메뉴 건너뛰기




Volumn 7, Issue 10, 2012, Pages 1797-1807

Designing and using RNA scaffolds to assemble proteins in vivo

Author keywords

[No Author keywords available]

Indexed keywords

MONOMER;

EID: 84870027847     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2012.102     Document Type: Article
Times cited : (50)

References (46)
  • 1
    • 79960697001 scopus 로고    scopus 로고
    • Organization of intracellular reactions with rationally designed RNA assemblies
    • Delebecque, C.J., Lindner, A.B., Silver, P.A. & Aldaye, F.A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470-474 (2011).
    • (2011) Science , vol.333 , pp. 470-474
    • Delebecque, C.J.1    Lindner, A.B.2    Silver, P.A.3    Aldaye, F.A.4
  • 2
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specifc ligands
    • Ellington, A.D. & Szostak, J.W. In vitro selection of RNA molecules that bind specifc ligands. Nature 346, 818-822 (1990).
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 3
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510 (1990).
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 5
    • 0035656688 scopus 로고    scopus 로고
    • Non-coding RNA genes and the modern RNA world
    • Eddy, S.R. Non-coding RNA genes and the modern RNA world. Nat. Rev. Genet. 2, 919-929 (2001).
    • (2001) Nat. Rev. Genet. , vol.2 , pp. 919-929
    • Eddy, S.R.1
  • 7
    • 54249113318 scopus 로고    scopus 로고
    • Higher-order cellular information processing with synthetic RNA devices
    • Win, M.N. & Smolke, C.D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456-460 (2008).
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 8
  • 9
    • 3042741121 scopus 로고    scopus 로고
    • Engineered riboregulators enable post-transcriptional control of gene expression
    • Isaacs, F.J. et al. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841-847 (2004).
    • (2004) Nat. Biotechnol. , vol.22 , pp. 841-847
    • Isaacs, F.J.1
  • 10
    • 53049107187 scopus 로고    scopus 로고
    • Engineering the spatial organization of metabolic enzymes: Mimicking nature's synergy
    • Conrado, R.J., Varner, J.D. & DeLisa, M.P. Engineering the spatial organization of metabolic enzymes: mimicking nature's synergy. Curr. Opin. Biotechnol. 19, 492-499 (2008).
    • (2008) Curr. Opin. Biotechnol. , vol.19 , pp. 492-499
    • Conrado, R.J.1    Varner, J.D.2    Delisa, M.P.3
  • 11
    • 77749264485 scopus 로고    scopus 로고
    • Spatially ordered dynamics of the bacterial carbon fxation machinery
    • Savage, D.F., Afonso, B., Chen, A.H. & Silver, P.A. Spatially ordered dynamics of the bacterial carbon fxation machinery. Science 327, 1258-1261 (2010).
    • (2010) Science , vol.327 , pp. 1258-1261
    • Savage, D.F.1    Afonso, B.2    Chen, A.H.3    Silver, P.A.4
  • 12
    • 0034009390 scopus 로고    scopus 로고
    • Signal transduction: Hanging on a scaffold
    • Burack, W.R. & Shaw, A.S. Signal transduction: hanging on a scaffold. Curr. Opin. Cell Biol. 12, 211-216 (2000).
    • (2000) Curr. Opin. Cell Biol. , vol.12 , pp. 211-216
    • Burack, W.R.1    Shaw, A.S.2
  • 13
    • 3042798454 scopus 로고    scopus 로고
    • Yeast telomerase RNA: A fexible scaffold for protein subunits
    • Zappulla, D.C. & Cech, T.R. Yeast telomerase RNA: a fexible scaffold for protein subunits. Proc. Natl. Acad. Sci. USA 101, 10024-10029 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 10024-10029
    • Zappulla, D.C.1    Cech, T.R.2
  • 14
    • 72249119445 scopus 로고    scopus 로고
    • A nanostructure made of a bacterial noncoding RNA
