CRISPR/Cas9-Based Genome Editing for Disease Modeling and Therapy: Challenges and Opportunities for Nonviral Delivery

Chemical Reviews

Volumn 117, Issue 15, 2017, Pages 9874-9906

  Wang, Hong Xia ^a   Li, Mingqiang ^a   Lee, Ciaran M ^b   Chakraborty, Syandan ^a   Kim, Hae Won ^c   Bao, Gang ^b   Leong, Kam W ^a  

^a Department of Earth and Environmental Sciences   (United States)

^b Rice University   (United States)

^c BK21 Plus NBM Global Research Center for Regenerative Medicine   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL MODIFICATION; DISEASE CONTROL; DNA SEQUENCES; ENZYME ACTIVITY; GENE EXPRESSION; GENE TRANSFER; NUCLEIC ACIDS; PROTEINS;

BIOINFORMATICS TOOLS; DISEASE MODELING; GENE CORRECTION; GENETIC DISORDERS; NON-VIRAL DELIVERIES; NON-VIRAL GENE DELIVERY; NONVIRAL VECTORS; RECENT PROGRESS;

GENES;

BIOLOGICAL MODEL; CRISPR CAS SYSTEM; GENE EDITING; GENE THERAPY; GENE TRANSFER; GENETICS; HUMAN; PROCEDURES;

CRISPR-CAS SYSTEMS; GENE EDITING; GENE TRANSFER TECHNIQUES; GENETIC THERAPY; HUMANS; MODELS, BIOLOGICAL;

EID: 85027368877     PISSN: 00092665     EISSN: 15206890     Source Type: Journal    
DOI: 10.1021/acs.chemrev.6b00799     Document Type: Review

References (301)

1. Kay, M. A. State-of-the-Art Gene-Based Therapies: The Road Ahead Nat. Rev. Genet. 2011, 12, 316-328 10.1038/nrg2971
2. Cox, D. B. T.; Platt, R. J.; Zhang, F. Therapeutic Genome Editing: Prospects and Challenges Nat. Med. 2015, 21, 121-131 10.1038/nm.3793
3. Capecchi, M. R. Altering the Genome by Homologous Recombination Science 1989, 244, 1288-1292 10.1126/science.2660260
4. Stoddard, B. L. Homing Endonucleases: From Microbial Genetic Invaders to Reagents for Targeted DNA Modification Structure 2011, 19, 7-15 10.1016/j.str.2010.12.003
5. Urnov, F. D.; Rebar, E. J.; Holmes, M. C.; Zhang, H. S.; Gregory, P. D. Genome Editing with Engineered Zinc Finger Nucleases Nat. Rev. Genet. 2010, 11, 636-646 10.1038/nrg2842
6. Bogdanove, A. J.; Voytas, D. F. TAL Effectors: Customizable Proteins for DNA Targeting Science 2011, 333, 1843-1846 10.1126/science.1204094
7. Brouns, S. J.; Jore, M. M.; Lundgren, M.; Westra, E. R.; Slijkhuis, R. J.; Snijders, A. P.; Dickman, M. J.; Makarova, K. S.; Koonin, E. V.; Van Der Oost, J. Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes Science 2008, 321, 960-964 10.1126/science.1159689
8. Hsu, P. D.; Lander, E. S.; Zhang, F. Development and Applications of CRISPR-Cas9 for Genome Engineering Cell 2014, 157, 1262-1278 10.1016/j.cell.2014.05.010
9. Wang, M.; Glass, Z.; Xu, Q. Non-Viral Delivery of Genome-Editing Nucleases for Gene Therapy Gene Ther. 2017, 24, 144 10.1038/gt.2016.72
10. Wu, Y.; Liang, D.; Wang, Y.; Bai, M.; Tang, W.; Bao, S.; Yan, Z.; Li, D.; Li, J. Correction of a Genetic Disease in Mouse via Use of CRISPR-Cas9 Cell Stem Cell 2013, 13, 659-662 10.1016/j.stem.2013.10.016
11. Wu, Y.; Zhou, H.; Fan, X.; Zhang, Y.; Zhang, M.; Wang, Y.; Xie, Z.; Bai, M.; Yin, Q.; Liang, D. et al. Correction of a Genetic Disease by CRISPR-Cas9-Mediated Gene Editing in Mouse Spermatogonial Stem Cells Cell Res. 2015, 25, 67-79 10.1038/cr.2014.160
12. Long, C.; McAnally, J. R.; Shelton, J. M.; Mireault, A. A.; Bassel-Duby, R.; Olson, E. N. Prevention of Muscular Dystrophy in Mice by CRISPR/Cas9-Mediated Editing of Germline DNA Science 2014, 345, 1184-1188 10.1126/science.1254445
13. Ye, L.; Wang, J.; Beyer, A. I.; Teque, F.; Cradick, T. J.; Qi, Z.; Chang, J. C.; Bao, G.; Muench, M. O.; Yu, J. Seamless Modification of Wild-Type Induced Pluripotent Stem Cells to the Natural CCR5Δ32 Mutation Confers Resistance to HIV Infection Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 9591-9596 10.1073/pnas.1407473111
14. Wells, D. Gene Therapy Progress and Prospects: Electroporation and Other Physical Methods Gene Ther. 2004, 11, 1363-1369 10.1038/sj.gt.3302337
15. Maurisse, R.; De Semir, D.; Emamekhoo, H.; Bedayat, B.; Abdolmohammadi, A.; Parsi, H.; Gruenert, D. C. Comparative Transfection of DNA into Primary and Transformed Mammalian Cells from Different Lineages BMC Biotechnol. 2010, 10, 9 10.1186/1472-6750-10-9
16. Ain, Q. U.; Chung, J. Y.; Kim, Y. H. Current and Future Delivery Systems for Engineered Nucleases: ZFN, TALEN and RGEN J. Controlled Release 2015, 205, 120-127 10.1016/j.jconrel.2014.12.036
17. Wang, T.; Wei, J. J.; Sabatini, D. M.; Lander, E. S. Genetic Screens in Human Cells Using the CRISPR-Cas9 System Science 2014, 343, 80-84 10.1126/science.1246981
18. Chakraborty, S.; Ji, H.; Kabadi, A. M.; Gersbach, C. A.; Christoforou, N.; Leong, K. W. A CRISPR/Cas9-Based System for Reprogramming Cell Lineage Specification Stem Cell Rep. 2014, 3, 940-947 10.1016/j.stemcr.2014.09.013
19. Ding, Q.; Strong, A.; Patel, K. M.; Ng, S.-L.; Gosis, B. S.; Regan, S. N.; Cowan, C. A.; Rader, D. J.; Musunuru, K. Permanent Alteration of PCSK9 with in vivo CRISPR-Cas9 Genome Editing Circ. Res. 2014, 115, 488-492 10.1161/CIRCRESAHA.115.304351
20. Ran, F. A.; Cong, L.; Yan, W. X.; Scott, D. A.; Gootenberg, J. S.; Kriz, A. J.; Zetsche, B.; Shalem, O.; Wu, X.; Makarova, K. S. et al. In vivo Genome Editing Using Staphylococcus Aureus Cas9 Nature 2015, 520, 186-191 10.1038/nature14299
21. Yin, H.; Kanasty, R. L.; Eltoukhy, A. A.; Vegas, A. J.; Dorkin, J. R.; Anderson, D. G. Non-Viral Vectors for Gene-Based Therapy Nat. Rev. Genet. 2014, 15, 541-555 10.1038/nrg3763
22. Liang, X.; Potter, J.; Kumar, S.; Zou, Y.; Quintanilla, R.; Sridharan, M.; Carte, J.; Chen, W.; Roark, N.; Ranganathan, S. et al. Rapid and Highly Efficient Mammalian Cell Engineering via Cas9 Protein Transfection J. Biotechnol. 2015, 208, 44-53 10.1016/j.jbiotec.2015.04.024
23. Zuris, J. A.; Thompson, D. B.; Shu, Y.; Guilinger, J. P.; Bessen, J. L.; Hu, J. H.; Maeder, M. L.; Joung, J. K.; Chen, Z.-Y.; Liu, D. R. Cationic Lipid-Mediated Delivery of Proteins Enables Efficient Protein-Based Genome Editing in vitro and in vivo Nat. Biotechnol. 2015, 33, 73-80 10.1038/nbt.3081
24. Wang, M.; Zuris, J. A.; Meng, F.; Rees, H.; Sun, S.; Deng, P.; Han, Y.; Gao, X.; Pouli, D.; Wu, Q. et al. Efficient Delivery of Genome-Editing Proteins Using Bioreducible Lipid Nanoparticles Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 2868-2873 10.1073/pnas.1520244113
25. Yin, H.; Song, C. Q.; Dorkin, J. R.; Zhu, L. J.; Li, Y.; Wu, Q.; Park, A.; Yang, J.; Suresh, S.; Bizhanova, A. et al. Therapeutic Genome Editing by Combined Viral and Non-Viral Delivery of CRISPR System Components in vivo Nat. Biotechnol. 2016, 34, 328-333 10.1038/nbt.3471
26. Miller, J. B.; Zhang, S.; Kos, P.; Xiong, H.; Zhou, K.; Perelman, S. S.; Zhu, H.; Siegwart, D. J. Non-Viral CRISPR/Cas Gene Editing in vitro and in vivo Enabled by Synthetic Nanoparticle Co-Delivery of Cas9 mRNA and sgRNA Angew. Chem., Int. Ed. 2017, 56, 1059-1063 10.1002/anie.201610209
27. Zhen, S.; Hua, L.; Liu, Y.; Gao, L.; Fu, J.; Wan, D.; Dong, L.; Song, H.; Gao, X. Harnessing the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-Associated Cas9 System to Disrupt the Hepatitis B Virus Gene Ther. 2015, 22, 404-412 10.1038/gt.2015.2
28. Ebina, H.; Misawa, N.; Kanemura, Y.; Koyanagi, Y. Harnessing the CRISPR/Cas9 System to Disrupt Latent HIV-1 Provirus Sci. Rep. 2013, 3, 2510 10.1038/srep02510
29. Kennedy, E. M.; Kornepati, A. V.; Goldstein, M.; Bogerd, H. P.; Poling, B. C.; Whisnant, A. W.; Kastan, M. B.; Cullen, B. R. Inactivation of the Human Papillomavirus E6 or E7 Gene in Cervical Carcinoma Cells by Using a Bacterial CRISPR/Cas RNA-Guided Endonuclease J. Virol. 2014, 88, 11965-11972 10.1128/JVI.01879-14
30. Ramakrishna, S.; Dad, A. K.; Beloor, J.; Gopalappa, R.; Lee, S. K.; Kim, H. Gene Disruption by Cell-Penetrating Peptide-Mediated Delivery of Cas9 Protein and Guide RNA Genome Res. 2014, 24, 1020-1027 10.1101/gr.171264.113
31. Platt, R. J.; Chen, S.; Zhou, Y.; Yim, M. J.; Swiech, L.; Kempton, H. R.; Dahlman, J. E.; PaRNAs, O.; Eisenhaure, T. M.; Jovanovic, M. et al. CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling Cell 2014, 159, 440-455 10.1016/j.cell.2014.09.014
32. Mout, R.; Ray, M.; Yesilbag Tonga, G.; Lee, Y. W.; Tay, T.; Sasaki, K.; Rotello, V. M. Direct Cytosolic Delivery of CRISPR/Cas9-Ribonucleoprotein for Efficient Gene Editing ACS Nano 2017, 11, 2452 10.1021/acsnano.6b07600
33. Li, L.; Song, L.; Liu, X.; Yang, X.; Li, X.; He, T.; Wang, N.; Yang, S.; Yu, C.; Yin, T. et al. Artificial Virus Delivers CRISPR-Cas9 System for Genome Editing of Cells in Mice ACS Nano 2017, 11, 95-111 10.1021/acsnano.6b04261
