Synthetic biological approaches for RNA labelling and imaging: design principles and future opportunities
Tài liệu tham khảo
Serganov, 2007, Ribozymes, riboswitches and beyond: regulation of gene expression without proteins, Nat. Rev. Genet., 8, 776, 10.1038/nrg2172
He, 2004, Micrornas: small RNAs with a big role in gene regulation, Nat. Rev. Genet., 5, 522, 10.1038/nrg1379
Fedor, 2005, The catalytic diversity of RNAs, Nat. Rev. Mol. Cell Biol., 6, 399, 10.1038/nrm1647
Matlin, 2005, Understanding alternative splicing: towards a cellular code, Nat. Rev. Mol. Cell Biol., 6, 386, 10.1038/nrm1645
Rath, 2015, Genetically encoded tools for RNA imaging in living cells, Curr. Opin. Biotechnol., 31, 42, 10.1016/j.copbio.2014.07.012
Pitchiaya, 2014, Single molecule fluorescence approaches shed light on intracellular RNAs, Chem. Rev., 114, 3224, 10.1021/cr400496q
Hövelmann, 2013, Brightness enhanced DNA fit-probes for wash-free RNA imaging in tissue, J. Am. Chem. Soc., 135, 19025, 10.1021/ja410674h
Lavergne, 2016, Fret characterization of complex conformational changes in a large 165 ribosomal RNA fragment site-specifically labeled using unnatural base pairs, ACS Chem. Biol., 11, 1347, 10.1021/acschembio.5b00952
Chen, 2016, The expanding world of DNA and RNA, Curr. Opin. Chem. Biol., 34, 80, 10.1016/j.cbpa.2016.08.001
Seo, 2011, Site-specific labeling of DNA and RNA using an efficiently replicated and transcribed class of unnatural base pairs, J. Am. Chem. Soc., 133, 19878, 10.1021/ja207907d
Someya, 2015, Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry, Nucleic Acids Res., 43, 6665, 10.1093/nar/gkv638
You, 2015, Structure and mechanism of RNA mimics of green fluorescent protein, Ann Rev Biophys., 44, 187, 10.1146/annurev-biophys-060414-033954
You, 2015, Imaging metabolite dynamics in living cells using a spinach-based riboswitch, Proc. Natl. Acad. Sci. U. S. A., 112, E2756, 10.1073/pnas.1504354112
Biffi, 2014, Visualization and selective chemical targeting of RNA G-quadruplex structures in the cytoplasm of human cells, Nat. Chem., 6, 75, 10.1038/nchem.1805
Nelles, 2016, Programmable RNA tracking in live cells with CRISPR/Cas9, Cell, 165, 488, 10.1016/j.cell.2016.02.054
Liu, 2015, Synthesis and applications of RNAs with position-selective labelling and mosaic composition, Nature, 522, 368, 10.1038/nature14352
Malyshev, 2015, The expanded genetic alphabet, Angew. Chem. Int. Ed., 54, 11930, 10.1002/anie.201502890
Taylor, 2014, Towards applications of synthetic genetic polymers in diagnosis and therapy, Curr. Opin. Chem. Biol., 22, 79, 10.1016/j.cbpa.2014.09.022
Zhang, 2015, Evolution of functional six-nucleotide DNA, J. Am. Chem. Soc., 137, 6734, 10.1021/jacs.5b02251
Leal, 2015, Transcription, reverse transcription, and analysis of RNA containing artificial genetic components, ACS Synth. Biol., 4, 407, 10.1021/sb500268n
Reichenbach, 2016, Structural basis of the mispairing of an artificially expanded genetic information system, Chem, 1, 946, 10.1016/j.chempr.2016.11.009
Kimoto, 2010, A new unnatural base pair system between fluorophore and quencher base analogues for nucleic acid-based imaging technology, J. Am. Chem. Soc., 132, 15418, 10.1021/ja1072383
Ishizuka, 2012, Site-specific functionalization of RNA molecules by an unnatural base pair transcription system via click chemistry, Chem. Commun., 48, 10835, 10.1039/c2cc36293g
Dhami, 2014, Systematic exploration of a class of hydrophobic unnatural base pairs yields multiple new candidates for the expansion of the genetic alphabet, Nucleic Acids Res., 42, 10235, 10.1093/nar/gku715
