Synthetic biology devices and circuits for RNA-based ‘smart vaccines’: a propositional review

References

• Elowitz M, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000;403(6767):335-8
   PubMed Web of Science ®Google Scholar
• Gardner T, Cantor C, Collins J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000;403(6767):339-42
   PubMed Web of Science ®Google Scholar
• Isaacs FJ, Dwyer DJ, Collins JJ. RNA synthetic biology. Nat Biotechnol 2006;24(5):545-54
   PubMed Web of Science ®Google Scholar
• Benenson Y. RNA-based computation in live cells. Curr Opin Biotechnol 2009;20(4):471-8
   PubMedGoogle Scholar
• Nandagopal N, Elowitz MB. Synthetic biology: integrated gene circuits. Science 2011;333(6047):1244-8
   PubMed Web of Science ®Google Scholar
• Brophy JA, Voigt CA. Principles of genetic circuit design. Nat Methods 2014;11(5):508-20
   PubMed Web of Science ®Google Scholar
• Chang AL, Wolf JJ, Smolke CD. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr Opin Biotechnol 2012;23(5):679-88
   PubMedGoogle Scholar
• Wang YH, Wei KY, Smolke CD. Synthetic biology: advancing the design of diverse genetic systems. Annu Rev Chem Biomol Eng 2013;4:69-102
   Google Scholar
• Benenson Y. Synthetic biology with RNA: progress report. Curr Opin Chem Biol 2012;16(3-4):278-84
   PubMedGoogle Scholar
• Auslander S, Fussenegger M. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol 2013;31(3):155-68
   PubMedGoogle Scholar
• Ye H, Aubel D, Fussenegger M. Synthetic mammalian gene circuits for biomedical applications. Curr Opin Chem Biol 2013;17(6):910-17
   PubMedGoogle Scholar
• Bacchus W, Aubel D, Fussenegger M. Biomedically relevant circuit-design strategies in mammalian synthetic biology. Mol Syst Biol 2013;9:691
   PubMedGoogle Scholar
• Lienert F, Lohmueller JJ, Garg A, Silver PA. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat Rev Mol Cell Biol 2014;15(2):95-107
   PubMed Web of Science ®Google Scholar
• Slusarczyk AL, Lin A, Weiss R. Foundations for the design and implementation of synthetic genetic circuits. Nat Rev Genetics 2012;13(6):406-20
   PubMed Web of Science ®Google Scholar
• Purnick PE, Weiss R. The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 2009;10(6):410-22
   PubMed Web of Science ®Google Scholar
• Xie Z, Wroblewska L, Prochazka L, et al. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 2011;333(6047):1307-11
   PubMed Web of Science ®Google Scholar
• Kemmer C, Gitzinger M, Daoud-El Baba M, et al. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat Biotechnol 2010;28(4):355-60
   PubMed Web of Science ®Google Scholar
• Ye H, Daoud-El Baba M, Peng RW, Fussenegger M. A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 2011;332(6037):1565-8
   PubMedGoogle Scholar
• Ye H, Charpin-El Hamri G, Zwicky K, et al. Pharmaceutically controlled designer circuit for the treatment of the metabolic syndrome. Proc Natl Acad Sci USA 2013;110(1):141-6
   PubMedGoogle Scholar
• Rossger K, Charpin-El Hamri G, Fussenegger M. Reward-based hypertension control by a synthetic brain-dopamine interface. Proc Natl Acad Sci USA 2013;110(45):18150-5
   PubMedGoogle Scholar
• Auslander D, Eggerschwiler B, Kemmer C, et al. A designer cell-based histamine-specific human allergy profiler. Nat Commun 2014;5:4408
   PubMedGoogle Scholar
• Lam AP, Dean DA. Progress and prospects: nuclear import of nonviral vectors. Gene Ther 2010;17(4):439-47
   PubMed Web of Science ®Google Scholar
• Andries O, De Filette M, Rejman J, et al. Comparison of the gene transfer efficiency of mRNA/GL67 and pDNA/GL67 complexes in respiratory cells. Mol Pharm 2012;9(8):2136-45