34. Sun, W.; Ji, W.; Hall, J. M.; Hu, Q.; Wang, C.; Beisel, C. L.; Gu, Z. Self-Assembled DNA Nanoclews for the Efficient Delivery of CRISPR-Cas9 for Genome Editing Angew. Chem. 2015, 127, 12197-12201 10.1002/ange.201506030
35. Doudna, J. A.; Charpentier, E. The New Frontier of Genome Engineering with CRISPR-Cas9 Science 2014, 346, 1258096 10.1126/science.1258096
36. Sander, J. D.; Joung, J. K. CRISPR-Cas Systems for Editing, Regulating and Targeting Genomes Nat. Biotechnol. 2014, 32, 347-355 10.1038/nbt.2842
37. Maggio, I.; Goncalves, M. Genome Editing at the Crossroads of Delivery, Specificity, and Fidelity Trends Biotechnol. 2015, 33, 280-291 10.1016/j.tibtech.2015.02.011
38. Gori, J. L.; Hsu, P. D.; Maeder, M. L.; Shen, S.; Welstead, G. G.; Bumcrot, D. Delivery and Specificity of CRISPR/Cas9 Genome Editing Technologies for Human Gene Therapy Hum. Gene Ther. 2015, 26, 443-451 10.1089/hum.2015.074
39. LaFountaine, J. S.; Fathe, K.; Smyth, H. D. C. Delivery and Therapeutic Applications of Gene Editing Technologies ZFNs, TALENs, and CRISPR/Cas9 Int. J. Pharm. 2015, 494, 180-194 10.1016/j.ijpharm.2015.08.029
40. Kirchner, M.; Schneider, S. CRISPR-Cas: From the Bacterial Adaptive Immune System to a Versatile Tool for Genome Engineering Angew. Chem., Int. Ed. 2015, 54, 13508-13514 10.1002/anie.201504741
41. Singh, A.; Chakraborty, D.; Maiti, S. CRISPR/Cas9: A Historical and Chemical Biology Perspective of Targeted Genome Engineering Chem. Soc. Rev. 2016, 45, 6666 10.1039/C6CS00197A
42. Hu, J. H.; Davis, K. M.; Liu, D. R. Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases Cell Chem. Biol. 2016, 23, 57-73 10.1016/j.chembiol.2015.12.009
43. Ishino, Y.; Shinagawa, H.; Makino, K.; Amemura, M.; Nakata, A. Nucleotide Sequence of the Iap Gene, Responsible for Alkaline Phosphatase Isozyme Conversion in Escherichia Coli, and Identification of the Gene Product J. Bacteriol. 1987, 169, 5429-5433 10.1128/jb.169.12.5429-5433.1987
44. Jansen, R.; Embden, J.; Gaastra, W.; Schouls, L. Identification of Genes That Are Associated with DNA Repeats in Prokaryotes Mol. Microbiol. 2002, 43, 1565-1575 10.1046/j.1365-2958.2002.02839.x
45. Mojica, F. J.; García-Martínez, J.; Soria, E. Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements J. Mol. Evol. 2005, 60, 174-182 10.1007/s00239-004-0046-3
46. Pourcel, C.; Salvignol, G.; Vergnaud, G. CRISPR Elements in Yersinia Pestis Acquire New Repeats by Preferential Uptake of Bacteriophage DNA, and Provide Additional Tools for Evolutionary Studies Microbiology 2005, 151, 653-663 10.1099/mic.0.27437-0
47. Bolotin, A.; Quinquis, B.; Sorokin, A.; Ehrlich, S. D. Clustered Regularly Interspaced Short Palindrome Repeats (CRISPRs) Have Spacers of Extrachromosomal Origin Microbiology 2005, 151, 2551-2561 10.1099/mic.0.28048-0
48. Barrangou, R.; Fremaux, C.; Deveau, H.; Richards, M.; Boyaval, P.; Moineau, S.; Romero, D. A.; Horvath, P. CRISPR Provides Acquired Resistance against Viruses in Prokaryotes Science 2007, 315, 1709-1712 10.1126/science.1138140
49. Marraffini, L. A.; Sontheimer, E. J. CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA Science 2008, 322, 1843-1845 10.1126/science.1165771
50. Jinek, M.; Chylinski, K.; Fonfara, I.; Hauer, M.; Doudna, J. A.; Charpentier, E. A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity Science 2012, 337, 816-821 10.1126/science.1225829
51. 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 2013, 339, 819-823 10.1126/science.1231143
52. Mali, P.; Yang, L.; Esvelt, K. M.; Aach, J.; Guell, M.; DiCarlo, J. E.; Norville, J. E.; Church, G. M. RNA-Guided Human Genome Engineering via Cas9 Science 2013, 339, 823-826 10.1126/science.1232033
53. Hwang, W. Y.; Fu, Y. F.; Reyon, D.; Maeder, M. L.; Tsai, S. Q.; Sander, J. D.; Peterson, R. T.; Yeh, J. R. J.; Joung, J. K. Efficient Genome Editing in Zebrafish Using a CRISPR-Cas System Nat. Biotechnol. 2013, 31, 227-229 10.1038/nbt.2501
54. Wang, H.; Yang, H.; Shivalila, C. S.; Dawlaty, M. M.; Cheng, A. W.; Zhang, F.; Jaenisch, R. One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering Cell 2013, 153, 910-918 10.1016/j.cell.2013.04.025
55. Niu, Y.; Shen, B.; Cui, Y.; Chen, Y.; Wang, J.; Wang, L.; Kang, Y.; Zhao, X.; Si, W.; Li, W. Generation of Gene-Modified Cynomolgus Monkey Via Cas9/Rna-Mediated Gene Targeting in One-Cell Embryos Cell 2014, 156, 836-843 10.1016/j.cell.2014.01.027
56. Chen, Y.; Zheng, Y.; Kang, Y.; Yang, W.; Niu, Y.; Guo, X.; Tu, Z.; Si, C.; Wang, H.; Xing, R. et al. Functional Disruption of the Dystrophin Gene in Rhesus Monkey Using CRISPR/Cas9 Hum. Mol. Genet. 2015, 24, 3764-3774 10.1093/hmg/ddv120
57. Yin, H.; Xue, W.; Chen, S.; Bogorad, R. L.; Benedetti, E.; Grompe, M.; Koteliansky, V.; Sharp, P. A.; Jacks, T.; Anderson, D. G. Genome Editing with Cas9 in Adult Mice Corrects a Disease Mutation and Phenotype Nat. Biotechnol. 2014, 32, 551-553 10.1038/nbt.2884
58. Mullard, A. Novartis Secures First CRISPR Pharma Collaborations Nat. Rev. Drug Discovery 2015, 14, 82-82 10.1038/nrd4546
59. Cyranoski, D. First Trial of CRISPR in People Nature 2016, 535, 476-477 10.1038/nature.2016.20302
60. Hsu, P. D.; Scott, D. A.; Weinstein, J. A.; Ran, F. A.; Konermann, S.; Agarwala, V.; Li, Y.; Fine, E. J.; Wu, X.; Shalem, O. DNA Targeting Specificity of RNA-Guided Cas9 Nucleases Nat. Biotechnol. 2013, 31, 827-832 10.1038/nbt.2647
61. Ran, F. A.; Hsu, P. D.; Lin, C.-Y.; Gootenberg, J. S.; Konermann, S.; Trevino, A. E.; Scott, D. A.; Inoue, A.; Matoba, S.; Zhang, Y. Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity Cell 2013, 154, 1380-1389 10.1016/j.cell.2013.08.021
62. Shen, B.; Zhang, W.; Zhang, J.; Zhou, J.; Wang, J.; Chen, L.; Wang, L.; Hodgkins, A.; Iyer, V.; Huang, X. et al. Efficient Genome Modification by CRISPR-Cas9 Nickase with Minimal Off-Target Effects Nat. Methods 2014, 11, 399-402 10.1038/nmeth.2857
63. Cho, S. W.; Kim, S.; Kim, Y.; Kweon, J.; Kim, H. S.; Bae, S.; Kim, J. S. Analysis of Off-Target Effects of CRISPR/Cas-Derived RNA-Guided Endonucleases and Nickases Genome Res. 2014, 24, 132-141 10.1101/gr.162339.113
64. Fu, Y. F.; Sander, J. D.; Reyon, D.; Cascio, V. M.; Joung, J. K. Improving CRISPR-Cas Nuclease Specificity Using Truncated Guide RNAs Nat. Biotechnol. 2014, 32, 279-284 10.1038/nbt.2808
65. Qi, L. S.; Larson, M. H.; Gilbert, L. A.; Doudna, J. A.; Weissman, J. S.; Arkin, A. P.; Lim, W. A. Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression Cell 2013, 152, 1173-1183 10.1016/j.cell.2013.02.022
66. Bikard, D.; Jiang, W.; Samai, P.; Hochschild, A.; Zhang, F.; Marraffini, L. A. Programmable Repression and Activation of Bacterial Gene Expression Using an Engineered CRISPR-Cas System Nucleic Acids Res. 2013, 41, 7429-7437 10.1093/nar/gkt520
67. Perez-Pinera, P.; Kocak, D. D.; Vockley, C. M.; Adler, A. F.; Kabadi, A. M.; Polstein, L. R.; Thakore, P. I.; Glass, K. A.; Ousterout, D. G.; Leong, K. W. et al. RNA-Guided Gene Activation by CRISPR-Cas9-Based Transcription Factors Nat. Methods 2013, 10, 973-976 10.1038/nmeth.2600
68. Mali, P.; Aach, J.; Stranges, P. B.; Esvelt, K. M.; Moosburner, M.; Kosuri, S.; Yang, L.; Church, G. M. Cas9 Transcriptional Activators for Target Specificity Screening and Paired Nickases for Cooperative Genome Engineering Nat. Biotechnol. 2013, 31, 833-838 10.1038/nbt.2675
69. Cheng, A. W.; Wang, H.; Yang, H.; Shi, L.; Katz, Y.; Theunissen, T. W.; Rangarajan, S.; Shivalila, C. S.; Dadon, D. B.; Jaenisch, R. Multiplexed Activation of Endogenous Genes by CRISPR-On, an RNA-Guided Transcriptional Activator System Cell Res. 2013, 23, 1163-1171 10.1038/cr.2013.122
70. Gilbert, L. A.; Larson, M. H.; Morsut, L.; Liu, Z.; Brar, G. A.; Torres, S. E.; Stern-Ginossar, N.; Brandman, O.; Whitehead, E. H.; Doudna, J. A. et al. CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes Cell 2013, 154, 442-451 10.1016/j.cell.2013.06.044
71. Konermann, S.; Brigham, M. D.; Trevino, A. E.; Hsu, P. D.; Heidenreich, M.; Cong, L.; Platt, R. J.; Scott, D. A.; Church, G. M.; Zhang, F. Optical Control of Mammalian Endogenous Transcription and Epigenetic States Nature 2013, 500, 472-476 10.1038/nature12466
72. Maeder, M. L.; Linder, S. J.; Cascio, V. M.; Fu, Y.; Ho, Q. H.; Joung, J. K. CRISPR RNA-Guided Activation of Endogenous Human Genes Nat. Methods 2013, 10, 977-979 10.1038/nmeth.2598
73. Konermann, S.; Brigham, M. D.; Trevino, A. E.; Joung, J.; Abudayyeh, O. O.; Barcena, C.; Hsu, P. D.; Habib, N.; Gootenberg, J. S.; Nishimasu, H. et al. Genome-Scale Transcriptional Activation by an Engineered CRISPR-Cas9 Complex Nature 2015, 517, 583-588 10.1038/nature14136
