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1
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84968903135
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Coming of age: ten years of next-generation sequencing technologies
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An excellent comprehensive review of sequencing technologies that describes and compares each approach.
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Goodwin, S., McPherson, J.D., McCombie, W.R., Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17 (2016), 333–351 An excellent comprehensive review of sequencing technologies that describes and compares each approach.
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Goodwin, S.1
McPherson, J.D.2
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Kosuri, S., Church, G.M., Large-scale de novo DNA synthesis: technologies and applications. Nat Methods 11 (2014), 499–507.
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Nat Methods
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Kosuri, S.1
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85014834845
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Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond
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This work describes a landmark in genome engineering — full yeast chromosome synthesis. This is part of the worldwide Yeast2.0 synthetic genome project. By organizing and condensing the yeast genome, unprecedented insight into gene function and genome biology is possible.
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Mitchell, L.A., Wang, A., Stracquadanio, G., Kuang, Z., Wang, X., Yang, K., Richardson, S., Martin, J.A., Zhao, Y., Walker, R., et al. Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond. Science, 2017, 355 This work describes a landmark in genome engineering — full yeast chromosome synthesis. This is part of the worldwide Yeast2.0 synthetic genome project. By organizing and condensing the yeast genome, unprecedented insight into gene function and genome biology is possible.
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Science
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Mitchell, L.A.1
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Richardson, S.7
Martin, J.A.8
Zhao, Y.9
Walker, R.10
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4
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Genetic circuit characterization and debugging using RNA-seq
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Gorochowski, T.E., Espah Borujeni, A., Park, Y., Nielsen, A.A., Zhang, J., Der, B.S., Gordon, D.B., Voigt, C.A., Genetic circuit characterization and debugging using RNA-seq. Mol Syst Biol, 13, 2017, 952.
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Mol Syst Biol
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Gordon, D.B.7
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A guide to genome engineering with programmable nucleases
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Kim, H., Kim, J.S., A guide to genome engineering with programmable nucleases. Nat Rev Genet 15 (2014), 321–334.
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Nat Rev Genet
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Kim, H.1
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Genome-scale CRISPR-Cas9 knockout screening in human cells
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Shalem, O., Sanjana, N.E., Hartenian, E., Shi, X., Scott, D.A., Mikkelsen, T.S., Heckl, D., Ebert, B.L., Root, D.E., Doench, J.G., et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343 (2014), 84–87.
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Science
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Shalem, O.1
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Mikkelsen, T.S.6
Heckl, D.7
Ebert, B.L.8
Root, D.E.9
Doench, J.G.10
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High efficiency hydrodynamic bacterial electrotransformation
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This work establishes electroporation in microfluidic channels, a new approach that could permit transformation of new microorganisms. The results suggest that the types of electric fields in this design allow increases in efficiency and scale over cuvettes.
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Garcia, P.A., Ge, Z., Kelley, L.E., Holcomb, S.J., Buie, C.R., High efficiency hydrodynamic bacterial electrotransformation. Lab Chip 17 (2017), 490–500 This work establishes electroporation in microfluidic channels, a new approach that could permit transformation of new microorganisms. The results suggest that the types of electric fields in this design allow increases in efficiency and scale over cuvettes.
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Lab Chip
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Garcia, P.A.1
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Garcia, P.A., Ge, Z., Moran, J.L., Buie, C.R., Microfluidic screening of electric fields for electroporation. Sci Rep, 6, 2016, 21238.
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Sci Rep
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Garcia, P.A.1
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Next-generation genome-scale models for metabolic engineering
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This review highlights progress and perspectives on Constraint Based Reconstruction and Analysis (COBRA). The authors describe recent achievement using this metabolic modeling approach and how additional predictions with COBRA models could advance metabolic engineering in the future.
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King, Z.A., Lloyd, C.J., Feist, A.M., Palsson, B.O., Next-generation genome-scale models for metabolic engineering. Curr Opin Biotechnol 35 (2015), 23–29 This review highlights progress and perspectives on Constraint Based Reconstruction and Analysis (COBRA). The authors describe recent achievement using this metabolic modeling approach and how additional predictions with COBRA models could advance metabolic engineering in the future.
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King, Z.A.1
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Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line
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e536
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Yusufi, F.N.K., Lakshmanan, M., Ho, Y.S., Loo, B.L.W., Ariyaratne, P., Yang, Y., Ng, S.K., Tan, T.R.M., Yeo, H.C., Lim, H.L., et al. Mammalian systems biotechnology reveals global cellular adaptations in a recombinant CHO cell line. Cell Syst 4 (2017), 530–542 e536.
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Yusufi, F.N.K.1
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Functional optimization of gene clusters by combinatorial design and assembly
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Smanski, M.J., Bhatia, S., Zhao, D., Park, Y., BAW, L., Giannoukos, G., Ciulla, D., Busby, M., Calderon, J., Nicol, R., et al. Functional optimization of gene clusters by combinatorial design and assembly. Nat Biotechnol 32 (2014), 1241–1249.