   PubMed Web of Science ®Google Scholar
• Sahin U, Kariko K, Tureci Ö. mRNA-based therapeutics - developing a new class of drugs. Nat Rev Drug Discov 2014;13(10):759-80
   PubMed Web of Science ®Google Scholar
• Geall AJ, Mandl CW, Ulmer JB. RNA: the new revolution in nucleic acid vaccines. Semin Immunol 2013;25(2):152-9
   PubMed Web of Science ®Google Scholar
• Lundstrom K. Alphavirus-based vaccines. Viruses 2014;6(6):2392-415
   PubMed Web of Science ®Google Scholar
• Ljungberg K, Liljestrom P. Self-replicating alphavirus RNA vaccines. Expert Rev Vaccines 2014;1-18
   Google Scholar
• Moser M, Leo O. Key concepts in immunology. Vaccine 2010;28(Suppl 3):C2-13
   PubMedGoogle Scholar
• Zepp F. Principles of vaccine design-Lessons from nature. Vaccine 2010;28(Suppl 3):C14-24
   PubMed Web of Science ®Google Scholar
• Leroux-Roels G. Unmet needs in modern vaccinology: adjuvants to improve the immune response. Vaccine 2010;28(Suppl 3):C25-36
   PubMedGoogle Scholar
• Sun L, Liu S, Chen ZJ. SnapShot: pathways of antiviral innate immunity. Cell 2010;140(3):436-436.e432
   PubMed Web of Science ®Google Scholar
• Yin H, Kanasty RL, Eltoukhy AA, et al. Non-viral vectors for gene-based therapy. Nat Rev Genet 2014;15(8):541-55
   PubMed Web of Science ®Google Scholar
• Warren L, Manos P, Ahfeldt T, et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 2010;7(5):618-30
   PubMed Web of Science ®Google Scholar
• Andries O, De Filette M, De Smedt SC, et al. Innate immune response and programmed cell death following carrier-mediated delivery of unmodified mRNA to respiratory cells. J Control Release 2013;167(2):157-66
   PubMed Web of Science ®Google Scholar
• Kariko K, Buckstein M, Ni H, Weissman D. Suppression of RNA recognition by Toll-like receptors: the impact of nucleoside modification and the evolutionary origin of RNA. Immunity 2005;23(2):165-75
   PubMed Web of Science ®Google Scholar
• Kariko K, Muramatsu H, Welsh FA, et al. Incorporation of pseudouridine into mRNA yields superior nonimmunogenic vector with increased translational capacity and biological stability. Mol Ther 2008;16(11):1833-40
   PubMed Web of Science ®Google Scholar
• Anderson BR, Muramatsu H, Nallagatla SR, et al. Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation. Nucleic Acids Res 2010;38(17):5884-92
   PubMed Web of Science ®Google Scholar
• Anderson BR, Muramatsu H, Jha BK, et al. Nucleoside modifications in RNA limit activation of 2’-5’-oligoadenylate synthetase and increase resistance to cleavage by RNase L. Nucleic Acids Res 2011;39(21):9329-38
   PubMed Web of Science ®Google Scholar
• Warren L, Manos PD, Ahfeldt T, et al. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell 2010;7(5):618-30
   PubMed Web of Science ®Google Scholar
• Kormann MS, Hasenpusch G, Aneja MK, et al. Expression of therapeutic proteins after delivery of chemically modified mRNA in mice. Nat Biotechnol 2011;29(2):154-7
   PubMed Web of Science ®Google Scholar
• Walsh D, Mathews MB, Mohr I. Tinkering with translation: protein synthesis in virus-infected cells. Cold Spring Harb Perspect Biol 2013;5(1):a012351
   Google Scholar
• Dormitzer PR, Mandl CW, Rappuoli R. Replicating vaccines A new generation. Springer; Basel: 2011
   Google Scholar
• Strauss J, Strauss E. The alphaviruses: gene expression, replication, and evolution. Microbiol Rev 1994;58(3):491-562
   PubMedGoogle Scholar
• Geall A, Verma A, Otten G, et al. Nonviral delivery of self-amplifying RNA vaccines. Proc Natl Acad Sci USA 2012;109(36):14604-9
   PubMed Web of Science ®Google Scholar
