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Siau JW, Siddiqui AA, Lau SY, Kannan S, Peter S, Zeng Y, Verma C, Droge P, Ghadessy JF. Expanding the DNA editing toolbox: Novel lambda integrase variants targeting microalgal and human genome sequences. PLoS One 2024; 19:e0292479. [PMID: 38349923 PMCID: PMC10863862 DOI: 10.1371/journal.pone.0292479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
Recombinase enzymes are extremely efficient at integrating very large DNA fragments into target genomes. However, intrinsic sequence specificities curtail their use to DNA sequences with sufficient homology to endogenous target motifs. Extensive engineering is therefore required to broaden applicability and robustness. Here, we describe the directed evolution of novel lambda integrase variants capable of editing exogenous target sequences identified in the diatom Phaeodactylum tricornutum and the algae Nannochloropsis oceanica. These microorganisms hold great promise as conduits for green biomanufacturing and carbon sequestration. The evolved enzyme variants show >1000-fold switch in specificity towards the non-natural target sites when assayed in vitro. A single-copy target motif in the human genome with homology to the Nannochloropsis oceanica site can also be efficiently targeted using an engineered integrase, both in vitro and in human cells. The developed integrase variants represent useful additions to the DNA editing toolbox, with particular application for targeted genomic insertion of large DNA cargos.
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Affiliation(s)
- Jia Wei Siau
- Protein and Peptide Engineering Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
| | - Asim Azhar Siddiqui
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sze Yi Lau
- Protein and Peptide Engineering Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
| | | | - Sabrina Peter
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yingying Zeng
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Chandra Verma
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, Singapore
| | - Peter Droge
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- LambdaGen Pte. Ltd., Singapore, Singapore
| | - John F. Ghadessy
- Protein and Peptide Engineering Research Laboratory, Institute of Molecular and Cell Biology, Agency for Science Technology and Research, Singapore, Singapore
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2
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Mahmoudian RA, Farshchian M, Golyan FF, Mahmoudian P, Alasti A, Moghimi V, Maftooh M, Khazaei M, Hassanian SM, Ferns GA, Mahaki H, Shahidsales S, Avan A. Preclinical tumor mouse models for studying esophageal cancer. Crit Rev Oncol Hematol 2023; 189:104068. [PMID: 37468084 DOI: 10.1016/j.critrevonc.2023.104068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Preclinical models are extensively employed in cancer research because they can be manipulated in terms of their environment, genome, molecular biology, organ systems, and physical activity to mimic human behavior and conditions. The progress made in in vivo cancer research has resulted in significant advancements, enabling the creation of spontaneous, metastatic, and humanized mouse models. Most recently, the remarkable and extensive developments in genetic engineering, particularly the utilization of CRISPR/Cas9, transposable elements, epigenome modifications, and liquid biopsies, have further facilitated the design and development of numerous mouse models for studying cancer. In this review, we have elucidated the production and usage of current mouse models, such as xenografts, chemical-induced models, and genetically engineered mouse models (GEMMs), for studying esophageal cancer. Additionally, we have briefly discussed various gene-editing tools that could potentially be employed in the future to create mouse models specifically for esophageal cancer research.
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Affiliation(s)
- Reihaneh Alsadat Mahmoudian
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Moein Farshchian
- Division of Oncology, Laboratory of Cellular Therapy, Department of Medical and Surgical Sciences for Children and Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Fatemeh Fardi Golyan
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvaneh Mahmoudian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Alasti
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Moghimi
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Mina Maftooh
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Majid Khazaei
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Hassanian
- Basic Sciences Research Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A Ferns
- Brighton & Sussex Medical School, Department of Medical Education, Falmer, Brighton, Sussex BN1 9PH, UK
| | - Hanie Mahaki
- Vascular & Endovascular Surgery Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq; Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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3
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Anzalone AV, Gao XD, Podracky CJ, Nelson AT, Koblan LW, Raguram A, Levy JM, Mercer JAM, Liu DR. Programmable deletion, replacement, integration and inversion of large DNA sequences with twin prime editing. Nat Biotechnol 2022; 40:731-740. [PMID: 34887556 PMCID: PMC9117393 DOI: 10.1038/s41587-021-01133-w] [Citation(s) in RCA: 222] [Impact Index Per Article: 111.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 10/22/2021] [Indexed: 12/17/2022]
Abstract
The targeted deletion, replacement, integration or inversion of genomic sequences could be used to study or treat human genetic diseases, but existing methods typically require double-strand DNA breaks (DSBs) that lead to undesired consequences, including uncontrolled indel mixtures and chromosomal abnormalities. Here we describe twin prime editing (twinPE), a DSB-independent method that uses a prime editor protein and two prime editing guide RNAs (pegRNAs) for the programmable replacement or excision of DNA sequences at endogenous human genomic sites. The two pegRNAs template the synthesis of complementary DNA flaps on opposing strands of genomic DNA, which replace the endogenous DNA sequence between the prime-editor-induced nick sites. When combined with a site-specific serine recombinase, twinPE enabled targeted integration of gene-sized DNA plasmids (>5,000 bp) and targeted sequence inversions of 40 kb in human cells. TwinPE expands the capabilities of precision gene editing and might synergize with other tools for the correction or complementation of large or complex human pathogenic alleles.
