메뉴 건너뛰기




Volumn 5, Issue 11, 2010, Pages 1065-1074

Combining SELEX screening and rational design to develop light-up fluorophore-RNA aptamer pairs for RNA tagging

Author keywords

[No Author keywords available]

Indexed keywords

APTAMER; FLUORESCENT DYE; RNA; SMALL MOLECULE FLUOROGEN; UNCLASSIFIED DRUG;

EID: 78649643879     PISSN: 15548929     EISSN: 15548937     Source Type: Journal    
DOI: 10.1021/cb1001894     Document Type: Article
Times cited : (41)

References (49)
  • 1
    • 0031663369 scopus 로고    scopus 로고
    • The green fluorescent protein
    • Tsien, R. Y. (1998) The green fluorescent protein Annu. Rev. Biochem. 67, 509-544
    • (1998) Annu. Rev. Biochem. , vol.67 , pp. 509-544
    • Tsien, R.Y.1
  • 2
    • 33746431492 scopus 로고    scopus 로고
    • Chemical labeling strategies for cell biology
    • Marks, K. M. and Nolan, G. P. (2006) Chemical labeling strategies for cell biology Nat. Methods 3, 591-596
    • (2006) Nat. Methods , vol.3 , pp. 591-596
    • Marks, K.M.1    Nolan, G.P.2
  • 3
    • 33947500247 scopus 로고    scopus 로고
    • Chemical tools for biomolecular imaging
    • Johnsson, N. and Johnsson, K. (2007) Chemical tools for biomolecular imaging ACS Chem. Biol. 2, 31-38
    • (2007) ACS Chem. Biol. , vol.2 , pp. 31-38
    • Johnsson, N.1    Johnsson, K.2
  • 4
    • 56749104130 scopus 로고    scopus 로고
    • Fluorescent probes for super-resolution imaging in living cells
    • Fernandez-Suarez, M. and Ting, A. Y. (2008) Fluorescent probes for super-resolution imaging in living cells Nat. Rev. Mol. Cell Biol. 9, 929-943
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 929-943
    • Fernandez-Suarez, M.1    Ting, A.Y.2
  • 5
    • 34547602169 scopus 로고    scopus 로고
    • Chemical labeling of protein in living cells
    • Dragulescu-Andrasi, A. and Rao, J. (2007) Chemical labeling of protein in living cells ChemBioChem 8, 1099-1101
    • (2007) ChemBioChem , vol.8 , pp. 1099-1101
    • Dragulescu-Andrasi, A.1    Rao, J.2
  • 6
    • 65449131152 scopus 로고    scopus 로고
    • Imaging intracellular RNA distribution and dynamics in living cells
    • Tyagi, S. (2009) Imaging intracellular RNA distribution and dynamics in living cells Nat. Methods 6, 331-338
    • (2009) Nat. Methods , vol.6 , pp. 331-338
    • Tyagi, S.1
  • 7
    • 70849088746 scopus 로고    scopus 로고
    • Subcellular mRNA localization in animal cells and why it matters
    • Holt, C. E. and Bullock, S. L. (2009) Subcellular mRNA localization in animal cells and why it matters Science 326, 1212-1216
    • (2009) Science , vol.326 , pp. 1212-1216
    • Holt, C.E.1    Bullock, S.L.2
  • 8
    • 67651151407 scopus 로고    scopus 로고
    • Fluorescent probes for live-cell RNA detection
    • Gang Bao, W. J. R. and Tsourkas, Andrew (2009) Fluorescent probes for live-cell RNA detection Annu. Rev. Biomed. Eng. 11, 25-47
    • (2009) Annu. Rev. Biomed. Eng. , vol.11 , pp. 25-47
    • Gang Bao, W.J.R.1    Tsourkas, A.2
  • 11
    • 2142662109 scopus 로고    scopus 로고
    • Poly(A)(+) RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells
    • Molenaar, C., Abdulle, A., Gena, A., Tanke, H. J., and Dirks, R. W. (2004) Poly(A)(+) RNAs roam the cell nucleus and pass through speckle domains in transcriptionally active and inactive cells J. Cell Biol. 165, 191-202
    • (2004) J. Cell Biol. , vol.165 , pp. 191-202
    • Molenaar, C.1    Abdulle, A.2    Gena, A.3    Tanke, H.J.4    Dirks, R.W.5
  • 12
    • 33646847806 scopus 로고    scopus 로고
    • Advances in fluorescent tracking of nucleic acids in living cells
    • Dirks, R. W. and Tanke, H. J. (2006) Advances in fluorescent tracking of nucleic acids in living cells Biotechniques 40, 489-496
    • (2006) Biotechniques , vol.40 , pp. 489-496