• Yoshioka N, Gros E, Li HR, et al. Efficient generation of human iPSCs by a synthetic self-replicative RNA. Cell Stem Cell 2013;13(2):246-54
   PubMed Web of Science ®Google Scholar
• Varble A, Benitez AA, Schmid S, et al. An in vivo RNAi screening approach to identify host determinants of virus replication. Cell Host Microbe 2013;14(3):346-56
   PubMedGoogle Scholar
• Beal J, Wagner TE, Kitada T, et al. Model-driven engineering of gene expression from RNA replicons. ACS Synth Biol 2014. [Epub ahead of print]
   Google Scholar
• Ferre-D’Amare AR, Scott WG. Small self-cleaving ribozymes. Cold Spring Harb Perspect Biol 2010;2(10):a003574
   PubMed Web of Science ®Google Scholar
• Grabow W, Jaeger L. RNA modularity for synthetic biology. F1000Prime Rep 2013;5:46
   PubMedGoogle Scholar
• Hershey JW, Sonenberg N, Mathews MB. Principles of translational control: an overview. Cold Spring Harb Perspect Biol 2012;4:12
   PubMed Web of Science ®Google Scholar
• Hinnebusch AG, Lorsch JR. The mechanism of eukaryotic translation initiation: new insights and challenges. Cold Spring Harb Perspect Biol 2012;4:10
   PubMedGoogle Scholar
• Babendure J, Babendure J, Ding J-H, Tsien R. Control of mammalian translation by mRNA structure near caps. RNA 2006;12(5):851-61
   PubMed Web of Science ®Google Scholar
• Rozhdestvensky TS, Tang TH, Tchirkova IV, et al. Binding of L7Ae protein to the K-turn of archaeal snoRNAs: a shared RNA binding motif for C/D and H/ACA box snoRNAs in Archaea. Nucleic Acids Res 2003;31(3):869-77
   PubMed Web of Science ®Google Scholar
• Gagnon KT, Zhang X, Qu G, et al. Signature amino acids enable the archaeal L7Ae box C/D RNP core protein to recognize and bind the K-loop RNA motif. Rna 2010;16(1):79-90
   PubMedGoogle Scholar
• Saito H, Kobayashi T, Hara T, et al. Synthetic translational regulation by an L7Ae-kink-turn RNP switch. Nat Chem Biol 2010;6(1):71-8
   PubMed Web of Science ®Google Scholar
• Stapleton JA, Endo K, Fujita Y, et al. Feedback control of protein expression in mammalian cells by tunable synthetic translational inhibition. ACS Synth Biol 2012;1(3):83-8
   PubMedGoogle Scholar
• Endo K, Stapleton JA, Hayashi K, et al. Quantitative and simultaneous translational control of distinct mammalian mRNAs. Nucleic Acids Res 2013;41(13):e135
   Google Scholar
• Endo K, Hayashi K, Inoue T, Saito H. A versatile cis-acting inverter module for synthetic translational switches. Nat Commun 2013;4:2393
   PubMed Web of Science ®Google Scholar
• Ohno H, Kobayashi T, Kabata R, et al. Synthetic RNA-protein complex shaped like an equilateral triangle. Nat Nanotechnol 2011;6(2):116-20
   PubMed Web of Science ®Google Scholar
• Osada E, Suzuki Y, Hidaka K, et al. Engineering RNA-protein complexes with different shapes for imaging and therapeutic applications. ACS Nano 2014;8(8):8130-40
   PubMed Web of Science ®Google Scholar
• Turner B, Melcher SE, Wilson TJ, et al. Induced fit of RNA on binding the L7Ae protein to the kink-turn motif. RNA 2005;11(8):1192-200
   PubMed Web of Science ®Google Scholar
• Keryer-Bibens C, Barreau C, Osborne H. Tethering of proteins to RNAs by bacteriophage proteins. Biol Cell 2008;100(2):125-38
   PubMedGoogle Scholar
• Stripecke R, Oliveira C, McCarthy J, Hentze M. Proteins binding to 5’ untranslated region sites: a general mechanism for translational regulation of mRNAs in human and yeast cells. Mol Cell Biol 1994;14(9):5898-909
   PubMedGoogle Scholar
• Culler S, Hoff K, Smolke C. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 2010;330(6008):1251-5
   PubMed Web of Science ®Google Scholar
• Gossen M, Bujard H. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc Natl Acad Sci USA 1992;89(12):5547-51