74. Zalatan, J. G.; Lee, M. E.; Almeida, R.; Gilbert, L. A.; Whitehead, E. H.; La Russa, M.; Tsai, J. C.; Weissman, J. S.; Dueber, J. E.; Qi, L. S. et al. Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds Cell 2015, 160, 339-350 10.1016/j.cell.2014.11.052
75. Hilton, I. B.; D'Ippolito, A. M.; Vockley, C. M.; Thakore, P. I.; Crawford, G. E.; Reddy, T. E.; Gersbach, C. A. Epigenome Editing by a CRISPR-Cas9-Based Acetyltransferase Activates Genes from Promoters and Enhancers Nat. Biotechnol. 2015, 33, 510-517 10.1038/nbt.3199
76. Thakore, P. I.; Black, J. B.; Hilton, I. B.; Gersbach, C. A. Editing the Epigenome: Technologies for Programmable Transcription and Epigenetic Modulation Nat. Methods 2016, 13, 127-137 10.1038/nmeth.3733
77. Tsai, S. Q.; Wyvekens, N.; Khayter, C.; Foden, J. A.; Thapar, V.; Reyon, D.; Goodwin, M. J.; Aryee, M. J.; Joung, J. K. Dimeric CRISPR RNA-Guided FokI Nucleases for Highly Specific Genome Editing Nat. Biotechnol. 2014, 32, 569-576 10.1038/nbt.2908
78. Guilinger, J. P.; Thompson, D. B.; Liu, D. R. Fusion of Catalytically Inactive Cas9 to FokI Nuclease Improves the Specificity of Genome Modification Nat. Biotechnol. 2014, 32, 287-305 10.1038/nbt.2909
79. Wang, S.; Su, J. H.; Feng, Z.; Zhuang, X. An RNA-Aptamer-Based Two-Color CRISPR Labeling System Sci. Rep. 2016, 6, 26857 10.1038/srep26857
80. Thierry, A.; Dujon, B. Nested Chromosomal Fragmentation in Yeast Using the Meganuclease I-Sce-I: a New Method for Physical Mapping of Eukaryotic Genomes Nucleic Acids Res. 1992, 20, 5625-5631 10.1093/nar/20.21.5625
81. Smith, J.; Grizot, S.; Arnould, S.; Duclert, A.; Epinat, J. C.; Chames, P.; Prieto, J.; Redondo, P.; Blanco, F. J.; Bravo, J. et al. A Combinatorial Approach to Create Artificial Homing Endonucleases Cleaving Chosen Sequences Nucleic Acids Res. 2006, 34, e149 10.1093/nar/gkl720
82. Boissel, S.; Jarjour, J.; Astrakhan, A.; Adey, A.; Gouble, A.; Duchateau, P.; Shendure, J.; Stoddard, B. L.; Certo, M. T.; Baker, D. et al. MegaTALs: A Rare-Cleaving Nuclease Architecture for Therapeutic Genome Engineering Nucleic Acids Res. 2014, 42, 2591-2601 10.1093/nar/gkt1224
83. Kim, Y. G.; Cha, J.; Chandrasegaran, S. Hybrid Restriction Enzymes: Zinc Finger Fusions to Fok I Cleavage Domain Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 1156-1160 10.1073/pnas.93.3.1156
84. Bibikova, M.; Golic, M.; Golic, K. G.; Carroll, D. Targeted Chromosomal Cleavage and Mutagenesis in Drosophila Using Zinc-Finger Nucleases Genetics 2002, 161, 1169-1175
85. Bibikova, M.; Beumer, K.; Trautman, J. K.; Carroll, D. Enhancing Gene Targeting with Designed Zinc Finger Nucleases Science 2003, 300, 764-764 10.1126/science.1079512
86. Miller, J. C.; Holmes, M. C.; Wang, J.; Guschin, D. Y.; Lee, Y. L.; Rupniewski, I.; Beausejour, C. M.; Waite, A. J.; Wang, N. S.; Kim, K. A. et al. An Improved Zinc-Finger Nuclease Architecture for Highly Specific Genome Editing Nat. Biotechnol. 2007, 25, 778-785 10.1038/nbt1319
87. Boch, J.; Scholze, H.; Schornack, S.; Landgraf, A.; Hahn, S.; Kay, S.; Lahaye, T.; Nickstadt, A.; Bonas, U. Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors Science 2009, 326, 1509-1512 10.1126/science.1178811
88. Moscou, M. J.; Bogdanove, A. J. A Simple Cipher Governs DNA Recognition by TAL Effectors Science 2009, 326, 1501-1501 10.1126/science.1178817
89. Miller, J. C.; Tan, S. Y.; Qiao, G. J.; Barlow, K. A.; Wang, J. B.; Xia, D. F.; Meng, X. D.; Paschon, D. E.; Leung, E.; Hinkley, S. J. et al. A TALE Nuclease Architecture for Efficient Genome Editing Nat. Biotechnol. 2011, 29, 143-149 10.1038/nbt.1755
90. Li, T.; Huang, S.; Jiang, W. Z.; Wright, D.; Spalding, M. H.; Weeks, D. P.; Yang, B. TAL Nucleases (TALNs): Hybrid Proteins Composed of TAL Effectors and FokI DNA-Cleavage Domain Nucleic Acids Res. 2011, 39, 359-372 10.1093/nar/gkq704
91. 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 2015, 163, 759-771 10.1016/j.cell.2015.09.038
92. Rosen, L. E.; Morrison, H. A.; Masri, S.; Brown, M. J.; Springstubb, B.; Sussman, D.; Stoddard, B. L.; Seligman, L. M. Homing Endonuclease I-CreI Derivatives with Novel DNA Target Specificities Nucleic Acids Res. 2006, 34, 4791-4800 10.1093/nar/gkl645
93. Seligman, L. M.; Chevalier, B. S.; Chadsey, M. S.; Edwards, S. T.; Savage, J. H.; Veillet, A. L. Mutations Altering the Cleavage Specificity of a Homing Endonuclease Nucleic Acids Res. 2002, 30, 3870-3879
94. Isalan, M. Zinc-Finger Nucleases: How to Play Two Good Hands Nat. Methods 2012, 9, 32-34 10.1038/nmeth.1805
95. Schmid-Burgk, J. L.; Schmidt, T.; Kaiser, V.; Honing, K.; Hornung, V. A Ligation-Independent Cloning Technique for High-Throughput Assembly of Transcription Activator-Like Effector Genes Nat. Biotechnol. 2013, 31, 76-81 10.1038/nbt.2460
96. Holkers, M.; Maggio, I.; Liu, J.; Janssen, J. M.; Miselli, F.; Mussolino, C.; Recchia, A.; Cathomen, T.; Goncalves, M. A. F. V. Differential Integrity of TALE Nuclease Genes Following Adenoviral and Lentiviral Vector Gene Transfer into Human Cells Nucleic Acids Res. 2013, 41, e63 10.1093/nar/gks1446
97. Cradick, T. J.; Fine, E. J.; Antico, C. J.; Bao, G. CRISPR/Cas9 Systems Targeting Beta-Globin and CCR5 Genes Have Substantial Off-Target Activity Nucleic Acids Res. 2013, 41, 9584-9592 10.1093/nar/gkt714
98. Fu, Y.; Foden, J. A.; Khayter, C.; Maeder, M. L.; Reyon, D.; Joung, J. K.; Sander, J. D. High-Frequency Off-Target Mutagenesis Induced by CRISPR-Cas Nucleases in Human Cells Nat. Biotechnol. 2013, 31, 822-826 10.1038/nbt.2623
99. Zetsche, B.; Volz, S. E.; Zhang, F. A Split-Cas9 Architecture for Inducible Genome Editing and Transcription Modulation Nat. Biotechnol. 2015, 33, 139-142 10.1038/nbt.3149
100. Davis, K. M.; Pattanayak, V.; Thompson, D. B.; Zuris, J. A.; Liu, D. R. Small Molecule-Triggered Cas9 Protein with Improved Genome-Editing Specificity Nat. Chem. Biol. 2015, 11, 316-318 10.1038/nchembio.1793
101. Fu, Y.; Sander, J. D.; Reyon, D.; Cascio, V. M.; Joung, J. K. Improving CRISPR-Cas Nuclease Specificity Using Truncated Guide RNAs Nat. Biotechnol. 2014, 32, 279-284 10.1038/nbt.2808
102. Bolukbasi, M. F.; Gupta, A.; Oikemus, S.; Derr, A. G.; Garber, M.; Brodsky, M. H.; Zhu, L. J.; Wolfe, S. A. DNA-Binding-Domain Fusions Enhance the Targeting Range and Precision of Cas9 Nat. Methods 2015, 12, 1150-1156 10.1038/nmeth.3624
103. Slaymaker, I. M.; Gao, L.; Zetsche, B.; Scott, D. A.; Yan, W. X.; Zhang, F. Rationally Engineered Cas9 Nucleases with Improved Specificity Science 2016, 351, 84-88 10.1126/science.aad5227
104. Kleinstiver, B. P.; Pattanayak, V.; Prew, M. S.; Tsai, S. Q.; Nguyen, N. T.; Zheng, Z. L.; Joung, J. K. High-Fidelity CRISPR-Cas9 Nucleases with No Detectable Genome-Wide Off-Target Effects Nature 2016, 529, 490-495 10.1038/nature16526
105. Smith, C.; Gore, A.; Yan, W.; Abalde-Atristain, L.; Li, Z.; He, C.; Wang, Y.; Brodsky, R. A.; Zhang, K.; Cheng, L. et al. Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs Cell Stem Cell 2014, 15, 12-13 10.1016/j.stem.2014.06.011
106. Suzuki, K.; Yu, C.; Qu, J.; Li, M.; Yao, X.; Yuan, T.; Goebl, A.; Tang, S.; Ren, R.; Aizawa, E. et al. Targeted Gene Correction Minimally Impacts Whole-Genome Mutational Load in Human-Disease-Specific Induced Pluripotent Stem Cell Clones Cell Stem Cell 2014, 15, 31-36 10.1016/j.stem.2014.06.016
107. Veres, A.; Gosis, B. S.; Ding, Q.; Collins, R.; Ragavendran, A.; Brand, H.; Erdin, S.; Cowan, C. A.; Talkowski, M. E.; Musunuru, K. Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing Cell Stem Cell 2014, 15, 27-30 10.1016/j.stem.2014.04.020
108. Yang, L.; Grishin, D.; Wang, G.; Aach, J.; Zhang, C. Z.; Chari, R.; Homsy, J.; Cai, X.; Zhao, Y.; Fan, J. B. et al. Targeted and Genome-Wide Sequencing Reveal Single Nucleotide Variations Impacting Specificity of Cas9 in Human Stem Cells Nat. Commun. 2014, 5, 5507 10.1038/ncomms6507
109. Siksnys, V.; Gasiunas, G. Rewiring Cas9 to Target New Pam Sequences Mol. Cell 2016, 61, 793-794 10.1016/j.molcel.2016.03.002
110. Hirano, S.; Nishimasu, H.; Ishitani, R.; Nureki, O. Structural Basis for the Altered Pam Specificities of Engineered CRISPR-Cas9 Mol. Cell 2016, 61, 886-894 10.1016/j.molcel.2016.02.018
111. Anders, C.; Bargsten, K.; Jinek, M. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9 Mol. Cell 2016, 61, 895-902 10.1016/j.molcel.2016.02.020
112. Makarova, K. S.; Wolf, Y. I.; Alkhnbashi, O. S.; Costa, F.; Shah, S. A.; Saunders, S. J.; Barrangou, R.; Brouns, S. J.; Charpentier, E.; Haft, D. H. et al. An Updated Evolutionary Classification of CRISPR-Cas Systems Nat. Rev. Microbiol. 2015, 13, 722-736 10.1038/nrmicro3569