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Smanski, M.J.1
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Leaf LIMS: a flexible laboratory information management system with a synthetic biology focus
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The authors present a freely available laboratory information management system specifically designed for synthetic biology. This software is a great resource for genetic engineering labs, where organization of DNA parts, for example, can be a challenge.
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Craig, T., Holland, R., D'Amore, R., Johnson, J.R., McCue, H.V., West, A., Zulkower, V., Tekotte, H., Cai, Y., Swan, D., et al. Leaf LIMS: a flexible laboratory information management system with a synthetic biology focus. ACS Synth Biol 6 (2017), 2273–2280 The authors present a freely available laboratory information management system specifically designed for synthetic biology. This software is a great resource for genetic engineering labs, where organization of DNA parts, for example, can be a challenge.
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ACS Synth Biol
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Craig, T.1
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Genetic circuit design automation
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The authors report 45 perfectly functioning circuits out of 60 designs without expert tuning. To accomplish this, the authors develop Cello, software that can output functional circuits composed of a set of well-characterized logic gates from user-inputted logic. This represents a landmark achievement for synthetic biology.
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Nielsen, A.A., Der, B.S., Shin, J., Vaidyanathan, P., Paralanov, V., Strychalski, E.A., Ross, D., Densmore, D., Voigt, C.A., Genetic circuit design automation. Science, 352, 2016, aac7341 The authors report 45 perfectly functioning circuits out of 60 designs without expert tuning. To accomplish this, the authors develop Cello, software that can output functional circuits composed of a set of well-characterized logic gates from user-inputted logic. This represents a landmark achievement for synthetic biology.
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Nielsen, A.A.1
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Automated multiplex genome-scale engineering in yeast
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An automated platform for multiplexed genome-scale engineering in S. cerevisiae was constructed. Genetic parts encoding overexpression and knockdown mutations were iteratively integrated by CRISPR-Cas in an automated workflow. This will greatly accelerate genome-scale engineering for a desired phenotype in S. cerevisiae, and could be adapted to other organisms.
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Si, T., Chao, R., Min, Y., Wu, Y., Ren, W., Zhao, H., Automated multiplex genome-scale engineering in yeast. Nat Commun, 8, 2017, 15187 An automated platform for multiplexed genome-scale engineering in S. cerevisiae was constructed. Genetic parts encoding overexpression and knockdown mutations were iteratively integrated by CRISPR-Cas in an automated workflow. This will greatly accelerate genome-scale engineering for a desired phenotype in S. cerevisiae, and could be adapted to other organisms.
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Nat Commun
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Si, T.1
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Kuznetsov, G., Goodman, D.B., Filsinger, G.T., Landon, M., Rohland, N., Aach, J., Lajoie, M.J., Church, G.M., Optimizing complex phenotypes through model-guided multiplex genome engineering. Genome Biol, 18, 2017, 100.
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Genome Biol
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Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes
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Melnikov, A., Rogov, P., Wang, L., Gnirke, A., Mikkelsen, T.S., Comprehensive mutational scanning of a kinase in vivo reveals substrate-dependent fitness landscapes. Nucleic Acids Res, 42, 2014, e112.
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Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor
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Zhou, H., Vonk, B., Roubos, J.A., Bovenberg, R.A., Voigt, C.A., Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor. Nucleic Acids Res 43 (2015), 10560–10570.
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18
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85012838041
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Improving metabolic pathway efficiency by statistical model-based multivariate regulatory metabolic engineering
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A promoter library was developed to allow different expression levels of the violacein pathway in E. coli. A combinatorial set of different expression variants was designed with a statistical model, specifically design-of-experiments (DoE). These models were used to correlate gene expression levels with violacein titer. Extracting useful design information from rationally reduced combinatorial libraries promises to significantly decrease the experimental effort needed to iterate towards high producing phenotypes.
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Xu, P., Rizzoni, E.A., Sul, S.Y., Stephanopoulos, G., Improving metabolic pathway efficiency by statistical model-based multivariate regulatory metabolic engineering. ACS Synth Biol 6 (2017), 148–158 A promoter library was developed to allow different expression levels of the violacein pathway in E. coli. A combinatorial set of different expression variants was designed with a statistical model, specifically design-of-experiments (DoE). These models were used to correlate gene expression levels with violacein titer. Extracting useful design information from rationally reduced combinatorial libraries promises to significantly decrease the experimental effort needed to iterate towards high producing phenotypes.
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ACS Synth Biol
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Xu, P.1
Rizzoni, E.A.2
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High substrate uptake rates empower Vibrio natriegens as production host for industrial biotechnology
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Hoffart, E., Grenz, S., Lange, J., Nitschel, R., Muller, F., Schwentner, A., Feith, A., Lenfers-Lucker, M., Takors, R., Blombach, B., High substrate uptake rates empower Vibrio natriegens as production host for industrial biotechnology. Appl Environ Microbiol 83 (2017), e01614–e01617.
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CHO cells in biotechnology for production of recombinant proteins: current state and further potential
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Kim, J.Y., Kim, Y.G., Lee, G.M., CHO cells in biotechnology for production of recombinant proteins: current state and further potential. Appl Microbiol Biotechnol 93 (2012), 917–930.