    • Dirks, R.W.1    Tanke, H.J.2
  • 13
    • 0035106632 scopus 로고    scopus 로고
    • Methods for visualizing RNA processing and transport pathways in living cells
    • Dirks, R. W., Molenaar, C., and Tanke, H. J. (2001) Methods for visualizing RNA processing and transport pathways in living cells Histochem. Cell Biol. 115, 3-11
    • (2001) Histochem. Cell Biol. , vol.115 , pp. 3-11
    • Dirks, R.W.1    Molenaar, C.2    Tanke, H.J.3
  • 14
  • 15
    • 0029670262 scopus 로고    scopus 로고
    • Molecular beacons: Probes that fluoresce upon hybridization
    • Tyagi, S. and Kramer, F. R. (1996) Molecular beacons: Probes that fluoresce upon hybridization Nat. Biotechnol. 14, 303-308
    • (1996) Nat. Biotechnol. , vol.14 , pp. 303-308
    • Tyagi, S.1    Kramer, F.R.2
  • 16
    • 0031983834 scopus 로고    scopus 로고
    • Multicolor molecular beacons for allele discrimination
    • Tyagi, S., Bratu, D. P., and Kramer, F. R. (1998) Multicolor molecular beacons for allele discrimination Nat. Biotechnol. 16, 49-53
    • (1998) Nat. Biotechnol. , vol.16 , pp. 49-53
    • Tyagi, S.1    Bratu, D.P.2    Kramer, F.R.3
  • 17
    • 10044298658 scopus 로고    scopus 로고
    • Imaging native beta-actin mRNA in motile fibroblasts
    • Tyagi, S. and Alsmadi, O. (2004) Imaging native beta-actin mRNA in motile fibroblasts Biophys. J. 87, 4153-4162
    • (2004) Biophys. J. , vol.87 , pp. 4153-4162
    • Tyagi, S.1    Alsmadi, O.2
  • 18
    • 70450206828 scopus 로고    scopus 로고
    • Efficient nucleic acid detection by templated reductive quencher release
    • Franzini, R. M. and Kool, E. T. (2009) Efficient nucleic acid detection by templated reductive quencher release J. Am. Chem. Soc. 131, 16021-16023
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 16021-16023
    • Franzini, R.M.1    Kool, E.T.2
  • 19
    • 33750008390 scopus 로고    scopus 로고
    • Detecting RNA and DNA with templated chemical reactions
    • Silverman, A. P. and Kool, E. T. (2006) Detecting RNA and DNA with templated chemical reactions Chem. Rev. 106, 3775-3789
    • (2006) Chem. Rev. , vol.106 , pp. 3775-3789
    • Silverman, A.P.1    Kool, E.T.2
  • 20
    • 59449100231 scopus 로고    scopus 로고
    • Imaging target mRNA and siRNA-mediated gene silencing in vivo with ribozyme-based reporters
    • So, M. K., Gowrishankar, G., Hasegawa, S., Chung, J. K., and Rao, J. (2008) Imaging target mRNA and siRNA-mediated gene silencing in vivo with ribozyme-based reporters ChemBioChem 9, 2682-2691
    • (2008) ChemBioChem , vol.9 , pp. 2682-2691
    • So, M.K.1    Gowrishankar, G.2    Hasegawa, S.3    Chung, J.K.4    Rao, J.5
  • 21
    • 34250191761 scopus 로고    scopus 로고
    • RNA visualization in live bacterial cells using fluorescent protein complementation
    • Valencia-Burton, M., McCullough, R. M., Cantor, C. R., and Broude, N. E. (2007) RNA visualization in live bacterial cells using fluorescent protein complementation Nat. Methods 4, 421-427
    • (2007) Nat. Methods , vol.4 , pp. 421-427
    • Valencia-Burton, M.1    McCullough, R.M.2    Cantor, C.R.3    Broude, N.E.4
  • 22
    • 34250210525 scopus 로고    scopus 로고
    • Imaging dynamics of endogenous mitochondrial RNA in single living cells
    • Ozawa, T., Natori, Y., Sato, M., and Umezawa, Y. (2007) Imaging dynamics of endogenous mitochondrial RNA in single living cells Nat. Methods 4, 413-419
    • (2007) Nat. Methods , vol.4 , pp. 413-419
    • Ozawa, T.1    Natori, Y.2    Sato, M.3    Umezawa, Y.4
  • 23
    • 0033519623 scopus 로고    scopus 로고
    • Localization and anchoring of mRNA in budding yeast
    • Beach, D. L., Salmon, E. D., and Bloom, K. (1999) Localization and anchoring of mRNA in budding yeast Curr. Biol. 9, 569-578