113. Shmakov, S.; Abudayyeh, O. O.; Makarova, K. S.; Wolf, Y. I.; Gootenberg, J. S.; Semenova, E.; Minakhin, L.; Joung, J.; Konermann, S.; Severinov, K. et al. Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems Mol. Cell 2015, 60, 385-397 10.1016/j.molcel.2015.10.008
114. Abudayyeh, O. O.; Gootenberg, J. S.; Konermann, S.; Joung, J.; Slaymaker, I. M.; Cox, D. B.; Shmakov, S.; Makarova, K. S.; Semenova, E.; Minakhin, L. et al. C2c2 Is a Single-Component Programmable RNA-Guided RNA-Targeting CRISPR Effector Science 2016, 353, aaf5573 10.1126/science.aaf5573
115. Jackson, A. L.; Linsley, P. S. Recognizing and Avoiding siRNA Off-Target Effects for Target Identification and Therapeutic Application Nat. Rev. Drug Discovery 2010, 9, 57-67 10.1038/nrd3010
116. Doench, J. G.; Hartenian, E.; Graham, D. B.; Tothova, Z.; Hegde, M.; Smith, I.; Sullender, M.; Ebert, B. L.; Xavier, R. J.; Root, D. E. Rational Design of Highly Active sgRNAs for CRISPR-Cas9-Mediated Gene Inactivation Nat. Biotechnol. 2014, 32, 1262-1267 10.1038/nbt.3026
117. Chari, R.; Mali, P.; Moosburner, M.; Church, G. M. Unraveling CRISPR-Cas9 Genome Engineering Parameters via a Library-on-Library Approach Nat. Methods 2015, 12, 823-826 10.1038/nmeth.3473
118. Moreno-Mateos, M. A.; Vejnar, C. E.; Beaudoin, J. D.; Fernandez, J. P.; Mis, E. K.; Khokha, M. K.; Giraldez, A. J. CRISPRscan: Designing Highly Efficient sgRNAs for CRISPR-Cas9 Targeting in vivo Nat. Methods 2015, 12, 982-988 10.1038/nmeth.3543
119. Xu, H.; Xiao, T.; Chen, C. H.; Li, W.; Meyer, C. A.; Wu, Q.; Wu, D.; Cong, L.; Zhang, F.; Liu, J. S. et al. Sequence Determinants of Improved CRISPR sgRNA Design Genome Res. 2015, 25, 1147-1157 10.1101/gr.191452.115
120. Wong, N.; Liu, W.; Wang, X. WU-CRISPR: Characteristics of Functional Guide RNAs for the CRISPR/Cas9 System Genome Biol. 2015, 16, 218 10.1186/s13059-015-0784-0
121. Haeussler, M.; Schonig, K.; Eckert, H.; Eschstruth, A.; Mianne, J.; Renaud, J. B.; Schneider-Maunoury, S.; Shkumatava, A.; Teboul, L.; Kent, J. et al. Evaluation of Off-Target and On-Target Scoring Algorithms and Integration into the Guide RNA Selection Tool CRISPOR Genome Biol. 2016, 17, 148 10.1186/s13059-016-1012-2
122. Tsai, S. Q.; Zheng, Z.; Nguyen, N. T.; Liebers, M.; Topkar, V. V.; Thapar, V.; Wyvekens, N.; Khayter, C.; Iafrate, A. J.; Le, L. P. et al. Guide-Seq Enables Genome-Wide Profiling of Off-Target Cleavage by CRISPR-Cas Nucleases Nat. Biotechnol. 2015, 33, 187-197 10.1038/nbt.3117
123. Lin, Y.; Cradick, T. J.; Brown, M. T.; Deshmukh, H.; Ranjan, P.; Sarode, N.; Wile, B. M.; Vertino, P. M.; Stewart, F. J.; Bao, G. CRISPR/Cas9 Systems Have Off-Target Activity with Insertions or Deletions between Target DNA and Guide RNA Sequences Nucleic Acids Res. 2014, 42, 7473-7485 10.1093/nar/gku402
124. Singh, R.; Kuscu, C.; Quinlan, A.; Qi, Y.; Adli, M. Cas9-Chromatin Binding Information Enables More Accurate CRISPR Off-Target Prediction Nucleic Acids Res. 2015, 43, e118 10.1093/nar/gkv575
125. Montague, T. G.; Cruz, J. M.; Gagnon, J. A.; Church, G. M.; Valen, E. CHOPCHOP: A CRISPR/Cas9 and TALEN Web Tool for Genome Editing Nucleic Acids Res. 2014, 42, W401-407 10.1093/nar/gku410
126. Stemmer, M.; Thumberger, T.; Del Sol Keyer, M.; Wittbrodt, J.; Mateo, J. L. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool PLoS One 2015, 10, e0124633 10.1371/journal.pone.0124633
127. Zhu, L. J.; Holmes, B. R.; Aronin, N.; Brodsky, M. H. CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems PLoS One 2014, 9, e108424 10.1371/journal.pone.0108424
128. Heigwer, F.; Kerr, G.; Boutros, M. E-CRISP: Fast CRISPR Target Site Identification Nat. Methods 2014, 11, 122-123 10.1038/nmeth.2812
129. Gratz, S. J.; Ukken, F. P.; Rubinstein, C. D.; Thiede, G.; Donohue, L. K.; Cummings, A. M.; O'Connor-Giles, K. M. Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair in Drosophila Genetics 2014, 196, 961-971 10.1534/genetics.113.160713
130. O'Brien, A.; Bailey, T. L. GT-Scan: Identifying Unique Genomic Targets Bioinformatics 2014, 30, 2673-2675 10.1093/bioinformatics/btu354
131. Xie, S.; Shen, B.; Zhang, C.; Huang, X.; Zhang, Y. sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites PLoS One 2014, 9, e100448 10.1371/journal.pone.0100448
132. Hodgkins, A.; Farne, A.; Perera, S.; Grego, T.; Parry-Smith, D. J.; Skarnes, W. C.; Iyer, V. WGE: A CRISPR Database for Genome Engineering Bioinformatics 2015, 31, 3078-3080 10.1093/bioinformatics/btv308
133. Cradick, T. J.; Qui, P.; Lee, C. M.; Fine, E. J.; Bao, G. COSMID: A Web-Based Tool for Identifying and Validating CRISPR/Cas Off-Target Sites Mol. Ther. - Nucleic Acids 2014, 3, e214 10.1038/mtna.2014.64
134. Bae, S.; Park, J.; Kim, J. S. Cas-OFFinder: A Fast and Versatile Algorithm That Searches for Potential Off-Target Sites of Cas9 RNA-Guided Endonucleases Bioinformatics 2014, 30, 1473-1475 10.1093/bioinformatics/btu048
135. Sander, J. D.; Zaback, P.; Joung, J. K.; Voytas, D. F.; Dobbs, D. Zinc Finger Targeter (ZiFiT): An Engineered Zinc Finger/Target Site Design Tool Nucleic Acids Res. 2007, 35, W599-W605 10.1093/nar/gkm349
136. Kim, D.; Bae, S.; Park, J.; Kim, E.; Kim, S.; Yu, H. R.; Hwang, J.; Kim, J. I.; Kim, J. S. Digenome-Seq: Genome-Wide Profiling of CRISPR-Cas9 Off-Target Effects in Human Cells Nat. Methods 2015, 12, 237-243 10.1038/nmeth.3284
137. Wang, X.; Wang, Y.; Wu, X.; Wang, J.; Qiu, Z.; Chang, T.; Huang, H.; Lin, R. J.; Yee, J. K. Unbiased Detection of Off-Target Cleavage by CRISPR-Cas9 and TALENs Using Integrase-Defective Lentiviral Vectors Nat. Biotechnol. 2015, 33, 175-178 10.1038/nbt.3127
138. Kuscu, C.; Arslan, S.; Singh, R.; Thorpe, J.; Adli, M. Genome-Wide Analysis Reveals Characteristics of Off-Target Sites Bound by the Cas9 Endonuclease Nat. Biotechnol. 2014, 32, 677-683 10.1038/nbt.2916
139. Kleinstiver, B. P.; Prew, M. S.; Tsai, S. Q.; Nguyen, N. T.; Topkar, V. V.; Zheng, Z.; Joung, J. K. Broadening the Targeting Range of Staphylococcus Aureus CRISPR-Cas9 by Modifying PAM Recognition Nat. Biotechnol. 2015, 33, 1293-1298 10.1038/nbt.3404
140. Friedland, A. E.; Baral, R.; Singhal, P.; Loveluck, K.; Shen, S.; Sanchez, M.; Marco, E.; Gotta, G. M.; Maeder, M. L.; Kennedy, E. M. et al. Characterization of Staphylococcus Aureus Cas9: A Smaller Cas9 for All-in-One Adeno-Associated Virus Delivery and Paired Nickase Applications Genome Biol. 2015, 16, 257 10.1186/s13059-015-0817-8
141. O'Geen, H.; Henry, I. M.; Bhakta, M. S.; Meckler, J. F.; Segal, D. J. A Genome-Wide Analysis of Cas9 Binding Specificity Using ChIP-Seq and Targeted Sequence Capture Nucleic Acids Res. 2015, 43, 3389-3404 10.1093/nar/gkv137
142. Wu, X.; Scott, D. A.; Kriz, A. J.; Chiu, A. C.; Hsu, P. D.; Dadon, D. B.; Cheng, A. W.; Trevino, A. E.; Konermann, S.; Chen, S. et al. Genome-Wide Binding of the CRISPR Endonuclease Cas9 in Mammalian Cells Nat. Biotechnol. 2014, 32, 670-676 10.1038/nbt.2889
143. Frock, R. L.; Hu, J.; Meyers, R. M.; Ho, Y. J.; Kii, E.; Alt, F. W. Genome-Wide Detection of DNA Double-Stranded Breaks Induced by Engineered Nucleases Nat. Biotechnol. 2015, 33, 179-186 10.1038/nbt.3101
144. Crosetto, N.; Mitra, A.; Silva, M. J.; Bienko, M.; Dojer, N.; Wang, Q.; Karaca, E.; Chiarle, R.; Skrzypczak, M.; Ginalski, K. et al. Nucleotide-Resolution DNA Double-Strand Break Mapping by Next-Generation Sequencing Nat. Methods 2013, 10, 361-365 10.1038/nmeth.2408
145. Sternberg, S. H.; LaFrance, B.; Kaplan, M.; Doudna, J. A. Conformational Control of DNA Target Cleavage by CRISPR-Cas9 Nature 2015, 527, 110-113 10.1038/nature15544
146. Kiani, S.; Chavez, A.; Tuttle, M.; Hall, R. N.; Chari, R.; Ter-Ovanesyan, D.; Qian, J.; Pruitt, B. W.; Beal, J.; Vora, S. et al. Cas9 gRNA Engineering for Genome Editing, Activation and Repression Nat. Methods 2015, 12, 1051-1054 10.1038/nmeth.3580
147. Xue, W.; Chen, S.; Yin, H.; Tammela, T.; Papagiannakopoulos, T.; Joshi, N. S.; Cai, W.; Yang, G.; Bronson, R.; Crowley, D. G. et al. CRISPR-Mediated Direct Mutation of Cancer Genes in the Mouse Liver Nature 2014, 514, 380-384 10.1038/nature13589
148. Choi, P. S.; Meyerson, M. Targeted Genomic Rearrangements Using CRISPR/Cas Technology Nat. Commun. 2014, 5, 3728 10.1038/ncomms4728
149. Matano, M.; Date, S.; Shimokawa, M.; Takano, A.; Fujii, M.; Ohta, Y.; Watanabe, T.; Kanai, T.; Sato, T. Modeling Colorectal Cancer Using CRISPR-Cas9-Mediated Engineering of Human Intestinal Organoids Nat. Med. 2015, 21, 256-262 10.1038/nm.3802
150. Zuckermann, M.; Hovestadt, V.; Knobbe-Thomsen, C. B.; Zapatka, M.; Northcott, P. A.; Schramm, K.; Belic, J.; Jones, D. T.; Tschida, B.; Moriarity, B. et al. Somatic CRISPR/Cas9-Mediated Tumour Suppressor Disruption Enables Versatile Brain Tumour Modelling Nat. Commun. 2015, 6, 7391 10.1038/ncomms8391
