References
Alam, K. K., Chang, J. L., & Burke, D. H. (2015). FASTAptamer: A
bioinformatic toolkit for high-throughput sequence analysis of
combinatorial selections. Molecular Therapy - Nucleic Acids .
https://doi.org/10.1038/mtna.2015.4
Anderson, C. W., Straus, J. W., & Dudock, B. S. (1983). Preparation of
a cell-free protein-synthesizing system from wheat germ. Methods
in Enzymology . https://doi.org/10.1016/0076-6879(83)01044-7
Bashiruddin, N. K., & Suga, H. (2015). Construction and screening of
vast libraries of natural product-like macrocyclic peptides using in
vitro display technologies. Current Opinion in Chemical Biology .
https://doi.org/10.1016/j.cbpa.2014.11.011
Bertschinger, J., & Neri, D. (2004). Covalent DNA display as a novel
tool for directed evolution of proteins in vitro. Protein
Engineering, Design and Selection .
https://doi.org/10.1093/protein/gzh082
Boder, E. T., & Wittrup, K. D. (1997). Yeast surface display for
screening combinatorial polypeptide libraries. Nature
Biotechnology . https://doi.org/10.1038/nbt0697-553
Bowie, J. U., Sherkhanov, S., Korman, T. P., Valliere, M. A., Opgenorth,
P. H., & Liu, H. (2020). Synthetic Biochemistry: The Bio-inspired
Cell-Free Approach to Commodity Chemical Production. Trends in
Biotechnology . https://doi.org/10.1016/j.tibtech.2019.12.024
Buntru, M., Vogel, S., Spiegel, H., & Schillberg, S. (2014). Tobacco
BY-2 cell-free lysate: An alternative and highly-productive plant-based
in vitro translation system. BMC Biotechnology .
https://doi.org/10.1186/1472-6750-14-37
Carlson, E. D., Gan, R., Hodgman, C. E., & Jewett, M. C. (2012).
Cell-free protein synthesis: Applications come of age.Biotechnology Advances , 30 (5), 1185–1194.
https://doi.org/10.1016/j.biotechadv.2011.09.016
Cherf, G. M., & Cochran, J. R. (2015). Applications of yeast surface
display for protein engineering. Methods in Molecular Biology .
https://doi.org/10.1007/978-1-4939-2748-7_8
Contreras-Llano, L. E., & Tan, C. (2018). High-throughput screening of
biomolecules using cell-free gene expression systems. Synthetic
Biology . https://doi.org/10.1093/synbio/ysy012
Crooks, G. E., Hon, G., Chandonia, J. M., & Brenner, S. E. (2004).
WebLogo: A sequence logo generator. Genome Research .
https://doi.org/10.1101/gr.849004
Didovyk, A., Tonooka, T., Tsimring, L., & Hasty, J. (2017). Rapid and
Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression.ACS Synthetic Biology . https://doi.org/10.1021/acssynbio.7b00253
Dodevski, I., Markou, G. C., & Sarkar, C. A. (2015). Conceptual and
methodological advances in cell-free directed evolution. Current
Opinion in Structural Biology .
https://doi.org/10.1016/j.sbi.2015.04.008
Doi, N., & Yanagawa, H. (1999). STABLE: Protein-DNA fusion system for
screening of combinatorial protein libraries in vitro. FEBS
Letters . https://doi.org/10.1016/S0014-5793(99)01041-8
Ezure, T., Suzuki, T., & Ando, E. (2014). A cell-free protein synthesis
system from insect cells. Methods in Molecular Biology .
https://doi.org/10.1007/978-1-62703-782-2_20
Fujii, S., Matsuura, T., Sunami, T., Kazuta, Y., & Yomo, T. (2013). In
vitro evolution of α-hemolysin using a liposome display.Proceedings of the National Academy of Sciences of the United
States of America . https://doi.org/10.1073/pnas.1314585110
Fujii, S., Matsuura, T., Sunami, T., Nishikawa, T., Kazuta, Y., & Yomo,
T. (2014). Liposome display for in vitro selection and evolution of
membrane proteins. Nature Protocols , 9 (7), 1578–1591.