Betz, 2013, Structural insights into DNA replication without hydrogen bonds, J. Am. Chem. Soc., 135, 18637, 10.1021/ja409609j
Malyshev, 2014, A semi-synthetic organism with an expanded genetic alphabet, Nature, 509, 385, 10.1038/nature13314
Giepmans, 2006, Review—the fluorescent toolbox for assessing protein location and function, Science, 312, 217, 10.1126/science.1124618
Song, 2013, Imaging bacterial protein expression using genetically encoded RNA sensors, Nat. Methods, 10, 873, 10.1038/nmeth.2568
Paige, 2012, Fluorescence imaging of cellular metabolites with RNA, Science, 335, 1194, 10.1126/science.1218298
Paige, 2011, RNA mimics of green fluorescent protein, Science, 333, 642, 10.1126/science.1207339
Huang, 2014, A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore, Nat. Chem. Biol., 10, 686, 10.1038/nchembio.1561
Warner, 2014, Structural basis for activity of highly efficient RNA mimics of green fluorescent protein, Nat. Struct. Mol. Biol., 21, 658, 10.1038/nsmb.2865
Strack, 2013, A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA, Nat. Methods, 10, 1219, 10.1038/nmeth.2701
Filonov, 2014, Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution, J. Am. Chem. Soc., 136, 16299, 10.1021/ja508478x
Autour, 2016, iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications, Nucleic Acids Res., 44, 2491, 10.1093/nar/gkw083
Ketterer, 2015, Systematic reconstruction of binding and stability landscapes of the fluorogenic aptamer spinach, Nucleic Acids Res., 43, 9564, 10.1093/nar/gkv944
Guet, 2015, Combining spinach-tagged RNA and gene localization to image gene expression in live yeast, Nat. Commun., 19, 8882, 10.1038/ncomms9882
Höfer, 2013, Universal aptamer-based real-time monitoring of enzymatic RNA synthesis, J. Am. Chem. Soc., 135, 13692, 10.1021/ja407142f
Nakayama, 2012, Nanomolar fluorescent detection of c-di-GMP using a modular aptamer strategy, Chem. Commun., 48, 9059, 10.1039/c2cc34379g
Wang, 2016, Next-generation RNA-based fluorescent biosensors enable anaerobic detection of cyclic di-GMP, Nucleic Acids Res., 44, 10, 10.1093/nar/gkw580
Ketterer, 2016, Engineering and characterization of fluorogenic glycine riboswitches, Nucleic Acids Res., 44, 5983, 10.1093/nar/gkw465
Su, 2016, In vitro and in vivo enzyme activity screening via RNA-based fluorescent biosensors for S-adenosyl-l-homocysteine (SAH), J. Am. Chem. Soc., 138, 7040, 10.1021/jacs.6b01621
Dolgosheina, 2014, RNA mango aptamer-fluorophore: a bright, high-affinity complex for RNA labeling and tracking, ACS Chem. Biol., 9, 2412, 10.1021/cb500499x
Jeng, 2016, Fluorophore ligand binding and complex stabilization of the RNA mango and RNA spinach aptamers, RNA, 22, 1884, 10.1261/rna.056226.116
Bertrand, 1998, Localization of ash1 mRNA particles in living yeast, Mol. Cell., 2, 437, 10.1016/S1097-2765(00)80143-4
Wang, 2002, Modular recognition of RNA by a human pumilio-homology domain, Cell, 110, 501, 10.1016/S0092-8674(02)00873-5
Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829
Jiang, 2013, RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat. Biotechnol., 31, 233, 10.1038/nbt.2508
Zhang, 2017, A semisynthetic organism engineered for the stable expansion of the genetic alphabet, Proc. Natl. Acad. Sci. U. S. A., 114, 1317, 10.1073/pnas.1616443114
Betz, 2012, KlenTaq polymerase replicates unnatural base pairs by inducing a Watson–Crick geometry, Nat. Chem. Biol., 8, 612, 10.1038/nchembio.966