    • Cayrol, B. et al. A nanostructure made of a bacterial noncoding RNA. J. Am. Chem. Soc. 131, 17270-17276 (2009).
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 17270-17276
    • Cayrol, B.1
  • 15
    • 79551593011 scopus 로고    scopus 로고
    • Nucleation of nuclear bodies by RNA
    • Shevtsov, S.P. & Dundr, M. Nucleation of nuclear bodies by RNA. Nat. Cell Biol. 13, 167-173 (2011).
    • (2011) Nat. Cell Biol. , vol.13 , pp. 167-173
    • Shevtsov, S.P.1    Dundr, M.2
  • 16
    • 0003064682 scopus 로고
    • Reduction of dimensionality in biological diffusion processes
    • Adam, G. & Delbriick, M. Reduction of dimensionality in biological diffusion processes. Struct. Chem. Mol. Biol. 198-215 (1968).
    • (1968) Struct. Chem. Mol. Biol. , pp. 198-215
    • Adam, G.1    Delbriick, M.2
  • 17
    • 68449088806 scopus 로고    scopus 로고
    • Synthetic protein scaffolds provide modular control over metabolic fux
    • Dueber, J.E. et al. Synthetic protein scaffolds provide modular control over metabolic fux. Nat. Biotechnol. 27, 753-759 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 753-759
    • Dueber, J.E.1
  • 18
    • 84859780045 scopus 로고    scopus 로고
    • Spatial organization of enzymes for metabolic engineering
    • Lee, H., DeLoache, W.C. & Dueber, J.E. Spatial organization of enzymes for metabolic engineering. Metab. Eng. 14, 242-251 (2012).
    • (2012) Metab. Eng. , vol.14 , pp. 242-251
    • Lee, H.1    Deloache, W.C.2    Dueber, J.E.3
  • 19
    • 0037436155 scopus 로고    scopus 로고
    • Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms
    • Park, S.-H., Zarrinpar, A. & Lim, W.A. Rewiring MAP kinase pathways using alternative scaffold assembly mechanisms. Science 299, 1061-1064 (2003).
    • (2003) Science , vol.299 , pp. 1061-1064
    • Park, S.-H.1    Zarrinpar, A.2    Lim, W.A.3
  • 20
    • 78651486207 scopus 로고    scopus 로고
    • Insulation of a synthetic hydrogen metabolism circuit in bacteria
    • Agapakis, C.M. et al. Insulation of a synthetic hydrogen metabolism circuit in bacteria. J. Biol. Eng. 4, 3-15 (2010).
    • (2010) J. Biol. Eng. , vol.4 , pp. 3-15
    • Agapakis, C.M.1
  • 21
    • 77950863739 scopus 로고    scopus 로고
    • Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli
    • Moon, T.S., Dueber, J.E., Shiue, E. & Prather, K.L.J. Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab. Eng. 12, 298-305 (2010).
    • (2010) Metab. Eng. , vol.12 , pp. 298-305
    • Moon, T.S.1    Dueber, J.E.2    Shiue, E.3    Prather, K.L.J.4
  • 22
    • 84863229940 scopus 로고    scopus 로고
    • DNA-guided assembly of biosynthetic pathways promotes improved catalytic effciency
    • Conrado, R.J. et al. DNA-guided assembly of biosynthetic pathways promotes improved catalytic effciency. Nucleic Acids Res. 40, 1879-1889 (2011).
    • (2011) Nucleic Acids Res. , vol.40 , pp. 1879-1889
    • Conrado, R.J.1
  • 23
    • 4644326818 scopus 로고    scopus 로고
    • Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology
    • Shu, D., Moll, W.-D., Deng, Z., Mao, C. & Guo, P. Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology. Nano Lett. 4, 1717-1723 (2004).
    • (2004) Nano Lett. , vol.4 , pp. 1717-1723
    • Shu, D.1    Moll, W.-D.2    Deng, Z.3    Mao, C.4    Guo, P.5
  • 24
    • 78649985789 scopus 로고    scopus 로고
    • The emerging feld of RNA nanotechnology
    • Guo, P. The emerging feld of RNA nanotechnology. Nat. Nanotechnol. 5, 833-842 (2010).
    • (2010) Nat. Nanotechnol. , vol.5 , pp. 833-842
    • Guo, P.1
  • 25
    • 77956422639 scopus 로고    scopus 로고
    • In vitro assembly of cubic RNA-based scaffolds designed in silico