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Affiliation(s)
- Andrew V Anzalone
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Xin D Gao
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Christopher J Podracky
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Andrew T Nelson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Luke W Koblan
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jonathan M Levy
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Jaron A M Mercer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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4
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Lansing F, Mukhametzyanova L, Rojo-Romanos T, Iwasawa K, Kimura M, Paszkowski-Rogacz M, Karpinski J, Grass T, Sonntag J, Schneider PM, Günes C, Hoersten J, Schmitt LT, Rodriguez-Muela N, Knöfler R, Takebe T, Buchholz F. Correction of a Factor VIII genomic inversion with designer-recombinases. Nat Commun 2022; 13:422. [PMID: 35058465 PMCID: PMC8776779 DOI: 10.1038/s41467-022-28080-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/22/2021] [Indexed: 01/16/2023] Open
Abstract
Despite advances in nuclease-based genome editing technologies, correcting human disease-causing genomic inversions remains a challenge. Here, we describe the potential use of a recombinase-based system to correct the 140 kb inversion of the F8 gene frequently found in patients diagnosed with severe Hemophilia A. Employing substrate-linked directed molecular evolution, we develop a coupled heterodimeric recombinase system (RecF8) achieving 30% inversion of the target sequence in human tissue culture cells. Transient RecF8 treatment of endothelial cells, differentiated from patient-derived induced pluripotent stem cells (iPSCs) of a hemophilic donor, results in 12% correction of the inversion and restores Factor VIII mRNA expression. In this work, we present designer-recombinases as an efficient and specific means towards treatment of monogenic diseases caused by large gene inversions. Correction of disease-causing large genomic inversions remains challenging. Here, the authors developed a dual designer-recombinase system (RecF8) that efficiently corrects a 140 kb inversion frequently found in patients with severe Hemophilia A.
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5
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Standage-Beier K, Brookhouser N, Balachandran P, Zhang Q, Brafman DA, Wang X. RNA-Guided Recombinase-Cas9 Fusion Targets Genomic DNA Deletion and Integration. CRISPR J 2020; 2:209-222. [PMID: 31436506 DOI: 10.1089/crispr.2019.0013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
CRISPR-based technologies have become central to genome engineering. However, CRISPR-based editing strategies are dependent on the repair of DNA breaks via endogenous DNA repair mechanisms, which increases susceptibility to unwanted mutations. Here we complement Cas9 with a recombinase's functionality by fusing a hyperactive mutant resolvase from transposon Tn3, a member of serine recombinases, to a catalytically inactive Cas9, which we term integrase Cas9 (iCas9). We demonstrate iCas9 targets DNA deletion and integration. First, we validate iCas9's function in Saccharomyces cerevisiae using a genome-integrated reporter. Cooperative targeting by CRISPR RNAs at spacings of 22 or 40 bp enables iCas9-mediated recombination. Next, iCas9's ability to target DNA deletion and integration in human HEK293 cells is demonstrated using dual GFP-mCherry fluorescent reporter plasmid systems. Finally, we show that iCas9 is capable of targeting integration into a genomic reporter locus. We envision targeting and design concepts of iCas9 will contribute to genome engineering and synthetic biology.