151. Heckl, D.; Kowalczyk, M. S.; Yudovich, D.; Belizaire, R.; Puram, R. V.; McConkey, M. E.; Thielke, A.; Aster, J. C.; Regev, A.; Ebert, B. L. Generation of Mouse Models of Myeloid Malignancy with Combinatorial Genetic Lesions Using CRISPR-Cas9 Genome Editing Nat. Biotechnol. 2014, 32, 941-946 10.1038/nbt.2951
152. Carroll, K. J.; Makarewich, C. A.; Mcanally, J.; Anderson, D. M.; Zentilin, L.; Liu, N.; Giacca, M.; Basselduby, R.; Olson, E. N. A Mouse Model for Adult Cardiac-Specific Gene Deletion with CRISPR/Cas9 Proc. Natl. Acad. Sci. U. S. A. 2016, 113, 338-343 10.1073/pnas.1523918113
153. Ma, Y.; Shen, B.; Zhang, X.; Lu, Y.; Chen, W.; Ma, J.; Huang, X.; Zhang, L. Heritable Multiplex Genetic Engineering in Rats Using CRISPR/Cas9 PLoS One 2014, 9, e89413 10.1371/journal.pone.0089413
154. Whitworth, K. M.; Lee, K.; Benne, J. A.; Beaton, B. P.; Spate, L. D.; Murphy, S. L.; Samuel, M. S.; Mao, J.; O'Gorman, C.; Walters, E. M. et al. Use of the CRISPR/Cas9 System to Produce Genetically Engineered Pigs from in vitro-Derived Oocytes and Embryos Biol. Reprod. 2014, 91, 78 10.1095/biolreprod.114.121723
155. Horii, T.; Tamura, D.; Morita, S.; Kimura, M.; Hatada, I. Generation of an ICF Syndrome Model by Efficient Genome Editing of Human Induced Pluripotent Stem Cells Using the CRISPR System Int. J. Mol. Sci. 2013, 14, 19774-19781 10.3390/ijms141019774
156. Paquet, D.; Kwart, D.; Chen, A.; Sproul, A.; Jacob, S.; Teo, S.; Olsen, K. M.; Gregg, A.; Noggle, S.; Tessierlavigne, M. Efficient Introduction of Specific Homozygous and Heterozygous Mutations Using CRISPR/Cas9 Nature 2016, 533, 125-129 10.1038/nature17664
157. Schwank, G.; Koo, B.-K.; Sasselli, V.; Dekkers, J. F.; Heo, I.; Demircan, T.; Sasaki, N.; Boymans, S.; Cuppen, E.; van der Ent, C. K. et al. Functional Repair of CFTR by CRISPR/Cas9 in Intestinal Stem Cell Organoids of Cystic Fibrosis Patients Cell stem cell 2013, 13, 653-658 10.1016/j.stem.2013.11.002
158. Long, C.; Amoasii, L.; Mireault, A. A.; McAnally, J. R.; Li, H.; Sanchez-Ortiz, E.; Bhattacharyya, S.; Shelton, J. M.; Bassel-Duby, R.; Olson, E. N. Postnatal Genome Editing Partially Restores Dystrophin Expression in a Mouse Model of Muscular Dystrophy Science 2016, 351, 400-403 10.1126/science.aad5725
159. Tabebordbar, M.; Zhu, K.; Cheng, J. K.; Chew, W. L.; Widrick, J. J.; Yan, W. X.; Maesner, C.; Wu, E. Y.; Xiao, R.; Ran, F. A. et al. In vivo Gene Editing in Dystrophic Mouse Muscle and Muscle Stem Cells Science 2016, 351, 407-411 10.1126/science.aad5177
160. Nelson, C. E.; Hakim, C. H.; Ousterout, D. G.; Thakore, P. I.; Moreb, E. A.; Rivera, R. M. C.; Madhavan, S.; Pan, X.; Ran, F. A.; Yan, W. X. et al. In vivo Genome Editing Improves Muscle Function in a Mouse Model of Duchenne Muscular Dystrophy Science 2016, 351, 403-407 10.1126/science.aad5143
161. Liu, Y.; Zeng, Y.; Liu, L.; Zhuang, C.; Fu, X.; Huang, W.; Cai, Z. Synthesizing and Gate Genetic Circuits Based on CRISPR-Cas9 for Identification of Bladder Cancer Cells Nat. Commun. 2014, 5, 5393 10.1038/ncomms6393
162. Antal, C. E.; Hudson, A. M.; Kang, E.; Zanca, C.; Wirth, C.; Stephenson, N. L.; Trotter, E. W.; Gallegos, L. L.; Miller, C. J.; Furnari, F. B. et al. Cancer-Associated Protein Kinase C Mutations Reveal Kinase's Role as Tumor Suppressor Cell 2015, 160, 489-502 10.1016/j.cell.2015.01.001
163. Kaminski, R.; Chen, Y.; Fischer, T.; Tedaldi, E.; Napoli, A.; Zhang, Y.; Karn, J.; Hu, W.; Khalili, K. Elimination of HIV-1 Genomes from Human T-Lymphoid Cells by CRISPR/Cas9 Gene Editing Sci. Rep. 2016, 6, 22555 10.1038/srep22555
164. Kaminski, R.; Bella, R.; Yin, C.; Otte, J.; Ferrante, P.; Gendelman, H.; Li, H.; Booze, R.; Gordon, J.; Hu, W. et al. Excision of HIV-1 DNA by Gene Editing: A Proof-of-Concept in vivo Study Gene Ther. 2016, 23, 690-695 10.1038/gt.2016.41
165. Dong, C.; Qu, L.; Wang, H.; Wei, L.; Dong, Y.; Xiong, S. Targeting Hepatitis B Virus cccDNA by CRISPR/Cas9 Nuclease Efficiently Inhibits Viral Replication Antiviral Res. 2015, 118, 110-117 10.1016/j.antiviral.2015.03.015
166. Price, A. A.; Sampson, T. R.; Ratner, H. K.; Grakoui, A.; Weiss, D. S. Cas9-Mediated Targeting of Viral RNA in Eukaryotic Cells Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 6164-6169 10.1073/pnas.1422340112
167. Roehm, P. C.; Shekarabi, M.; Wollebo, H. S.; Bellizzi, A.; He, L.; Salkind, J.; Khalili, K. Inhibition of HSV-1 Replication by Gene Editing Strategy Sci. Rep. 2016, 6, 23146 10.1038/srep23146
168. Wang, J.; Quake, S. R. RNA-Guided Endonuclease Provides a Therapeutic Strategy to Cure Latent Herpesviridae Infection Proc. Natl. Acad. Sci. U. S. A. 2014, 111, 13157-13162 10.1073/pnas.1410785111
169. O'Connell, M. R.; Oakes, B. L.; Sternberg, S. H.; East-Seletsky, A.; Kaplan, M.; Doudna, J. A. Programmable RNA Recognition and Cleavage by CRISPR/Cas9 Nature 2014, 516, 263-266 10.1038/nature13769
170. Nelles, D. A.; Fang, M. Y.; Aigner, S.; Yeo, G. W. Applications of Cas9 as an RNA-Programmed RNA-Binding Protein BioEssays 2015, 37, 732-739 10.1002/bies.201500001
171. Sampson, T. R.; Saroj, S. D.; Llewellyn, A. C.; Tzeng, Y.-L.; Weiss, D. S. A CRISPR/Cas System Mediates Bacterial Innate Immune Evasion and Virulence Nature 2013, 497, 254-257 10.1038/nature12048
172. Tsai, S. Q.; Joung, J. K. Defining and Improving the Genome-Wide Specificities of CRISPR-Cas9 Nucleases Nat. Rev. Genet. 2016, 17, 300-312 10.1038/nrg.2016.28
173. Chew, W. L.; Tabebordbar, M.; Cheng, J. K.; Mali, P.; Wu, E. Y.; Ng, A. H.; Zhu, K.; Wagers, A. J.; Church, G. M. A Multifunctional AAV-CRISPR-Cas9 and Its Host Response Nat. Methods 2016, 13, 868-874 10.1038/nmeth.3993
174. Wang, D.; Mou, H.; Li, S.; Li, Y.; Hough, S.; Tran, K.; Li, J.; Yin, H.; Anderson, D. G.; Sontheimer, E. J. et al. Adenovirus-Mediated Somatic Genome Editing of PTEN by CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses Hum. Gene Ther. 2015, 26, 432-442 10.1089/hum.2015.087
175. Ran, F. A.; Hsu, P. D.; Wright, J.; Agarwala, V.; Scott, D. A.; Zhang, F. Genome Engineering Using the CRISPR-Cas9 System Nat. Protoc. 2013, 8, 2281-2308 10.1038/nprot.2013.143
176. Chen, S.; Sanjana, N. E.; Zheng, K.; Shalem, O.; Lee, K.; Shi, X.; Scott, D. A.; Song, J.; Pan, J. Q.; Weissleder, R. et al. Genome-Wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis Cell 2015, 160, 1246-1260 10.1016/j.cell.2015.02.038
177. Hemmi, H.; Takeuchi, O.; Kawai, T.; Kaisho, T.; Sato, S.; Sanjo, H.; Matsumoto, M.; Hoshino, K.; Wagner, H.; Takeda, K. et al. A Toll-Like Receptor Recognizes Bacterial DNA Nature 2000, 408, 740-745 10.1038/35047123
178. Han, X.; Liu, Z.; Chan, Jo. M.; Zhang, K.; Li, Y.; Zeng, Z.; Li, N.; Zu, Y.; Qin, L. CRISPR-Cas9 Delivery to Hard-to-Transfect Cells via Membrane Deformation Sci. Adv. 2015, 1, e1500454 10.1126/sciadv.1500454
179. Ousterout, D. G.; Kabadi, A. M.; Thakore, P. I.; Majoros, W. H.; Reddy, T. E.; Gersbach, C. A. Multiplex CRISPR/Cas9-Based Genome Editing for Correction of Dystrophin Mutations That Cause Duchenne Muscular Dystrophy Nat. Commun. 2015, 6, 6244 10.1038/ncomms7244
180. Sakuma, T.; Nishikawa, A.; Kume, S.; Chayama, K.; Yamamoto, T. Multiplex Genome Engineering in Human Cells Using All-in-One CRISPR/Cas9 Vector System Sci. Rep. 2015, 4, 5400 10.1038/srep05400
181. Yang, H.; Wang, H.; Shivalila, C. S.; Cheng, A. W.; Shi, L.; Jaenisch, R. One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering Cell 2013, 154, 1370-1379 10.1016/j.cell.2013.08.022
182. Kim, S.; Kim, D.; Cho, S. W.; Kim, J.; Kim, J.-S. Highly Efficient RNA-Guided Genome Editing in Human Cells via Delivery of Purified Cas9 Ribonucleoproteins Genome Res. 2014, 24, 1012-1019 10.1101/gr.171322.113
183. Schumann, K.; Lin, S.; Boyer, E.; Simeonov, D. R.; Subramaniam, M.; Gate, R. E.; Haliburton, G. E.; Chun, J. Y.; Bluestone, J. A.; Doudna, J. A. et al. Generation of Knock-in Primary Human T Cells Using Cas9 Ribonucleoproteins Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 10437-10442 10.1073/pnas.1512503112
184. Peer, D.; Karp, J. M.; Hong, S.; Farokhzad, O. C.; Margalit, R.; Langer, R. Nanocarriers as an Emerging Platform for Cancer Therapy Nat. Nanotechnol. 2007, 2, 751-760 10.1038/nnano.2007.387
185. Wisse, E.; Jacobs, F.; Topal, B.; Frederik, P.; De Geest, B. The Size of Endothelial Fenestrae in Human Liver Sinusoids: Implications for Hepatocyte-Directed Gene Transfer Gene Ther. 2008, 15, 1193-1199 10.1038/gt.2008.60