    • Afonin, K.A. et al. In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat. Nanotechnol. 5, 676-682 (2010).
    • (2010) Nat. Nanotechnol. , vol.5 , pp. 676-682
    • Afonin, K.A.1
  • 26
    • 0042622372 scopus 로고    scopus 로고
    • RNAsoft: A suite of RNA secondary structure prediction and design software tools
    • Andronescu, M., Aguirre-Hernandez, R., Condon, A. & Hoos, H.H. RNAsoft: a suite of RNA secondary structure prediction and design software tools. Nucleic Acids Res. 31, 3416-3422 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3416-3422
    • Andronescu, M.1    Aguirre-Hernandez, R.2    Condon, A.3    Hoos, H.H.4
  • 27
    • 37849019313 scopus 로고    scopus 로고
    • Structural basis for the coevolution of a viral RNA-protein complex
    • Chao, J.A., Patskovsky, Y., Almo, S.C. & Singer, R.H. Structural basis for the coevolution of a viral RNA-protein complex. Nat. Struct. Mol. Biol. 15, 103-105 (2008).
    • (2008) Nat. Struct. Mol. Biol. , vol.15 , pp. 103-105
    • Chao, J.A.1    Patskovsky, Y.2    Almo, S.C.3    Singer, R.H.4
  • 28
    • 0031951789 scopus 로고    scopus 로고
    • Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution
    • Convery, M.A. et al. Crystal structure of an RNA aptamer-protein complex at 2.8 A resolution. Nat. Struct. Biol. 5, 133-139 (1998).
    • (1998) Nat. Struct. Biol. , vol.5 , pp. 133-139
    • Convery, M.A.1
  • 29
    • 0035933720 scopus 로고    scopus 로고
    • Translational repression and specifc RNA binding by the coat protein of the Pseudomonas phage PP7
    • Lim, F., Downey, T.P. & Peabody, D.S. Translational repression and specifc RNA binding by the coat protein of the Pseudomonas phage PP7. J. Biol. Chem. 276, 22507-22513 (2001).
    • (2001) J. Biol. Chem. , vol.276 , pp. 22507-22513
    • Lim, F.1    Downey, T.P.2    Peabody, D.S.3
  • 30
    • 0034650498 scopus 로고    scopus 로고
    • RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour
    • Parrott, A.M. et al. RNA aptamers for the MS2 bacteriophage coat protein and the wild-type RNA operator have similar solution behaviour. Nucleic Acids Res. 28, 489-497 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 489-497
    • Parrott, A.M.1
  • 31
    • 3843126332 scopus 로고    scopus 로고
    • RNA dynamics in live Escherichia coli cells
    • Golding, I. & Cox, E.C. RNA dynamics in live Escherichia coli cells. Proc. Natl. Acad. Sci. USA 101, 11310-11315 (2004).
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 11310-11315
    • Golding, I.1    Cox, E.C.2
  • 32
    • 34250191761 scopus 로고    scopus 로고
    • RNA visualization in live bacterial cells using fuorescent protein complementation
    • Valencia-Burton, M., McCullough, R.M., Cantor, C.R. & Broude, N.E. RNA visualization in live bacterial cells using fuorescent protein complementation. Nat. Methods 4, 421-427 (2007).
    • (2007) Nat. Methods , vol.4 , pp. 421-427
    • Valencia-Burton, M.1    McCullough, R.M.2    Cantor, C.R.3    Broude, N.E.4
  • 33
    • 52949116414 scopus 로고    scopus 로고
    • Assembling materials with DNA as the guide
    • Aldaye, F.A., Palmer, A.L. & Sleiman, H.F. Assembling materials with DNA as the guide. Science 321, 1795-1799 (2008).
    • (2008) Science , vol.321 , pp. 1795-1799
    • Aldaye, F.A.1    Palmer, A.L.2    Sleiman, H.F.3
  • 34
    • 36949030704 scopus 로고    scopus 로고
    • An overview of structural DNA nanotechnology
    • Seeman, N.C. An overview of structural DNA nanotechnology. Mol. Biotechnol. 37, 246-257 (2007).
    • (2007) Mol. Biotechnol. , vol.37 , pp. 246-257
    • Seeman, N.C.1