https://doi.org/10.1038/nprot.2014.107
Fujimori, S., Hirai, N., Ohashi, H., Masuoka, K., Nishikimi, A., Fukui,
Y., … Miyamoto-Sato, E. (2012). Next-generation sequencing
coupled with a cell-free display technology for high-throughput
production of reliable interactome data. Scientific Reports .
https://doi.org/10.1038/srep00691
Fujiwara, K., & Doi, N. (2016). Biochemical preparation of cell extract
for cell-free protein synthesis without physical disruption. PLoS
ONE . https://doi.org/10.1371/journal.pone.0154614
Hammerling, M. J., Krüger, A., & Jewett, M. C. (2019). Strategies for
in vitro engineering of the translation machinery. Nucleic Acids
Research . https://doi.org/10.1093/nar/gkz1011
Hino, M., Kataoka, M., Kajimoto, K., Yamamoto, T., Kido, J. I.,
Shinohara, Y., & Baba, Y. (2008). Efficiency of cell-free protein
synthesis based on a crude cell extract from Escherichia coli, wheat
germ, and rabbit reticulocytes. Journal of Biotechnology .
https://doi.org/10.1016/j.jbiotec.2007.08.008
Hodgman, C. E., & Jewett, M. C. (2012). Cell-free synthetic biology:
Thinking outside the cell. Metabolic Engineering .
https://doi.org/10.1016/j.ymben.2011.09.002
Jackson, R. J., & Hunt, T. (1983). Preparation and use of
nuclease-treated rabbit reticulocyte lysates for the translation of
eukaryotic messenger RNA. Methods in Enzymology .
https://doi.org/10.1016/S0076-6879(83)96008-1
Josephson, K., Ricardo, A., & Szostak, J. W. (2014). MRNA display: From
basic principles to macrocycle drug discovery. Drug Discovery
Today . https://doi.org/10.1016/j.drudis.2013.10.011
Kanamori, T., Fujino, Y., & Ueda, T. (2014). PURE ribosome display and
its application in antibody technology. Biochimica et Biophysica
Acta - Proteins and Proteomics .
https://doi.org/10.1016/j.bbapap.2014.04.007
Kay, J. E., & Jewett, M. C. (2020). A cell-free system for production
of 2,3-butanediol is robust to growth-toxic compounds. Metabolic
Engineering Communications . https://doi.org/10.1016/j.mec.2019.e00114
Kazuta, Y., Matsuura, T., Ichihashi, N., & Yomo, T. (2014). Synthesis
of milligram quantities of proteins using a reconstituted in vitro
protein synthesis system. Journal of Bioscience and
Bioengineering . https://doi.org/10.1016/j.jbiosc.2014.04.019
Keasling, J. D. (2012). Synthetic biology and the development of tools
for metabolic engineering. Metab Eng , 14 (1096-7184
(Electronic)), 189–195. https://doi.org/10.1016/j.ymben.2012.01.004
Kuruma, Y., & Ueda, T. (2015). The PURE system for the cell-free
synthesis of membrane proteins. Nature Protocols .
https://doi.org/10.1038/nprot.2015.082
Lavickova, B., & Maerkl, S. J. (2019). A Simple, Robust, and Low-Cost
Method to Produce the PURE Cell-Free System. ACS Synthetic
Biology . https://doi.org/10.1021/acssynbio.8b00427
Layton, C. J., McMahon, P. L., & Greenleaf, W. J. (2019). Large-Scale,
Quantitative Protein Assays on a High-Throughput DNA Sequencing Chip.Molecular Cell . https://doi.org/10.1016/j.molcel.2019.02.019
Ledsgaard, L., Kilstrup, M., Karatt-Vellatt, A., McCafferty, J., &
Laustsen, A. H. (2018). Basics of antibody phage display technology.Toxins . https://doi.org/10.3390/toxins10060236
Miceli, R. M., DeGraaf, M. E., & Fischer, H. D. (1994). Two-stage
selection of sequences from a random phage display library delineates
both core residues and permitted structural range within an epitope.Journal of Immunological Methods .
https://doi.org/10.1016/0022-1759(94)90097-3
Nagumo, Y., Fujiwara, K., Horisawa, K., Yanagawa, H., & Doi, N. (2016).