    • (1999) Curr. Biol. , vol.9 , pp. 569-578
    • Beach, D.L.1    Salmon, E.D.2    Bloom, K.3
  • 25
    • 0037154985 scopus 로고    scopus 로고
    • Mechanisms of subcellular mRNA localization
    • Kloc, M., Zearfoss, N. R., and Etkin, L. D. (2002) Mechanisms of subcellular mRNA localization Cell 108, 533-544
    • (2002) Cell , vol.108 , pp. 533-544
    • Kloc, M.1    Zearfoss, N.R.2    Etkin, L.D.3
  • 26
    • 0041919397 scopus 로고    scopus 로고
    • RNA localization: Visualization in real-time
    • Singer, R. H. (2003) RNA localization: Visualization in real-time Curr. Biol. 13, R673-R675
    • (2003) Curr. Biol. , vol.13
    • Singer, R.H.1
  • 27
    • 0038376482 scopus 로고    scopus 로고
    • Live imaging of endogenous RNA reveals a diffusion and entrapment mechanism for nanos mRNA localization in Drosophila
    • 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
    • (2003) Curr. Biol. , vol.13 , pp. 1159-1168
    • Forrest, K.M.1    Gavis, E.R.2
  • 31
    • 0344430112 scopus 로고    scopus 로고
    • Aptamers switch on fluorescence of triphenylmethane dyes
    • Babendure, J. R., Adams, S. R., and Tsien, R. Y. (2003) Aptamers switch on fluorescence of triphenylmethane dyes J. Am. Chem. Soc. 125, 14716-14717
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 14716-14717
    • Babendure, J.R.1    Adams, S.R.2    Tsien, R.Y.3
  • 33
    • 65849084573 scopus 로고    scopus 로고
    • Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers
    • Pei, R., Rothman, J., Xie, Y. L., and Stojanovic, M. N. (2009) Light-up properties of complexes between thiazole orange-small molecule conjugates and aptamers Nucleic Acids Res. 37 e59
    • (2009) Nucleic Acids Res. , vol.37
    • Pei, R.1    Rothman, J.2    Xie, Y.L.3    Stojanovic, M.N.4
  • 34
    • 27544478113 scopus 로고    scopus 로고
    • A strategy for the development of small-molecule-based sensors that strongly fluoresce when bound to a specific RNA
    • Sparano, B. A. and Koide, K. (2005) A strategy for the development of small-molecule-based sensors that strongly fluoresce when bound to a specific RNA J. Am. Chem. Soc. 127, 14954-14955
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 14954-14955
    • Sparano, B.A.1    Koide, K.2
  • 35
    • 0032213173 scopus 로고    scopus 로고
    • Isolation of a fluorophore-specific DNA aptamer with weak redox activity
    • Wilson, C. and Szostak, J. W. (1998) Isolation of a fluorophore-specific DNA aptamer with weak redox activity Chem. Biol. 5, 609-617
    • (1998) Chem. Biol. , vol.5 , pp. 609-617
    • Wilson, C.1    Szostak, J.W.2
  • 36
    • 50249150245 scopus 로고    scopus 로고
    • Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: A blue fluorescent RNA
    • Sando, S., Narita, A., Hayami, M., and Aoyama, Y. (2008) Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: A blue fluorescent RNA Chem. Commun. 3858-3860
    • (2008) Chem. Commun. , pp. 3858-3860
    • Sando, S.1    Narita, A.2    Hayami, M.3    Aoyama, Y.4
  • 37
    • 0000469474 scopus 로고    scopus 로고
    • Solvent dependence of the fluorescence lifetimes of xanthene dyes
    • Magde, D., Rojas, G. E., and Seybold, P. G. (1999) Solvent dependence of the fluorescence lifetimes of xanthene dyes Photochem. Photobiol. 70, 737-744
    • (1999) Photochem. Photobiol. , vol.70 , pp. 737-744
    • Magde, D.1    Rojas, G.E.2    Seybold, P.G.3
  • 38
    • 14644407473 scopus 로고    scopus 로고
    • Synthesis of isomerically pure carboxylate- and sulfonate-substituted xanthene fluorophores
    • Woodroofe, C. C., Lim, M. H., Bu, W. M., and Lippard, S. J. (2005) Synthesis of isomerically pure carboxylate- and sulfonate-substituted xanthene fluorophores Tetrahedron 61, 3097-3105