  • 35
    • 33746281403 scopus 로고    scopus 로고
    • Approaching the limit: Can one DNA oligonucleotide assemble into large nanostructures?
    • Liu, H., Chen, Y., He, Y., Ribbe, A.E. & Mao, C. Approaching the limit: can one DNA oligonucleotide assemble into large nanostructures? Angew. Chem. Int. Ed. Engl. 45, 1942-1945 (2006).
    • (2006) Angew. Chem. Int. Ed. Engl. , vol.45 , pp. 1942-1945
    • Liu, H.1    Chen, Y.2    He, Y.3    Ribbe, A.E.4    Mao, C.5
  • 36
    • 28844504657 scopus 로고    scopus 로고
    • Two-dimensional (2D) DNA crystals assembled from two DNA strands
    • Liu, H., He, Y., Ribbe, A.E. & Mao, C. Two-dimensional (2D) DNA crystals assembled from two DNA strands. Biomacromolecules 6, 2943-2945 (2005).
    • (2005) Biomacromolecules , vol.6 , pp. 2943-2945
    • Liu, H.1    He, Y.2    Ribbe, A.E.3    Mao, C.4
  • 37
    • 38349121586 scopus 로고    scopus 로고
    • Programming biomolecular self-assembly pathways
    • Yin, P., Choi, H.M.T., Calvert, C.R. & Pierce, N.A. Programming biomolecular self-assembly pathways. Nature 451, 318-322 (2008).
    • (2008) Nature , vol.451 , pp. 318-322
    • Yin, P.1    Choi, H.M.T.2    Calvert, C.R.3    Pierce, N.A.4
  • 38
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31, 3406-3415 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 39
    • 78149355812 scopus 로고    scopus 로고
    • NUPACK: Analysis and design of nucleic acid systems
    • Zadeh, J.N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170-173 (2011).
    • (2011) J. Comput. Chem. , vol.32 , pp. 170-173
    • Zadeh, J.N.1
  • 40
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis, H.M., Mirsky, E.A. & Voigt, C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27, 946-950 (2009).
    • (2009) Nat. Biotechnol. , vol.27 , pp. 946-950
    • Salis, H.M.1    Mirsky, E.A.2    Voigt, C.A.3
  • 41
    • 77649201708 scopus 로고    scopus 로고
    • Expression profling of microRNA using real-time quantitative PCR, how to use it and what is available
    • Benes, V. & Castoldi, M. Expression profling of microRNA using real-time quantitative PCR, how to use it and what is available. Methods 50, 244-249 (2010).
    • (2010) Methods , vol.50 , pp. 244-249
    • Benes, V.1    Castoldi, M.2
  • 42
    • 0037315564 scopus 로고    scopus 로고
    • Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation
    • Selinger, D.W. Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation. Genome Res. 13, 216-223 (2003).
    • (2003) Genome Res. , vol.13 , pp. 216-223
    • Selinger, D.W.1
  • 44
    • 0029129682 scopus 로고
    • Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: Thermodynamic and spectroscopic applications
    • Molinaro, M. & Tinoco, I. Use of ultra stable UNCG tetraloop hairpins to fold RNA structures: thermodynamic and spectroscopic applications. Nucleic Acids Res. 23, 3056-3063 (1995).
    • (1995) Nucleic Acids Res. , vol.23 , pp. 3056-3063
    • Molinaro, M.1    Tinoco, I.2
  • 45
    • 31344474305 scopus 로고    scopus 로고
    • Strategies for protein coexpression in Escherichia coli
    • Tolia, N.H. & Joshua-Tor, L. Strategies for protein coexpression in Escherichia coli. Nat. Methods 3, 55-64 (2006).
    • (2006) Nat. Methods , vol.3 , pp. 55-64
    • Tolia, N.H.1    Joshua-Tor, L.2
  • 46
    • 1542301827 scopus 로고    scopus 로고
    • Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes
    • Vandesompele, J. et al. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3, 1-12 (2002).
    • (2002) Genome Biol. , vol.3 , pp. 1-12
    • Vandesompele, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.