PURE mRNA display for in vitro selection of single-chain antibodies.Journal of Biochemistry . https://doi.org/10.1093/jb/mvv131
Naimuddin, M., Kobayashi, S., Tsutsui, C., MacHida, M., Nemoto, N.,
Sakai, T., & Kubo, T. (2011). Directed evolution of a three-finger
neurotoxin by using cDNA display yields antagonists as well as agonists
of interleukin-6 receptor signaling. Molecular Brain .
https://doi.org/10.1186/1756-6606-4-2
Naimuddin, M., & Kubo, T. (2016). A High Performance Platform Based on
cDNA Display for Efficient Synthesis of Protein Fusions and Accelerated
Directed Evolution. ACS Combinatorial Science .
https://doi.org/10.1021/acscombsci.5b00139
Nemoto, N., Miyamoto-Sato, E., Husimi, Y., & Yanagawa, H. (1997). In
vitro virus: Bonding of mRNA bearing puromycin at the 3’-terminal end to
the C-terminal end of its encoded protein on the ribosome in vitro.FEBS Letters . https://doi.org/10.1016/S0014-5793(97)01026-0
Newton, M. S., Cabezas-Perusse, Y., Tong, C. L., & Seelig, B. (2020).
In Vitro Selection of Peptides and Proteins - Advantages of mRNA
Display. ACS Synthetic Biology .
https://doi.org/10.1021/acssynbio.9b00419
Nishigaki, K., Taguchi, K., Kinoshita, Y., Aita, T., & Husimi, Y.
(1998). Y-ligation: An efficient method for ligating single-stranded
DNAs and RNAs with T4 RNA ligase. Molecular Diversity .
https://doi.org/10.1023/A:1009644028931
Opyrchal, M., Anderson, J. R., Sokoloski, K. J., Wilusz, C. J., &
Wilusz, J. (2005). A cell-free mRNA stability assay reveals conservation
of the enzymes and mechanisms of mRNA decay between mosquito and
mammalian cell lines. Insect Biochemistry and Molecular Biology .
https://doi.org/10.1016/j.ibmb.2005.08.004
Osada, E., Shimizu, Y., Akbar, B. K., Kanamori, T., & Ueda, T. (2009).
Epitope mapping using ribosome display in a reconstituted cell-free
protein synthesis system. Journal of Biochemistry .
https://doi.org/10.1093/jb/mvp027
Perez, J. G., Stark, J. C., & Jewett, M. C. (2016). Cell-free synthetic
biology: Engineering beyond the cell. Cold Spring Harbor
Perspectives in Biology . https://doi.org/10.1101/cshperspect.a023853
Roberts, R. W., & Szostak, J. W. (1997). RNA-peptide fusions for the in
vitro selection of peptides and proteins. Proceedings of the
National Academy of Sciences of the United States of America .
https://doi.org/10.1073/pnas.94.23.12297
Roosild, T. P., Castronovo, S., & Choe, S. (2006). Structure of
anti-FLAG M2 Fab domain and its use in the stabilization of engineered
membrane proteins. Acta Crystallographica Section F: Structural
Biology and Crystallization Communications .
https://doi.org/10.1107/S1744309106029125
Seelig, B. (2011). MRNA display for the selection and evolution of
enzymes from in vitro-translated protein libraries. Nature
Protocols . https://doi.org/10.1038/nprot.2011.312
Shimizu, Y, Inoue, a, Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa,
K., & Ueda, T. (2001). Cell-free translation reconstituted with
purified components. Nature Biotechnology , 19 (8),
751–755. https://doi.org/10.1038/90802
Shimizu, Yoshihiro, Kanamori, T., & Ueda, T. (2005). Protein synthesis
by pure translation systems. Methods .
