUORESCENT DYES; HUMANS; MICRORNAS; MICROSCOPY, FLUORESCENCE; OPTICAL IMAGING; PEPTIDE NUCLEIC ACIDS; PHOSPHINES; RHODAMINES; TIME FACTORS;

EID: 84892900469     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-553-8_15     Document Type: Article

References (24)

1. Winter J, Jung S, Keller S, Gregory RI, Diederichs S (2009) Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 11:228-234
2. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E et al (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99:15524-15529
3. Chin LJ, Ratner E, Leng S, Zhai R, Nallur S, Babar I et al (2008) A SNP in a let-7 microRNA complementary site in the KRAS 3' untranslated region increases non-small cell lung cancer risk. Cancer Res 68:8535-8540
4. Metzler M, Wilda M, Busch K, Viehmann S, Borkhardt A (2004) High expression of precursor microRNA-155/BIC RNA in children with Burkitt lymphoma. Genes Chromosomes Cancer 39:167-169
5. Jay C, Nemunaitis J, Chen P, Fulgham P, Tong AW (2007) miRNA profi ling for diagnosis and prognosis of human cancer. DNA Cell Biol 26:293-300
6. Pena JT, Sohn-Lee C, Rouhanifard SH, Ludwig J, Hafner M, Mihailovic A et al (2009) miRNA in situ hybridization in formaldehyde and EDC-fi xed tissues. Nat Methods 6: 139-141
7. Politz JC, Zhang F, Pederson T (2006) MicroRNA-206 colocalizes with ribosome-rich regions in both the nucleolus and cytoplasm of rat myogenic cells. Proc Natl Acad Sci USA 103:18957-18962
8. Lu J, Tsourkas A (2011) Quantifi cation of miRNA abundance in single cells using locked nucleic acid-FISH and enzyme-labeled fl uorescence. Methods Mol Biol 680:77-88
9. Silverman AP, Kool ET (2006) Detecting RNA and DNA with templated chemical reactions. Chem Rev 106:3775-3789
10. Grossmann TN, Strohbach A, Seitz O (2008) Achieving turnover in DNA-templated reactions. Chembiochem 9:2185-2192
11. Franzini RM, Kool ET (2009) Effi cient nucleic acid detection by templated reductive quencher release. J Am Chem Soc 131:16021-16023
12. Franzini RM, Kool ET (2011) Two successive reactions on a DNA template: a strategy for improving background fl uorescence and specifi city in nucleic acid detection. Chemistry 17:2168-2175
13. Sando S, Kool ET (2002) Imaging of RNA in bacteria with self-ligating quenched probes. J Am Chem Soc 124:9686-9687
14. Silverman AP, Baron EJ, Kool ET (2006) RNA-templated chemistry in cells: discrimination of Escherichia, Shigella and Salmonella bacterial strains with a new two-color FRET strategy. Chembiochem 7:1890-1894
15. Silverman AP, Kool ET (2005) Quenched autoligation probes allow discrimination of live bacterial species by single nucleotide differences in rRNA. Nucleic Acids Res 33: 4978-4986
16. Abe H, Kool ET (2006) Flow cytometric detection of specifi c RNAs in native human cells with quenched autoligating FRET probes. Proc Natl Acad Sci USA 103:263-268
17. Pianowski Z, Gorska K, Oswald L, Merten CA, Winssinger N (2009) Imaging of mRNA in live cells using nucleic acid-templated reduction of azidorhodamine probes. J Am Chem Soc 131:6492-6497
18. Furukawa K, Abe H, Hibino K, Sako Y, Tsuneda S, Ito Y (2009) Reduction-triggered fl uorescent amplifi cation probe for the detection of endogenous RNAs in living human cells. Bioconjug Chem 20:1026-1036
19. Abe H, Wang J, Furukawa K, Oki K, Uda M, Tsuneda S et al (2008) A reduction-triggered fl uorescence probe for sensing nucleic acids. Bioconjug Chem 19:1219-1226
20. Franzini RM, Kool ET (2008) 7-Azidomethoxycoumarins as profl uorophores for templated nucleic acid detection. Chembiochem 9: 2981-2988
21. Zhou P, Wang M, Du L, Fisher GW, Waggoner A, Ly DH (2003) Novel binding and effi cient cellular uptake of guanidine-based peptide nucleic acids (GPNA). J Am Chem Soc 125: 6878-6879
22. Gorska K, Keklikoglou I, Tschulena I, Winssingera N (2011) Rapid fl uorescence imaging of miRNAs in human cells using templated Staudinger reaction. Chem Sci 2: 1969-1975
23. Egholm M, Buchardt O, Christensen L, Behrens C, Freier SM, Driver DA et al (1993) PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogenbonding rules. Nature 365:566-568
24. Nielsen PE (2004) PNA technology. Mol Biotechnol 26:233-248