   PubMed Web of Science ®Google Scholar
• Gossen M, Freundlieb S, Bender G, et al. Transcriptional activation by tetracyclines in mammalian cells. Science 1995;268(5218):1766-9
   PubMed Web of Science ®Google Scholar
• Tuerk C, Gold L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 1990;249(4968):505-10
   PubMed Web of Science ®Google Scholar
• Ellington AD, Szostak JW. In vitro selection of RNA molecules that bind specific ligands. Nature 1990;346(6287):818-22
   PubMed Web of Science ®Google Scholar
• Hunsicker A, Steber M, Mayer G, et al. An RNA aptamer that induces transcription. Chem Biol 2009;16(2):173-80
   PubMedGoogle Scholar
• Belmont B, Niles J. Engineering a direct and inducible protein-RNA interaction to regulate RNA biology. ACS Chem Biol 2010;5(9):851-61
   PubMedGoogle Scholar
• Steber M, Arora A, Hofmann J, et al. Mechanistic basis for RNA aptamer-based induction of TetR. Chembiochem 2011;12(17):2608-14
   PubMedGoogle Scholar
• Goldfless S, Belmont B, Paz A, et al. Direct and specific chemical control of eukaryotic translation with a synthetic RNA-protein interaction. Nucleic Acids Res 2012;40(9):e64-4
   PubMedGoogle Scholar
• Quenault T, Lithgow T, Traven A. PUF proteins: repression, activation and mRNA localization. Trends Cell Biol 2011;21(2):104-12
   PubMed Web of Science ®Google Scholar
• Wang X, McLachlan J, Zamore PD, Hall TM. Modular recognition of RNA by a human pumilio-homology domain. Cell 2002;110(4):501-12
   PubMed Web of Science ®Google Scholar
• Hall TM. Expanding the RNA-recognition code of PUF proteins. Nat Struct Mol Biol 2014;21(8):653-5
   PubMed Web of Science ®Google Scholar
• Wang Y, Cheong CG, Hall TM, Wang Z. Engineering splicing factors with designed specificities. Nat Methods 2009;6(11):825-30
   PubMedGoogle Scholar
• Choudhury R, Tsai YS, Dominguez D, et al. Engineering RNA endonucleases with customized sequence specificities. Nat Commun 2012;3:1147
   Google Scholar
• Cooke A, Prigge A, Opperman L, Wickens M. Targeted translational regulation using the PUF protein family scaffold. Proc Natl Acad Sci USA 2011;108(38):15870-5
   PubMedGoogle Scholar
• Campbell ZT, Valley CT, Wickens M. A protein-RNA specificity code enables targeted activation of an endogenous human transcript. Nat Struct Mol Biol 2014;21(8):732-8
   PubMed Web of Science ®Google Scholar
• Cao J, Arha M, Sudrik C, et al. Bidirectional regulation of mRNA translation in mammalian cells by using PUF domains. Angew Chem 2014;53(19):4900-4
   Google Scholar
• Abil Z, Denard CA, Zhao H. Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA. J Biol Eng 2014;8(1):7
   PubMedGoogle Scholar
• Engler C, Kandzia R, Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS One 2008;3(11):e3647
   PubMed Web of Science ®Google Scholar
• Filipovska A, Razif MF, Nygard KK, Rackham O. A universal code for RNA recognition by PUF proteins. Nat Chem Biol 2011;7(7):425-7
   PubMed Web of Science ®Google Scholar
• Barkan A, Rojas M, Fujii S, et al. A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 2012;8(8):e1002910
   PubMed Web of Science ®Google Scholar
• Yin P, Li Q, Yan C, et al. Structural basis for the modular recognition of single-stranded RNA by PPR proteins. Nature 2013;504(7478):168-71
   PubMed Web of Science ®Google Scholar
• Yagi Y, Nakamura T, Small I. The potential for manipulating RNA with pentatricopeptide repeat proteins. Plant J 2014;78(5):772-82
   PubMedGoogle Scholar
• Serganov A, Nudler E. A decade of riboswitches. Cell 2013;152(1-2):17-24
   PubMed Web of Science ®Google Scholar