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Affiliation(s)
- Kylie Standage-Beier
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona.,Molecular and Cellular Biology Graduate Program, Arizona State University, Tempe, Arizona; University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Nicholas Brookhouser
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona.,Graduate Program in Clinical Translational Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Parithi Balachandran
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Qi Zhang
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - David A Brafman
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Xiao Wang
- School of Biological and Health Systems Engineering and University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
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6
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Huang M, Song J, Huang P, Chen X, Wang W, Zhu Z, Song Y, Yang C. Molecular Crowding Evolution for Enabling Discovery of Enthalpy-Driven Aptamers for Robust Biomedical Applications. Anal Chem 2019; 91:10879-10886. [PMID: 31347355 DOI: 10.1021/acs.analchem.9b02697] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An enthalpy-driven ligand is an ideal probe for practical applications because of the formation of abundant specific bonds between the ligand and target, compared to an entropy-driven ligand with a similar Gibbs free energy change. However, there has been a lack of direct discovery strategy for identifying enthalpy-driven ligands. In this work, a molecular crowding SELEX (systematic evolution of ligands by exponential enrichment) strategy for discovering enthalpy-driven aptamers was developed to improve the affinity and selectivity of aptamers in complex samples. Three aptamer sequences were successfully evolved against a tumor biomarker protein, and all proved to be enthalpy-driven by thermodynamics analysis, establishing the feasibility of molecular crowding SELEX for effective discovery of enthalpy-driven aptamers. Further comparison of aptamers evolved from conventional SELEX in buffer and molecular crowding SELEX (SYL-H2C) revealed much higher affinity of SYL-H2C. With its improved thermodynamic properties, the enthalpy-driven SYL-H2C aptamer was able to detect circulating tumor cells in real cancer patient blood samples with excellent detection accuracy (10/10). The proposed molecular crowding screening strategy offers a promising direction for discovering robust binding probes for a great variety of biomedical applications.
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Affiliation(s)
- Mengjiao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Jia Song
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Peifeng Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Xiaofeng Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Wei Wang
- Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Zhi Zhu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Collaborative Innovation Center of Chemistry for Energy Materials, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology , College of Chemistry and Chemical Engineering, Xiamen University , Xiamen , 361005 , China.,Institute of Molecular Medicine, Renji Hospital , Shanghai Jiao Tong University School of Medicine , Shanghai , 200127 , China
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7
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Yu S, Yao P, Li J, Feng J, Wu Q, Zhu D. Improving the catalytic efficiency and stereoselectivity of a nitrilase from Synechocystis sp. PCC6803 by semi-rational engineering en route to chiral γ-amino acids. Catal Sci Technol 2019. [DOI: 10.1039/c8cy02455c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Simultaneously improving activity and stereoselectivity of a nitrilase to catalyze the desymmetrization of 3-substituted glutaronitriles is presented.
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Affiliation(s)
- Shanshan Yu
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Engineering Research Center of Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Peiyuan Yao
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Engineering Research Center of Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Jinlong Li
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Engineering Research Center of Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Jinhui Feng
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Engineering Research Center of Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Qiaqing Wu
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Engineering Research Center of Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
| | - Dunming Zhu
- National Engineering Laboratory for Industrial Enzymes
- Tianjin Engineering Research Center of Biocatalytic Technology
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin 300308
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8
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Nomura W. Development of Toolboxes for Precision Genome/Epigenome Editing and Imaging of Epigenetics. CHEM REC 2018; 18:1717-1726. [PMID: 30066981 DOI: 10.1002/tcr.201800036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
Zinc finger (ZF) proteins are composed of repeated ββα modules and coordinate a zinc ion. ZF domains recognizing specific DNA target sequences can be substituted for the binding domains of various DNA-modifying enzymes to create designer nucleases, recombinases, and methyltransferases with programmable sequence specificity. Enzymatic genome editing and modification can be applied to many fields of basic research and medicine. The recent development of new platforms using transcription activator-like effector (TALE) proteins or the CRISPR-Cas9 system has expanded the range of possibilities for genome-editing technologies. In addition, these DNA binding domains can also be utilized to build a toolbox for epigenetic controls by fusing them with protein- or DNA-modifying enzymes. Here, our research on epigenome editing including the development of artificial zinc finger recombinase (ZFR), split DNA methyltransferase, and fluorescence imaging of histone proteins by ZIP tag-probe system is introduced. Advances in the ZF, TALE, and CRISPR-Cas9 platforms have paved the way for the next generation of genome/epigenome engineering approaches.