https://doi.org/10.1016/j.ymeth.2005.04.006
Shimizu, Yoshihiro, Kuruma, Y., Kanamori, T., & Ueda, T. (2014). The
PURE system for protein production. Methods in Molecular Biology ,1118 , 275–284. https://doi.org/10.1007/978-1-62703-782-2-19
Shin, J., & Noireaux, V. (2010). Study of messenger RNA inactivation
and protein degradation in an Escherichia coli cell-free expression
system. Journal of Biological Engineering .
https://doi.org/10.1186/1754-1611-4-9
Silverman, A. D., Karim, A. S., & Jewett, M. C. (2019). Cell-free gene
expression: an expanded repertoire of applications. Nature Reviews
Genetics . https://doi.org/10.1038/s41576-019-0186-3
Srila, W., & Yamabhai, M. (2013). Identification of amino acid residues
responsible for the binding to anti-FLAGTM M2 antibody
using a phage display combinatorial peptide library. Applied
Biochemistry and Biotechnology .
https://doi.org/10.1007/s12010-013-0326-8
Sun, Z. Z., Hayes, C. A., Shin, J., Caschera, F., Murray, R. M., &
Noireaux, V. (2013). Protocols for implementing an Escherichia coli
based TX-TL cell-free expression system for synthetic biology.Journal of Visualized Experiments : JoVE , (79), e50762.
https://doi.org/10.3791/50762
Takahashi, T. T., Austin, R. J., & Roberts, R. W. (2003). mRNA display:
Ligand discovery, interaction analysis and beyond. Trends in
Biochemical Sciences . https://doi.org/10.1016/S0968-0004(03)00036-7
Tinafar, A., Jaenes, K., & Pardee, K. (2019). Synthetic Biology Goes
Cell-Free. BMC Biology . https://doi.org/10.1186/s12915-019-0685-x
Ueno, S., & Nemoto, N. (2012). CDNA display: Rapid stabilization of
mrna display. Methods in Molecular Biology .
https://doi.org/10.1007/978-1-61779-379-0_8
Van Der Mast, C. A., & Bloemers, H. P. J. (1973). The puromycin
reaction mediated by yeast ribosomes in high salt. Molecular
Biology Reports . https://doi.org/10.1007/BF00357646
Villarreal, F., & Tan, C. (2017). Cell-free systems in the new age of
synthetic biology. Frontiers of Chemical Science and Engineering .
https://doi.org/10.1007/s11705-017-1610-x
Wang, P. H., Fujishima, K., Berhanu, S., Kuruma, Y., Jia, T. Z.,
Khusnutdinova, A. N., … McGlynn, S. E. (2019). A Bifunctional
Polyphosphate Kinase Driving the Regeneration of Nucleoside Triphosphate
and Reconstituted Cell-Free Protein Synthesis. ACS Synthetic
Biology . https://doi.org/10.1021/acssynbio.9b00456
Wang, X., Zhao, L., & Zhao, K. N. (2014). An optimized yeast cell-free
lysate system for in vitro translation of human virus mRNA.Methods in Molecular Biology .
https://doi.org/10.1007/978-1-62703-782-2_14
Yadavalli, R., & Sam-Yellowe, T. (2015). Hela based cell free
expression systems for expression of Plasmodium rhoptry proteins.Journal of Visualized Experiments . https://doi.org/10.3791/52772
Yamaguchi, J., Naimuddin, M., Biyani, M., Sasaki, T., Machida, M., Kubo,
T., … Nemoto, N. (2009). cDNA display: A novel screening method
for functional disulfide-rich peptides by solid-phase synthesis and
stabilization of mRNA-protein fusions. Nucleic Acids Research .
https://doi.org/10.1093/nar/gkp514
Yonezawa, M., Doi, N., Kawahashi, Y., Higashinakagawa, T., & Yanagawa,
H. (2003). DNA display for in vitro selection of diverse peptide
libraries. Nucleic Acids Research .
https://doi.org/10.1093/nar/gng119
Zahnd, C., Amstutz, P., & Plückthun, A. (2007). Ribosome display:
Selecting and evolving proteins in vitro that specifically bind to a
target. Nature Methods . https://doi.org/10.1038/nmeth1003