• Stoltenburg R, Reinemann C, Strehlitz B. SELEX–a (r)evolutionary method to generate high-affinity nucleic acid ligands. Biomol Eng 2007;24(4):381-403
   PubMedGoogle Scholar
• Weigand J, Schmidtke S, Will T, et al. Mechanistic insights into an engineered riboswitch: a switching element which confers riboswitch activity. Nucleic Acids Res 2011;39(8):3363-72
   PubMedGoogle Scholar
• Groher F, Suess B. Synthetic riboswitches – a tool comes of age. Biochim Biophys Acta 2014;1839(10):964-73
   PubMedGoogle Scholar
• Weigand J, Sanchez M, Gunnesch E-B, et al. Screening for engineered neomycin riboswitches that control translation initiation. RNA 2008;14(1):89-97
   PubMedGoogle Scholar
• Werstuck G, Green M. Controlling gene expression in living cells through small molecule-RNA interactions. Science 1998;282(5387):296-8
   PubMedGoogle Scholar
• Harvey I, Garneau P, Pelletier J. Inhibition of translation by RNA-small molecule interactions. RNA 2002;8(4):452-63
   PubMedGoogle Scholar
• Suess B, Hanson S, Berens C, et al. Conditional gene expression by controlling translation with tetracycline-binding aptamers. Nucleic Acids Res 2003;31(7):1853-8
   PubMedGoogle Scholar
• Hanson S, Berthelot K, Fink B, et al. Tetracycline-aptamer-mediated translational regulation in yeast. Mol Microbiol 2003;49(6):1627-37
   PubMedGoogle Scholar
• Kötter P, Weig J, Weigand J, et al. A fast and efficient translational control system for conditional expression of yeast genes. Nucleic Acids Res 2009;37(18):e120
   Google Scholar
• Bayer TS, Smolke CD. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat Biotechnol 2005;23(3):337-43
   PubMed Web of Science ®Google Scholar
• Ogawa A. Rational design of artificial riboswitches based on ligand-dependent modulation of internal ribosome entry in wheat germ extract and their applications as label-free biosensors. RNA 2011;17(3):478-88
   PubMedGoogle Scholar
• Ogawa A. Ligand-dependent upregulation of ribosomal shunting. ChemBioChem 2013;14(13):1539-43; 1509
   PubMedGoogle Scholar
• Kim D-S, Gusti V, Pillai S, Gaur R. An artificial riboswitch for controlling pre-mRNA splicing. RNA 2005;11(11):1667-77
   PubMedGoogle Scholar
• Kim D-S, Gusti V, Dery K, Gaur R. Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing. BMC Mol Biol 2008;9:23
   PubMedGoogle Scholar
• Weigand J, Suess B. Tetracycline aptamer-controlled regulation of pre-mRNA splicing in yeast. Nucleic Acids Res 2007;35(12):4179-85
   PubMed Web of Science ®Google Scholar
• Wang S, Mortazavi L, White K. Higher-order RNA structural requirements and small-molecule induction of tombusvirus subgenomic mRNA transcription. J Virol 2008;82(8):3864-71
   PubMedGoogle Scholar
• Ausländer D, Wiel M, Wieland M, et al. Rational design of a small molecule-responsive intramer controlling transgene expression in mammalian cells. Nucleic Acids Res 2011;39(22):e155
   PubMedGoogle Scholar
• Tang J, Breaker R. Rational design of allosteric ribozymes. Chem Biol 1997;4(6):453-9
   PubMedGoogle Scholar
• Khvorova A, Lescoute A, Westhof E, Jayasena S. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 2003;10(9):708-12
   PubMedGoogle Scholar
• Win M, Smolke C. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci USA 2007;104(36):14283-8
   PubMedGoogle Scholar
• Win M, Smolke C. Higher-order cellular information processing with synthetic RNA devices. Science 2008;322(5900):456-60
   PubMed Web of Science ®Google Scholar
• Ausländer S, Ketzer P, Hartig J. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol Biosyst 2010;6(5):807-14
   PubMedGoogle Scholar
• Chen YY, Jensen MC, Smolke CD. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc Natl Acad Sci USA 2010;107(19):8531-6