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Multiplex genome engineering using CRISPR/Cas systems
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Cong, L., Ran, F.A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P.D., Wu, X., Jiang, W., Marraffini, L.A., et al. Multiplex genome engineering using CRISPR/Cas systems. Science 339 (2013), 819–823.
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A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
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Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J.A., Charpentier E: A., A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337 (2012), 816–821.
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Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation
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An informative review of alternative uses of the Cas9 nuclease, including strategies for inducible gene regulation, genome-wide screens, and cell fate engineering.
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Dominguez, A.A., Lim, W.A., Qi, L.S., Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 17 (2016), 5–15 An informative review of alternative uses of the Cas9 nuclease, including strategies for inducible gene regulation, genome-wide screens, and cell fate engineering.
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Dominguez, A.A.1
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Digital logic circuits in yeast with CRISPR-dCas9 NOR gates
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Gander, M.W., Vrana, J.D., Voje, W.E., Carothers, J.M., Klavins, E., Digital logic circuits in yeast with CRISPR-dCas9 NOR gates. Nat Commun, 8, 2017, 15459.
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Nat Commun
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New CRISPR-Cas systems from uncultivated microbes
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Burstein, D., Harrington, L.B., Strutt, S.C., Probst, A.J., Anantharaman, K., Thomas, B.C., Doudna, J.A., Banfield, J.F., New CRISPR-Cas systems from uncultivated microbes. Nature 542 (2017), 237–241.
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84975678715
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Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system
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Zetsche, B., Gootenberg, J.S., Abudayyeh, O.O., Slaymaker, I.M., Makarova, K.S., Essletzbichler, P., Volz, S.E., Joung, J., van der Oost, J., Regev, A., et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163 (2015), 759–771.
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In vivo high-throughput profiling of CRISPR-Cpf1 activity
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Kim, H.K., Song, M., Lee, J., Menon, A.V., Jung, S., Kang, Y.M., Choi, J.W., Woo, E., Koh, H.C., Nam, J.W., et al. In vivo high-throughput profiling of CRISPR-Cpf1 activity. Nat Methods 14 (2017), 153–159.
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Begemann, M.B., Gray, B.N., January, E., Gordon, G.C., He, Y., Liu, H., Wu, X., Brutnell, T.P., Mockler, T.C., Oufattole, M., Precise insertion and guided editing of higher plant genomes using Cpf1 CRISPR nucleases. Sci Rep, 7, 2017, 11606.
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Zetsche, B., Heidenreich, M., Mohanraju, P., Fedorova, I., Kneppers, J., DeGennaro, E.M., Winblad, N., Choudhury, S.R., Abudayyeh, O.O., Gootenberg, J.S., et al. Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. Nat Biotechnol 35 (2017), 31–34.
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Tak, Y.E., Kleinstiver, B.P., Nunez, J.K., Hsu, J.Y., Horng, J.E., Gong, J., Weissman, J.S., Joung, J.K., Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods 14 (2017), 1163–1166.
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The CCTL (Cpf1-assisted Cutting and Taq DNA ligase-assisted Ligation) method for efficient editing of large DNA constructs in vitro
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In this work, the recently discovered Cpf1 nuclease was adapted as a flexible cloning tool. DNA cleavage with the Cpf1 nuclease domain creates sticky ends, which the authors show can facilitate in vitro molecular cloning reactions. Like Gibson assembly, Cpf1 cloning is scarless, but has the added advantage of being much more efficient with high GC regions.
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Lei, C., Li, S.Y., Liu, J.K., Zheng, X., Zhao, G.P., Wang, J., The CCTL (Cpf1-assisted Cutting and Taq DNA ligase-assisted Ligation) method for efficient editing of large DNA constructs in vitro. Nucleic Acids Res, 45, 2017, e74 In this work, the recently discovered Cpf1 nuclease was adapted as a flexible cloning tool. DNA cleavage with the Cpf1 nuclease domain creates sticky ends, which the authors show can facilitate in vitro molecular cloning reactions. Like Gibson assembly, Cpf1 cloning is scarless, but has the added advantage of being much more efficient with high GC regions.
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Nucleic Acids Res
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Lei, C.1
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Li, S.Y., Zhao, G.P., Wang, J., C-Brick: a new standard for assembly of biological parts using Cpf1. ACS Synth Biol 5 (2016), 1383–1388.
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Kweon, J., Jang, A.H., Kim, D.E., Yang, J.W., Yoon, M., Rim Shin, H., Kim, J.S., Kim, Y., Fusion guide RNAs for orthogonal gene manipulation with Cas9 and Cpf1. Nat Commun, 8, 2017, 1723.
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Yang, H., Gao, P., Rajashankar, K.R., Patel, D.J., PAM-dependent target DNA recognition and cleavage by C2c1 CRISPR-Cas endonuclease. Cell 167 (2016), 1814–1828 e1812.
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Biotechnol Bioeng
, vol.112
, pp. 521-535
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Fan, Y.1
Jimenez Del Val, I.2
Muller, C.3
Wagtberg Sen, J.4
Rasmussen, S.K.5
Kontoravdi, C.6
Weilguny, D.7
Andersen, M.R.8
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