186. D'Astolfo, D. S.; Pagliero, R. J.; Pras, A.; Karthaus, W. R.; Clevers, H.; Prasad, V.; Lebbink, R. J.; Rehmann, H.; Geijsen, N. Efficient Intracellular Delivery of Native Proteins Cell 2015, 161, 674-690 10.1016/j.cell.2015.03.028
187. 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 2014, 343, 84-87 10.1126/science.1247005
188. Koike-Yusa, H.; Li, Y.; Tan, E.-P.; Velasco-Herrera, M. D. C.; Yusa, K. Genome-Wide Recessive Genetic Screening in Mammalian Cells with a Lentiviral CRISPR-Guide RNA Library Nat. Biotechnol. 2014, 32, 267-273 10.1038/nbt.2800
189. Mátrai, J.; Chuah, M. K.; VandenDriessche, T. Recent Advances in Lentiviral Vector Development and Applications Mol. Ther. 2010, 18, 477-490 10.1038/mt.2009.319
190. Chen, X.; Goncalves, M. A. F. V. Engineered Viruses as Genome Editing Devices Mol. Ther. 2016, 24, 447-457 10.1038/mt.2015.164
191. Kotterman, M. A.; Schaffer, D. V. Engineering Adeno-Associated Viruses for Clinical Gene Therapy Nat. Rev. Genet. 2014, 15, 445-451 10.1038/nrg3742
192. Kotterman, M. A.; Chalberg, T. W.; Schaffer, D. V. Viral Vectors for Gene Therapy: Translational and Clinical Outlook Annu. Rev. Biomed. Eng. 2015, 17, 63-89 10.1146/annurev-bioeng-071813-104938
193. McCarty, D. M.; Young, S. M., Jr.; Samulski, R. J. Integration of Adeno-Associated Virus (AAV) and Recombinant AAV Vectors Annu. Rev. Genet. 2004, 38, 819-845 10.1146/annurev.genet.37.110801.143717
194. Wu, Z.; Yang, H.; Colosi, P. Effect of Genome Size on AAV Vector Packaging Mol. Ther. 2010, 18, 80-86 10.1038/mt.2009.255
195. Esvelt, K. M.; Mali, P.; Braff, J. L.; Moosburner, M.; Yaung, S. J.; Church, G. M. Orthogonal Cas9 Proteins for RNA-Guided Gene Regulation and Editing Nat. Methods 2013, 10, 1116-1121 10.1038/nmeth.2681
196. Swiech, L.; Heidenreich, M.; Banerjee, A.; Habib, N.; Li, Y.; Trombetta, J.; Sur, M.; Zhang, F. In vivo Interrogation of Gene Function in the Mammalian Brain Using CRISPR-Cas9 Nat. Biotechnol. 2015, 33, 102-106 10.1038/nbt.3055
197. Truong, D. J. J.; Kuhner, K.; Kuhn, R.; Werfel, S.; Engelhardt, S.; Wurst, W.; Ortiz, O. Development of an Intein-Mediated Split-Cas9 System for Gene Therapy Nucleic Acids Res. 2015, 43, 6450-6458 10.1093/nar/gkv601
198. Pack, D. W.; Hoffman, A. S.; Pun, S.; Stayton, P. S. Design and Development of Polymers for Gene Delivery Nat. Rev. Drug Discovery 2005, 4, 581-593 10.1038/nrd1775
199. Mintzer, M. A.; Simanek, E. E. Nonviral Vectors for Gene Delivery Chem. Rev. 2008, 109, 259-302 10.1021/cr800409e
200. Graessmann, M.; Graessmann, A. Microinjection of Tissue Culture Cells Methods Enzymol. 1983, 101, 482-492 10.1016/0076-6879(83)01033-2
201. Kimura, Y.; Hisano, Y.; Kawahara, A.; Higashijima, S.-i. Efficient Generation of Knock-in Transgenic Zebrafish Carrying Reporter/Driver Genes by CRISPR/Cas9-Mediated Genome Engineering Sci. Rep. 2015, 4, 6545 10.1038/srep06545
202. Yang, H.; Wang, H. Y.; Shivalila, C. S.; Cheng, A. W.; Shi, L. Y.; Jaenisch, R. One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering Cell 2013, 154, 1370-1379 10.1016/j.cell.2013.08.022
203. Yang, D.; Xu, J.; Zhu, T.; Fan, J.; Lai, L.; Zhang, J.; Chen, Y. E. Effective Gene Targeting in Rabbits Using RNA-Guided Cas9 Nucleases J. Mol. Cell Biol. 2014, 6, 97-99 10.1093/jmcb/mjt047
204. Crispo, M.; Mulet, A.; Tesson, L.; Barrera, N.; Cuadro, F.; dos Santos-Neto, P.; Nguyen, T.; Crénéguy, A.; Brusselle, L.; Anegon, I. et al. Efficient Generation of Myostatin Knock-out Sheep Using CRISPR/Cas9 Technology and Microinjection into Zygotes PLoS One 2015, 10, e0136690 10.1371/journal.pone.0136690
205. Goodwin, T.; Huang, L. Nonviral Vectors: We Have Come a Long Way Adv. Genet. 2014, 88, 1-12 10.1016/B978-0-12-800148-6.00001-8
206. Lin, S.-R.; Yang, H.-C.; Kuo, Y.-T.; Liu, C.-J.; Yang, T.-Y.; Sung, K.-C.; Lin, Y.-Y.; Wang, H.-Y.; Wang, C.-C.; Shen, Y.-C. et al. The CRISPR/Cas9 System Facilitates Clearance of the Intrahepatic HBV Templates in vivo Mol. Ther. - Nucleic Acids 2014, 3, e186 10.1038/mtna.2014.38
207. Tlaxca, J. L.; Rychak, J. J.; Ernst, P. B.; Konkalmatt, P. R.; Shevchenko, T. I.; Pizzaro, T. T.; Rivera-Nieves, J.; Klibanov, A. L.; Lawrence, M. B. Ultrasound-Based Molecular Imaging and Specific Gene Delivery to Mesenteric Vasculature by Endothelial Adhesion Molecule Targeted Microbubbles in a Mouse Model of Crohn's Disease J. Controlled Release 2013, 165, 216-225 10.1016/j.jconrel.2012.10.021
208. Sun, L.; Huang, C.-W.; Wu, J.; Chen, K.-J.; Li, S.-H.; Weisel, R. D.; Rakowski, H.; Sung, H.-W.; Li, R.-K. The Use of Cationic Microbubbles to Improve Ultrasound-Targeted Gene Delivery to the Ischemic Myocardium Biomaterials 2013, 34, 2107-2116 10.1016/j.biomaterials.2012.11.041
209. Lin, C.-Y.; Hsieh, H.-Y.; Pitt, W. G.; Huang, C.-Y.; Tseng, I.-C.; Yeh, C.-K.; Wei, K.-C.; Liu, H.-L. Focused Ultrasound-Induced Blood-Brain Barrier Opening for Non-Viral, Non-Invasive, and Targeted Gene Delivery J. Controlled Release 2015, 212, 1-9 10.1016/j.jconrel.2015.06.010
210. Tirlapur, U. K.; König, K. Cell Biology: Targeted Transfection by Femtosecond Laser Nature 2002, 418, 290-291 10.1038/418290a
211. Sharei, A.; Zoldan, J.; Adamo, A.; Sim, W. Y.; Cho, N.; Jackson, E.; Mao, S.; Schneider, S.; Han, M.-J.; Lytton-Jean, A. et al. A Vector-Free Microfluidic Platform for Intracellular Delivery Proc. Natl. Acad. Sci. U. S. A. 2013, 110, 2082-2087 10.1073/pnas.1218705110
212. Wightman, L.; Kircheis, R.; Rössler, V.; Carotta, S.; Ruzicka, R.; Kursa, M.; Wagner, E. Different Behavior of Branched and Linear Polyethylenimine for Gene Delivery in vitro and in vivo J. Gene Med. 2001, 3, 362-372 10.1002/jgm.187
213. Godbey, W.; Wu, K. K.; Mikos, A. G. Size Matters: Molecular Weight Affects the Efficiency of Poly (Ethyleneimine) as a Gene Delivery Vehicle J. Biomed. Mater. Res. 1999, 45, 268-275 10.1002/(SICI)1097-4636(19990605)45:3<268::AID-JBM15>3.0.CO;2-Q
214. Buscail, L.; Bournet, B.; Vernejoul, F.; Cambois, G.; Lulka, H.; Hanoun, N.; Dufresne, M.; Meulle, A.; Vignolle-Vidoni, A.; Ligat, L. et al. First-in-Man Phase 1 Clinical Trial of Gene Therapy for Advanced Pancreatic Cancer: Safety, Biodistribution, and Preliminary Clinical Findings Mol. Ther. 2015, 23, 779-789 10.1038/mt.2015.1
215. Hanna, N.; Ohana, P.; Konikoff, F.; Leichtmann, G.; Hubert, A.; Appelbaum, L.; Kopelman, Y.; Czerniak, A.; Hochberg, A. Phase 1/2a, Dose-Escalation, Safety, Pharmacokinetic and Preliminary Efficacy Study of Intratumoral Administration of BC-819 in Patients with Unresectable Pancreatic Cancer Cancer Gene Ther. 2012, 19, 374-381 10.1038/cgt.2012.10
216. Francis, S. M.; Taylor, C. A.; Tang, T.; Liu, Z.; Zheng, Q.; Dondero, R.; Thompson, J. E. SNS01-T Modulation of eIF5A Inhibits B-Cell Cancer Progression and Synergizes with Bortezomib and Lenalidomide Mol. Ther. 2014, 22, 1643-1652 10.1038/mt.2014.24
217. Dash, M.; Chiellini, F.; Ottenbrite, R. M.; Chiellini, E. Chitosan-a Versatile Semi-Synthetic Polymer in Biomedical Applications Prog. Polym. Sci. 2011, 36, 981-1014 10.1016/j.progpolymsci.2011.02.001
218. Kiang, T.; Wen, J.; Lim, H. W.; Leong, K. W. The Effect of the Degree of Chitosan Deacetylation on the Efficiency of Gene Transfection Biomaterials 2004, 25, 5293-5301 10.1016/j.biomaterials.2003.12.036
219. Huang, M.; Fong, C.-W.; Khor, E.; Lim, L.-Y. Transfection Efficiency of Chitosan Vectors: Effect of Polymer Molecular Weight and Degree of Deacetylation J. Controlled Release 2005, 106, 391-406 10.1016/j.jconrel.2005.05.004
220. Kim, Y. H.; Gihm, S. H.; Park, C. R.; Lee, K. Y.; Kim, T. W.; Kwon, I. C.; Chung, H.; Jeong, S. Y. Structural Characteristics of Size-Controlled Self-Aggregates of Deoxycholic Acid-Modified Chitosan and Their Application as a DNA Delivery Carrier Bioconjugate Chem. 2001, 12, 932-938 10.1021/bc015510c
221. Xu, X.; Capito, R. M.; Spector, M. Plasmid Size Influences Chitosan Nanoparticle Mediated Gene Transfer to Chondrocytes J. Biomed. Mater. Res., Part A 2008, 84, 1038-1048 10.1002/jbm.a.31479
222. Oliveira, A. V. V; Silva, G. A.; Chung, D. C. Enhancement of Chitosan-Mediated Gene Delivery through Combination with PhiC31 Integrase Acta Biomater. 2015, 17 (17) 89-97 10.1016/j.actbio.2015.01.013
223. Konstan, M. W.; Davis, P. B.; Wagener, J. S.; Hilliard, K. A.; Stern, R. C.; Milgram, L. J. H.; Kowalczyk, T. H.; Hyatt, S. L.; Fink, T. L.; Gedeon, C. R. et al. Compacted DNA Nanoparticles Administered to the Nasal Mucosa of Cystic Fibrosis Subjects Are Safe and Demonstrate Partial to Complete Cystic Fibrosis Transmembrane Regulator Reconstitution Hum. Gene Ther. 2004, 15, 1255-1269 10.1089/hum.2004.15.1255