   PubMed Web of Science ®Google Scholar
• Nomura Y, Zhou L, Miu A, Yokobayashi Y. Controlling mammalian gene expression by allosteric hepatitis delta virus ribozymes. ACS Synth Biol 2013;2(12):684-9
   PubMedGoogle Scholar
• Burnett JC, Rossi JJ. RNA-based therapeutics: current progress and future prospects. Chem Biol 2012;19(1):60-71
   PubMed Web of Science ®Google Scholar
• Han J, Lee Y, Yeom K-H, et al. Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 2006;125(5):887-901
   PubMed Web of Science ®Google Scholar
• Wilson R, Doudna J. Molecular mechanisms of RNA interference. Annu Rev Biophys 2013;42:217-39
   PubMed Web of Science ®Google Scholar
• An C-I, Trinh V, Yokobayashi Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 2006;12(5):710-16
   PubMedGoogle Scholar
• Kumar D, An C-I, Yokobayashi Y. Conditional RNA interference mediated by allosteric ribozyme. J Am Chem Soc 2009;131(39):13906-7
   PubMedGoogle Scholar
• Kumar D, Kim S, Yokobayashi Y. Combinatorially inducible RNA interference triggered by chemically modified oligonucleotides. J Am Chem Soc 2011;133(8):2783-8
   PubMedGoogle Scholar
• Beisel C, Chen Y, Culler S, et al. Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing. Nucleic Acids Res 2011;39(7):2981-94
   PubMedGoogle Scholar
• Saito H, Fujita Y, Kashida S, et al. Synthetic human cell fate regulation by protein-driven RNA switches. Nat Commun 2011;2:160
   PubMedGoogle Scholar
• Velagapudi S, Gallo S, Disney M. Sequence-based design of bioactive small molecules that target precursor microRNAs. Nat Chem Biol 2014;10(4):291-7
   PubMed Web of Science ®Google Scholar
• Disney M, Labuda L, Paul D, et al. Two-dimensional combinatorial screening identifies specific aminoglycoside-RNA internal loop partners. J Am Chem Soc 2008;130(33):11185-94
   PubMed Web of Science ®Google Scholar
• Paul D, Seedhouse S, Disney M. Two-dimensional combinatorial screening and the RNA Privileged Space Predictor program efficiently identify aminoglycoside-RNA hairpin loop interactions. Nucleic Acids Res 2009;37(17):5894-907
   PubMed Web of Science ®Google Scholar
• Velagapudi S, Seedhouse S, Disney M. Structure-activity relationships through sequencing (StARTS) defines optimal and suboptimal RNA motif targets for small molecules. Angew Chem Int Ed Engl 2010;49(22):3816-18
   PubMed Web of Science ®Google Scholar
• Griffiths-Jones S, Saini H, Dongen S, Enright A. miRBase: tools for microRNA genomics. Nucleic Acids Res 2008;36(Database issue):D154-8
   PubMed Web of Science ®Google Scholar
• Mathews D, Disney M, Childs J, et al. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 2004;101(19):7287-92
   PubMed Web of Science ®Google Scholar
• Ebert MS, Neilson JR, Sharp PA. MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells. Nat Methods 2007;4(9):721-6
   PubMed Web of Science ®Google Scholar
• Banaszynski LA, Chen LC, Maynard-Smith LA, et al. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules. Cell 2006;126(5):995-1004
   PubMed Web of Science ®Google Scholar
• Banaszynski LA, Sellmyer MA, Contag CH, et al. Chemical control of protein stability and function in living mice. Nat Med 2008;14(10):1123-7
   PubMed Web of Science ®Google Scholar
• Iwamoto M, Bjorklund T, Lundberg C, et al. A general chemical method to regulate protein stability in the mammalian central nervous system. Chem Biol 2010;17(9):981-8
   PubMed Web of Science ®Google Scholar
• Miyazaki Y, Imoto H, Chen LC, Wandless TJ. Destabilizing domains derived from the human estrogen receptor. J Am Chem Soc 2012;134(9):3942-5