    • (2005) Tetrahedron , vol.61 , pp. 3097-3105
    • Woodroofe, C.C.1    Lim, M.H.2    Bu, W.M.3    Lippard, S.J.4
  • 39
    • 16844362313 scopus 로고    scopus 로고
    • Evolution of fluorescein as a platform for finely tunable fluorescence probes
    • Urano, Y., Kamiya, M., Kanda, K., Ueno, T., Hirose, K., and Nagano, T. (2005) Evolution of fluorescein as a platform for finely tunable fluorescence probes J. Am. Chem. Soc. 127, 4888-4894
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 4888-4894
    • Urano, Y.1    Kamiya, M.2    Kanda, K.3    Ueno, T.4    Hirose, K.5    Nagano, T.6
  • 40
    • 0034837073 scopus 로고    scopus 로고
    • Rational design of fluorescein-based fluorescence probes, mechanism-based design of a maximum fluorescence probe for singlet oxygen
    • Tanaka, K., Miura, T., Umezawa, N., Urano, Y., Kikuchi, K., Higuchi, T., and Nagano, T. (2001) Rational design of fluorescein-based fluorescence probes, mechanism-based design of a maximum fluorescence probe for singlet oxygen J. Am. Chem. Soc. 123, 2530-2536
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 2530-2536
    • Tanaka, K.1    Miura, T.2    Umezawa, N.3    Urano, Y.4    Kikuchi, K.5    Higuchi, T.6    Nagano, T.7
  • 41
    • 0038037163 scopus 로고    scopus 로고
    • Rational design principle for modulating fluorescence properties of fluorescein-based probes by photoinduced electron transfer
    • Miura, T., Urano, Y., Tanaka, K., Nagano, T., Ohkubo, K., and Fukuzumi, S. (2003) Rational design principle for modulating fluorescence properties of fluorescein-based probes by photoinduced electron transfer J. Am. Chem. Soc. 125, 8666-8671
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 8666-8671
    • Miura, T.1    Urano, Y.2    Tanaka, K.3    Nagano, T.4    Ohkubo, K.5    Fukuzumi, S.6
  • 43
    • 0027488624 scopus 로고
    • Isolation of new ribozymes from a large pool of random sequences
    • Bartel, D. P. and Szostak, J. W. (1993) Isolation of new ribozymes from a large pool of random sequences Science 261, 1411-1418
    • (1993) Science , vol.261 , pp. 1411-1418
    • Bartel, D.P.1    Szostak, J.W.2
  • 44
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A. D. and Szostak, J. W. (1990) In vitro selection of RNA molecules that bind specific ligands Nature 346, 818-822
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 45
    • 0025332385 scopus 로고
    • Selection in vitro of an RNA enzyme that specifically cleaves single-stranded-DNA
    • Robertson, D. L. and Joyce, G. F. (1990) Selection in vitro of an RNA enzyme that specifically cleaves single-stranded-DNA Nature 344, 467-468
    • (1990) Nature , vol.344 , pp. 467-468
    • Robertson, D.L.1    Joyce, G.F.2
  • 46
    • 0027180473 scopus 로고
    • An RNA motif that binds ATP
    • Sassanfar, M. and Szostak, J. W. (1993) An RNA motif that binds ATP Nature 364, 550-553
    • (1993) Nature , vol.364 , pp. 550-553
    • Sassanfar, M.1    Szostak, J.W.2
  • 47
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment- RNA ligands to bacteriophage-T4 DNA-polymerase
    • Tuerk, C. and Gold, L. (1990) Systematic evolution of ligands by exponential enrichment-RNA ligands to bacteriophage-T4 DNA-polymerase Science 249, 505-510
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 48
    • 0028911845 scopus 로고
    • In vitro evolution of a self-alkylating ribozyme
    • Wilson, C. and Szostak, J. W. (1995) In vitro evolution of a self-alkylating ribozyme Nature 374, 777-782
    • (1995) Nature , vol.374 , pp. 777-782
    • Wilson, C.1    Szostak, J.W.2
  • 49
    • 78649646931 scopus 로고    scopus 로고
    • http://www.dow.com/glycerine/resources/table12-020.htm.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.