224. Fink, T.; Klepcyk, P.; Oette, S.; Gedeon, C.; Hyatt, S.; Kowalczyk, T.; Moen, R.; Cooper, M. Plasmid Size up to 20 Kbp Does Not Limit Effective in vivo Lung Gene Transfer Using Compacted DNA Nanoparticles Gene Ther. 2006, 13, 1048-1051 10.1038/sj.gt.3302761
225. Allen, T. M.; Cullis, P. R. Liposomal Drug Delivery Systems: From Concept to Clinical Applications Adv. Drug Delivery Rev. 2013, 65, 36-48 10.1016/j.addr.2012.09.037
226. Luo, D.; Saltzman, W. M. Enhancement of Transfection by Physical Concentration of DNA at the Cell Surface Nat. Biotechnol. 2000, 18, 893-895 10.1038/78523
227. Ghosh, P.; Han, G.; De, M.; Kim, C. K.; Rotello, V. M. Gold Nanoparticles in Delivery Applications Adv. Drug Delivery Rev. 2008, 60, 1307-1315 10.1016/j.addr.2008.03.016
228. Bates, K.; Kostarelos, K. Carbon Nanotubes as Vectors for Gene Therapy: Past Achievements, Present Challenges and Future Goals Adv. Drug Delivery Rev. 2013, 65, 2023-2033 10.1016/j.addr.2013.10.003
229. Wang, T.; Upponi, J. R.; Torchilin, V. P. Design of Multifunctional Non-Viral Gene Vectors to Overcome Physiological Barriers: Dilemmas and Strategies Int. J. Pharm. 2012, 427, 3-20 10.1016/j.ijpharm.2011.07.013
230. Kogure, K.; Moriguchi, R.; Sasaki, K.; Ueno, M.; Futaki, S.; Harashima, H. Development of a Non-Viral Multifunctional Envelope-Type Nano Device by a Novel Lipid Film Hydration Method J. Controlled Release 2004, 98, 317-323 10.1016/j.jconrel.2004.04.024
231. Nakamura, T.; Akita, H.; Yamada, Y.; Hatakeyama, H.; Harashima, H. A Multifunctional Envelope-Type Nanodevice for Use in Nanomedicine: Concept and Applications Acc. Chem. Res. 2012, 45, 1113-1121 10.1021/ar200254s
232. Kormann, M. S.; Hasenpusch, G.; Aneja, M. K.; Nica, G.; Flemmer, A. W.; Herber-Jonat, S.; Huppmann, M.; Mays, L. E.; Illenyi, M.; Schams, A. et al. Expression of Therapeutic Proteins after Delivery of Chemically Modified mRNA in Mice Nat. Biotechnol. 2011, 29, 154-157 10.1038/nbt.1733
233. Thess, A.; Grund, S.; Mui, B. L.; Hope, M. J.; Baumhof, P.; Fotin-Mleczek, M.; Schlake, T. Sequence-Engineered mRNA without Chemical Nucleoside Modifications Enables an Effective Protein Therapy in Large Animals Mol. Ther. 2015, 23, 1456-1464 10.1038/mt.2015.103
234. Karikó, K.; Muramatsu, H.; Keller, J. M.; Weissman, D. Increased Erythropoiesis in Mice Injected with Submicrogram Quantities of Pseudouridine-Containing mRNA Encoding Erythropoietin Mol. Ther. 2012, 20, 948-953 10.1038/mt.2012.7
235. Pollard, C.; Rejman, J.; De Haes, W.; Verrier, B.; Van Gulck, E.; Naessens, T.; De Smedt, S.; Bogaert, P.; Grooten, J.; Vanham, G. et al. Type I IFN Counteracts the Induction of Antigen-Specific Immune Responses by Lipid-Based Delivery of mRNA Vaccines Mol. Ther. 2013, 21, 251-259 10.1038/mt.2012.202
236. Rejman, J.; Tavernier, G.; Bavarsad, N.; Demeester, J.; De Smedt, S. C. mRNA Transfection of Cervical Carcinoma and Mesenchymal Stem Cells Mediated by Cationic Carriers J. Controlled Release 2010, 147, 385-391 10.1016/j.jconrel.2010.07.124
237. Geall, A. J.; Verma, A.; Otten, G. R.; Shaw, C. A.; Hekele, A.; Banerjee, K.; Cu, Y.; Beard, C. W.; Brito, L. A.; Krucker, T. et al. Nonviral Delivery of Self-Amplifying RNA Vaccines Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 14604-14609 10.1073/pnas.1209367109
238. Kauffman, K. J.; Dorkin, J. R.; Yang, J. H.; Heartlein, M. W.; DeRosa, F.; Mir, F. F.; Fenton, O. S.; Anderson, D. G. Optimization of Lipid Nanoparticle Formulations for mRNA Delivery in vivo with Fractional Factorial and Definitive Screening Designs Nano Lett. 2015, 15, 7300-7306 10.1021/acs.nanolett.5b02497
239. Mahiny, A. J.; Dewerth, A.; Mays, L. E.; Alkhaled, M.; Mothes, B.; Malaeksefat, E.; Loretz, B.; Rottenberger, J.; Brosch, D. M.; Reautschnig, P. et al. In vivo Genome Editing Using Nuclease-Encoding mRNA Corrects SP-B Deficiency Nat. Biotechnol. 2015, 33, 584-586 10.1038/nbt.3241
240. Kallen, K.-J.; Heidenreich, R.; Schnee, M.; Petsch, B.; Schlake, T.; Thess, A.; Baumhof, P.; Scheel, B.; Koch, S. D.; Fotin-Mleczek, M. A Novel, Disruptive Vaccination Technology: Self-Adjuvanted RNActive® Vaccines Hum. Vaccines Immunother. 2013, 9, 2263-2276 10.4161/hv.25181
241. Fotin-Mleczek, M.; Duchardt, K. M.; Lorenz, C.; Pfeiffer, R.; Ojkic-Zrna, S.; Probst, J.; Kallen, K.-J. Messenger RNA-Based Vaccines with Dual Activity Induce Balanced TLR-7 Dependent Adaptive Immune Responses and Provide Antitumor Activity J. Immunother. 2011, 34, 1-15 10.1097/CJI.0b013e3181f7dbe8
242. Üzgün, S.; Nica, G.; Pfeifer, C.; Bosinco, M.; Michaelis, K.; Lutz, J.-F.; Schneider, M.; Rosenecker, J.; Rudolph, C. Pegylation Improves Nanoparticle Formation and Transfection Efficiency of Messenger RNA Pharm. Res. 2011, 28, 2223-2232 10.1007/s11095-011-0464-z
243. Phua, K. K.; Leong, K. W.; Nair, S. K. Transfection Efficiency and Transgene Expression Kinetics of mRNA Delivered in Naked and Nanoparticle Format J. Controlled Release 2013, 166, 227-233 10.1016/j.jconrel.2012.12.029
244. Weide, B.; Pascolo, S.; Scheel, B.; Derhovanessian, E.; Pflugfelder, A.; Eigentler, T. K.; Pawelec, G.; Hoerr, I.; Rammensee, H.-G.; Garbe, C. Direct Injection of Protamine-Protected mRNA: Results of a Phase 1/2 Vaccination Trial in Metastatic Melanoma Patients J. Immunother. 2009, 32, 498-507 10.1097/CJI.0b013e3181a00068
245. Hendel, A.; Bak, R. O.; Clark, J. T.; Kennedy, A. B.; Ryan, D. E.; Roy, S.; Steinfeld, I.; Lunstad, B. D.; Kaiser, R. J.; Wilkens, A. B. et al. Chemically Modified Guide RNAs Enhance CRISPR-Cas Genome Editing in Human Primary Cells Nat. Biotechnol. 2015, 33, 985-989 10.1038/nbt.3290
246. Lu, Y.; Sun, W.; Gu, Z. Stimuli-Responsive Nanomaterials for Therapeutic Protein Delivery J. Controlled Release 2014, 194, 1-19 10.1016/j.jconrel.2014.08.015
247. Gu, Z.; Biswas, A.; Zhao, M.; Tang, Y. Tailoring Nanocarriers for Intracellular Protein Delivery Chem. Soc. Rev. 2011, 40, 3638-3655 10.1039/c0cs00227e
248. Paix, A.; Folkmann, A.; Rasoloson, D.; Seydoux, G. High Efficiency, Homology-Directed Genome Editing in Caenorhabditis Elegans Using CRISPR-Cas9 Ribonucleoprotein Complexes Genetics 2015, 201, 47-54 10.1534/genetics.115.179382
249. Woo, J. W.; Kim, J.; Kwon, S. I.; Corvalan, C.; Cho, S. W.; Kim, H.; Kim, S. G.; Kim, S. T.; Choe, S.; Kim, J. S. DNA-Free Genome Editing in Plants with Preassembled CRISPR-Cas9 Ribonucleoproteins Nat. Biotechnol. 2015, 33, 1162-1164 10.1038/nbt.3389
250. Cho, S. W.; Lee, J.; Carroll, D.; Kim, J.-S.; Lee, J. Heritable Gene Knockout in Caenorhabditis Elegans by Direct Injection of Cas9-sgRNA Ribonucleoproteins Genetics 2013, 195, 1177-1180 10.1534/genetics.113.155853
251. Roberts, M. J.; Bentley, M. D.; Harris, J. M. Chemistry for Peptide and Protein Pegylation Adv. Drug Delivery Rev. 2012, 64, 116-127 10.1016/j.addr.2012.09.025
252. Alconcel, S. N. S.; Baas, A. S.; Maynard, H. D. FDA-Approved Poly(Ethylene Glycol)-Protein Conjugate Drugs Polym. Chem. 2011, 2, 1442-1448 10.1039/c1py00034a
253. Cárdenas-Bailón, F.; Osorio-Revilla, G.; Gallardo-Velázquez, T. Microencapsulation of Insulin Using a W/O/W Double Emulsion Followed by Complex Coacervation to Provide Protection in the Gastrointestinal Tract J. Microencapsulation 2015, 32, 1-9 10.3109/02652048.2015.1017619
254. Davis, M. E. The First Targeted Delivery of siRNA in Humans via a Self-Assembling, Cyclodextrin Polymer-Based Nanoparticle: From Concept to Clinic Mol. Pharmaceutics 2009, 6, 659-668 10.1021/mp900015y
255. Zimmermann, T. S.; Lee, A. C.; Akinc, A.; Bramlage, B.; Bumcrot, D.; Fedoruk, M. N.; Harborth, J.; Heyes, J. A.; Jeffs, L. B.; John, M. et al. RNAi-Mediated Gene Silencing in Non-Human Primates Nature 2006, 441, 111-114 10.1038/nature04688
256. Kontermann, R. E. Strategies for Extended Serum Half-Life of Protein Therapeutics Curr. Opin. Biotechnol. 2011, 22, 868-876 10.1016/j.copbio.2011.06.012
257. Rahdar, M.; McMahon, M. A.; Prakash, T. P.; Swayze, E. E.; Bennett, C. F.; Cleveland, D. W. Synthetic CRISPR RNA-Cas9-Guided Genome Editing in Human Cells Proc. Natl. Acad. Sci. U. S. A. 2015, 112, E7110-E7117 10.1073/pnas.1520883112
258. Scheule, R. K.; George, J. A. S.; Bagley, R. G.; Marshall, J.; Kaplan, J. M.; Akita, G. Y.; Wang, K. X.; Lee, E. R.; Harris, D. J.; Jiang, C. et al. Basis of Pulmonary Toxicity Associated with Cationic Lipid-Mediated Gene Transfer to the Mammalian Lung Hum. Gene Ther. 1997, 8, 689-707 10.1089/hum.1997.8.6-689
259. Li, S.; Tseng, W.; Stolz, D. B.; Wu, S.; Watkins, S.; Huang, L. Dynamic Changes in the Characteristics of Cationic Lipidic Vectors after Exposure to Mouse Serum: Implications for Intravenous Lipofection Gene Ther. 1999, 6, 585-594 10.1038/sj.gt.3300865