   PubMedGoogle Scholar
• Bonger KM, Chen LC, Liu CW, Wandless TJ. Small-molecule displacement of a cryptic degron causes conditional protein degradation. Nat Chem Biol 2011;7(8):531-7
   PubMedGoogle Scholar
• Auslander D, Auslander S, Charpin-El Hamri G, et al. A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol Cell 2014;55(3):397-408
   PubMed Web of Science ®Google Scholar
• Brown BD, Venneri MA, Zingale A, et al. Endogenous microRNA regulation suppresses transgene expression in hematopoietic lineages and enables stable gene transfer. Nat Med 2006;12(5):585-91
   PubMed Web of Science ®Google Scholar
• Langlois RA, Albrecht RA, Kimble B, et al. MicroRNA-based strategy to mitigate the risk of gain-of-function influenza studies. Nat Biotechnol 2013;31(9):844-7
   PubMed Web of Science ®Google Scholar
• Rinaudo K, Bleris L, Maddamsetti R, et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 2007;25(7):795-801
   PubMed Web of Science ®Google Scholar
• Leisner M, Bleris L, Lohmueller J, et al. Rationally designed logic integration of regulatory signals in mammalian cells. Nat Nanotechnol 2010;5(9):666-70
   PubMed Web of Science ®Google Scholar
• Xie Z, Liu S, Bleris L, Benenson Y. Logic integration of mRNA signals by an RNAi-based molecular computer. Nucleic Acids Res 2010;38(8):2692-701
   PubMedGoogle Scholar
• Kashida S, Inoue T, Saito H. Three-dimensionally designed protein-responsive RNA devices for cell signaling regulation. Nucleic Acids Res 2012;40(18):9369-78
   PubMedGoogle Scholar
• Regot S, Hughey JJ, Bajar BT, et al. High-sensitivity measurements of multiple kinase activities in live single cells. Cell 2014;157(7):1724-34
   PubMed Web of Science ®Google Scholar
• Ausländer S, Ausländer D, Müller M, et al. Programmable single-cell mammalian biocomputers. Nature 2012;487(7405):123-7
   PubMedGoogle Scholar
• Pollard C, De Koker S, Saelens X, et al. Challenges and advances towards the rational design of mRNA vaccines. Trends Mol Med 2013;19(12):705-13
   PubMed Web of Science ®Google Scholar
• Pascolo S. Vaccination with messenger RNA (mRNA). Handb Exp Pharmacol 2008(183):221-35
   PubMedGoogle Scholar
• Zhou J, Rossi JJ. Cell-type-specific, aptamer-functionalized agents for targeted disease therapy. Mol Ther Nucleic Acids 2014;3:e169
   PubMedGoogle Scholar
• Wengerter BC, Katakowski JA, Rosenberg JM, et al. Aptamer-targeted Antigen Delivery. Mol Ther 2014;22(7):1375-87
   PubMed Web of Science ®Google Scholar
• Pastor F, Kolonias D, Giangrande PH, Gilboa E. Induction of tumour immunity by targeted inhibition of nonsense-mediated mRNA decay. Nature 2010;465(7295):227-30
   PubMedGoogle Scholar
• Chadambuka A, Chimusoro A, Apollo T, et al. The need for innovative strategies to improve immunisation services in rural Zimbabwe. Disasters 2012;36(1):161-73
   PubMedGoogle Scholar
• Palmowski MJ, Choi EM, Hermans IF, et al. Competition between CTL narrows the immune response induced by prime-boost vaccination protocols. J Immunol 2002;168(9):4391-8
   PubMedGoogle Scholar
• Probst HC, Tschannen K, Gallimore A, et al. Immunodominance of an antiviral cytotoxic T cell response is shaped by the kinetics of viral protein expression. J Immunol 2003;171(10):5415-22
   PubMedGoogle Scholar
• Kim JH, Lee SR, Li LH, et al. High cleavage efficiency of a 2A peptide derived from porcine teschovirus-1 in human cell lines, zebrafish and mice. PLoS One 2011;6(4):e18556
   PubMed Web of Science ®Google Scholar
• Belmont B, Niles J. Inducible control of subcellular RNA localization using a synthetic protein-RNA aptamer interaction. PLoS One 2012;7(10):e46868
   Google Scholar