260. Knop, K.; Hoogenboom, R.; Fischer, D.; Schubert, U. S. Poly (Ethylene Glycol) in Drug Delivery: Pros and Cons as Well as Potential Alternatives Angew. Chem., Int. Ed. 2010, 49, 6288-6308 10.1002/anie.200902672
261. McManus, J. J.; Rädler, J. O.; Dawson, K. A. Observation of a Rectangular Columnar Phase in a DNA-Calcium-Zwitterionic Lipid Complex J. Am. Chem. Soc. 2004, 126, 15966-15967 10.1021/ja046105+
262. Rodriguez, P. L.; Harada, T.; Christian, D. A.; Pantano, D. A.; Tsai, R. K.; Discher, D. E. Minimal ″Self″ Peptides That Inhibit Phagocytic Clearance and Enhance Delivery of Nanoparticles Science 2013, 339, 971-975 10.1126/science.1229568
263. Cabral, H.; Matsumoto, Y.; Mizuno, K.; Chen, Q.; Murakami, M.; Kimura, M.; Terada, Y.; Kano, M.; Miyazono, K.; Uesaka, M. et al. Accumulation of Sub-100 nm Polymeric Micelles in Poorly Permeable Tumours Depends on Size Nat. Nanotechnol. 2011, 6, 815-823 10.1038/nnano.2011.166
264. Li, L.; Wang, H.; Ong, Z. Y.; Xu, K.; Ee, P. L. R.; Zheng, S.; Hedrick, J. L.; Yang, Y.-Y. Polymer-and Lipid-Based Nanoparticle Therapeutics for the Treatment of Liver Diseases Nano Today 2010, 5, 296-312 10.1016/j.nantod.2010.06.007
265. Schratzberger, P.; Krainin, J. G.; Schratzberger, G.; Silver, M.; Ma, H.; Kearney, M.; Zuk, R. F.; Brisken, A. F.; Losordo, D. W.; Isner, J. M. Transcutaneous Ultrasound Augments Naked DNA Transfection of Skeletal Muscle Mol. Ther. 2002, 6, 576-583 10.1006/mthe.2002.0715
266. Capecchi, M. R. High Efficiency Transformation by Direct Microinjection of DNA into Cultured Mammalian Cells Cell 1980, 22, 479-488 10.1016/0092-8674(80)90358-X
267. Brandén, L. J.; Mohamed, A. J.; Smith, C. E. A Peptide Nucleic Acid-Nuclear Localization Signal Fusion That Mediates Nuclear Transport of DNA Nat. Biotechnol. 1999, 17, 784-787 10.1038/11726
268. Schaffer, D. V.; Fidelman, N. A.; Dan, N.; Lauffenburger, D. A. Vector Unpacking as a Potential Barrier for Receptor-Mediated Polyplex Gene Delivery Biotechnol. Bioeng. 2000, 67, 598-606 10.1002/(SICI)1097-0290(20000305)67:5<598::AID-BIT10>3.0.CO;2-G
269. Benner, S. A.; Kim, H. J.; Carrigan, M. A. Asphalt, Water, and the Prebiotic Synthesis of Ribose, Ribonucleosides, and RNA Acc. Chem. Res. 2012, 45, 2025-2034 10.1021/ar200332w
270. Deleavey, G. F.; Damha, M. J. Designing Chemically Modified Oligonucleotides for Targeted Gene Silencing Chem. Biol. 2012, 19, 937-954 10.1016/j.chembiol.2012.07.011
271. Braasch, D. A.; Jensen, S.; Liu, Y.; Kaur, K.; Arar, K.; White, M. A.; Corey, D. R. RNA Interference in Mammalian Cells by Chemically-Modified RNA Biochemistry 2003, 42, 7967-7975 10.1021/bi0343774
272. Sundaram, P.; Kurniawan, H.; Byrne, M. E.; Wower, J. Therapeutic RNA Aptamers in Clinical Trials Eur. J. Pharm. Sci. 2013, 48, 259-271 10.1016/j.ejps.2012.10.014
273. Jordheim, L. P.; Durantel, D.; Zoulim, F.; Dumontet, C. Advances in the Development of Nucleoside and Nucleotide Analogues for Cancer and Viral Diseases Nat. Rev. Drug Discovery 2013, 12, 447-464 10.1038/nrd4010
274. Kanasty, R.; Dorkin, J. R.; Vegas, A.; Anderson, D. Delivery Materials for siRNA Therapeutics Nat. Mater. 2013, 12, 967-977 10.1038/nmat3765
275. Peacock, H.; Kannan, A.; Beal, P. A.; Burrows, C. J. Chemical Modification of siRNA Bases to Probe and Enhance RNA Interference J. Org. Chem. 2011, 76, 7295-7300 10.1021/jo2012225
276. Bramsen, J. B.; Laursen, M. B.; Nielsen, A. F.; Hansen, T. B.; Bus, C.; Langkjaer, N.; Babu, B. R.; Hojland, T.; Abramov, M.; Van Aerschot, A. et al. A Large-Scale Chemical Modification Screen Identifies Design Rules to Generate siRNAs with High Activity, High Stability and Low Toxicity Nucleic Acids Res. 2009, 37, 2867-2881 10.1093/nar/gkp106
277. Pottier, N.; Cauffiez, C.; Perrais, M.; Barbry, P.; Mari, B. FibromiRs: Translating Molecular Discoveries into New Anti-Fibrotic Drugs Trends Pharmacol. Sci. 2014, 35, 119-126 10.1016/j.tips.2014.01.003
278. Meyers, B. C.; Green, P. J. Plant MicroRNAs: Methods and Protocols; Humana Press: Totowa, NJ, 2010; p 137.
279. Lennox, K. A.; Behlke, M. A. Chemical Modification and Design of Anti-miRNA Oligonucleotides Gene Ther. 2011, 18, 1111-1120 10.1038/gt.2011.100
280. Peng, B.; Chen, Y.; Leong, K. W. MicroRNA Delivery for Regenerative Medicine Adv. Drug Delivery Rev. 2015, 88, 108-122 10.1016/j.addr.2015.05.014
281. Li, Z.; Rana, T. M. Therapeutic Targeting of MicroRNAs: Current Status and Future Challenges Nat. Rev. Drug Discovery 2014, 13, 622-638 10.1038/nrd4359
282. Lao, Y. H.; Phua, K. K.; Leong, K. W. Aptamer Nanomedicine for Cancer Therapeutics: Barriers and Potential for Translation ACS Nano 2015, 9, 2235-2254 10.1021/nn507494p
283. Rusconi, C. P.; Scardino, E.; Layzer, J.; Pitoc, G. A.; Ortel, T. L.; Monroe, D.; Sullenger, B. A. RNA Aptamers as Reversible Antagonists of Coagulation Factor IXa Nature 2002, 419, 90-94 10.1038/nature00963
284. Dellinger, D. J.; Sheehan, D. M.; Christensen, N. K.; Lindberg, J. G.; Caruthers, M. H. Solid-Phase Chemical Synthesis of Phosphonoacetate and Thiophosphonoacetate Oligodeoxynucleotides J. Am. Chem. Soc. 2003, 125, 940-950 10.1021/ja027983f
285. Sharma, V. K.; Sharma, R. K.; Singh, S. K. Antisense Oligonucleotides: Modifications and Clinical Trials MedChemComm 2014, 5, 1454-1471 10.1039/C4MD00184B
286. Wagner, E. Biomaterials in RNAi Therapeutics: Quo Vadis? Biomater. Sci. 2013, 1, 804-809 10.1039/c3bm60071h
287. Gagnon, K. T.; Corey, D. R. Stepping toward Therapeutic CRISPR Proc. Natl. Acad. Sci. U. S. A. 2015, 112, 15536-15537 10.1073/pnas.1521670112
288. Putnam, D. Polymers for Gene Delivery Across Length Scales Nat. Mater. 2006, 5, 439-451 10.1038/nmat1645
289. Williford, J. M.; Wu, J.; Ren, Y.; Archang, M. M.; Leong, K. W.; Mao, H. Q. Recent Advances in Nanoparticle-Mediated Sirna Delivery Annu. Rev. Biomed. Eng. 2014, 16, 347-370 10.1146/annurev-bioeng-071813-105119
290. Ho, Y. P.; Chen, H. H.; Leong, K. W.; Wang, T. H. The Convergence of Quantum-Dot-Mediated Fluorescence Resonance Energy Transfer and Microfluidics for Monitoring DNA Polyplex Self-Assembly in Real Time Nanotechnology 2009, 20, 095103 10.1088/0957-4484/20/9/095103
291. Ho, Y. P.; Grigsby, C. L.; Zhao, F.; Leong, K. W. Tuning Physical Properties of Nanocomplexes through Microfluidics-Assisted Confinement Nano Lett. 2011, 11, 2178-2182 10.1021/nl200862n
292. Grigsby, C. L.; Ho, Y. P.; Lin, C.; Engbersen, J. F.; Leong, K. W. Microfluidic Preparation of Polymer-Nucleic Acid Nanocomplexes Improves Nonviral Gene Transfer Sci. Rep. 2013, 3, 3155 10.1038/srep03155
293. Lu, M.; Ho, Y. P.; Grigsby, C. L.; Nawaz, A. A.; Leong, K. W.; Huang, T. J. Three-Dimensional Hydrodynamic Focusing Method for Polyplex Synthesis ACS Nano 2014, 8, 332-339 10.1021/nn404193e
294. Valencia, P. M.; Farokhzad, O. C.; Karnik, R.; Langer, R. Microfluidic Technologies for Accelerating the Clinical Translation of Nanoparticles Nat. Nanotechnol. 2012, 7, 623-629 10.1038/nnano.2012.168
295. Perry, J. L.; Herlihy, K. P.; Napier, M. E.; Desimone, J. M. Print: A Novel Platform toward Shape and Size Specific Nanoparticle Theranostics Acc. Chem. Res. 2011, 44, 990-998 10.1021/ar2000315
296. Campbell, T. A.; Ivanova, O. S. 3d Printing of Multifunctional Nanocomposites Nano Today 2013, 8, 119-120 10.1016/j.nantod.2012.12.002
297. Tekin, E.; Smith, P. J.; Schubert, U. S. Inkjet Printing as a Deposition and Patterning Tool for Polymers and Inorganic Particles Soft Matter 2008, 4, 703-713 10.1039/b711984d
298. Dunn, S. S.; Tian, S. M.; Blake, S.; Wang, J.; Galloway, A. L.; Murphy, A.; Pohlhaus, P. D.; Rolland, J. P.; Napier, M. E.; DeSimone, J. M. Reductively Responsive siRNA-Conjugated Hydrogel Nanoparticles for Gene Silencing J. Am. Chem. Soc. 2012, 134, 7423-7430 10.1021/ja300174v
299. Petros, R. A.; Ropp, P. A.; DeSimone, J. M. Reductively Labile Print Particles for the Delivery of Doxorubicin to Hela Cells J. Am. Chem. Soc. 2008, 130, 5008 10.1021/ja801436j
300. Hasan, W.; Chu, K.; Gullapalli, A.; Dunn, S. S.; Enlow, E. M.; Luft, J. C.; Tian, S. M.; Napier, M. E.; Pohlhaus, P. D.; Rolland, J. P. et al. Delivery of Multiple siRNAs Using Lipid-Coated PLGA Nanoparticles for Treatment of Prostate Cancer Nano Lett. 2012, 12, 287-292 10.1021/nl2035354
301. Xu, J.; Luft, J. C.; Yi, X. W.; Tian, S. M.; Owens, G.; Wang, J.; Johnson, A.; Berglund, P.; Smith, J.; Napier, M. E. et al. RNA Replicon Delivery Via Lipid-Complexed Print Protein Particles Mol. Pharmaceutics 2013, 10, 3366-3374 10.1021/mp400190z