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Affiliation(s)
- Wataru Nomura
- Institute of Biomaterials and Bioenginerring, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
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9
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Bogdanove AJ, Bohm A, Miller JC, Morgan RD, Stoddard BL. Engineering altered protein-DNA recognition specificity. Nucleic Acids Res 2018; 46:4845-4871. [PMID: 29718463 PMCID: PMC6007267 DOI: 10.1093/nar/gky289] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 04/03/2018] [Accepted: 04/06/2018] [Indexed: 02/07/2023] Open
Abstract
Protein engineering is used to generate novel protein folds and assemblages, to impart new properties and functions onto existing proteins, and to enhance our understanding of principles that govern protein structure. While such approaches can be employed to reprogram protein-protein interactions, modifying protein-DNA interactions is more difficult. This may be related to the structural features of protein-DNA interfaces, which display more charged groups, directional hydrogen bonds, ordered solvent molecules and counterions than comparable protein interfaces. Nevertheless, progress has been made in the redesign of protein-DNA specificity, much of it driven by the development of engineered enzymes for genome modification. Here, we summarize the creation of novel DNA specificities for zinc finger proteins, meganucleases, TAL effectors, recombinases and restriction endonucleases. The ease of re-engineering each system is related both to the modularity of the protein and the extent to which the proteins have evolved to be capable of readily modifying their recognition specificities in response to natural selection. The development of engineered DNA binding proteins that display an ideal combination of activity, specificity, deliverability, and outcomes is not a fully solved problem, however each of the current platforms offers unique advantages, offset by behaviors and properties requiring further study and development.
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Affiliation(s)
- Adam J Bogdanove
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Andrew Bohm
- Sackler School of Graduate Biomedical Sciences, Tufts University, 136 Harrison Avenue, Boston, MA 02111, USA
| | - Jeffrey C Miller
- Sangamo Therapeutics Inc. 501 Canal Blvd., Richmond, CA 94804, USA
| | - Richard D Morgan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98019, USA
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10
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Abstract
Recent exponential advances in genome sequencing and engineering technologies have enabled an unprecedented level of interrogation into the impact of DNA variation (genotype) on cellular function (phenotype). Furthermore, these advances have also prompted realistic discussion of writing and radically re-writing complex genomes. In this Perspective, we detail the motivation for large-scale engineering, discuss the progress made from such projects in bacteria and yeast and describe how various genome-engineering technologies will contribute to this effort. Finally, we describe the features of an ideal platform and provide a roadmap to facilitate the efficient writing of large genomes.
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Affiliation(s)
- Raj Chari
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts, 02115, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, Massachusetts, 02115, USA
- Wyss Institute for Biologically Inspired Engineering, 3 Blackfan Circle, Boston, Massachusetts, 02115, USA
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11
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Kim MS, Kini AG. Engineering and Application of Zinc Finger Proteins and TALEs for Biomedical Research. Mol Cells 2017; 40:533-541. [PMID: 28835021 PMCID: PMC5582299 DOI: 10.14348/molcells.2017.0139] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 08/10/2017] [Accepted: 08/11/2017] [Indexed: 12/13/2022] Open
Abstract
Engineered DNA-binding domains provide a powerful technology for numerous biomedical studies due to their ability to recognize specific DNA sequences. Zinc fingers (ZF) are one of the most common DNA-binding domains and have been extensively studied for a variety of applications, such as gene regulation, genome engineering and diagnostics. Another novel DNA-binding domain known as a transcriptional activator-like effector (TALE) has been more recently discovered, which has a previously undescribed DNA-binding mode. Due to their modular architecture and flexibility, TALEs have been rapidly developed into artificial gene targeting reagents. Here, we describe the methods used to design these DNA-binding proteins and their key applications in biomedical research.
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Affiliation(s)
- Moon-Soo Kim
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
| | - Anu Ganesh Kini
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, KY 42101,
USA
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12
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Davies JP, Kumar S, Sastry-Dent L. Use of Zinc-Finger Nucleases for Crop Improvement. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2017; 149:47-63. [PMID: 28712500 DOI: 10.1016/bs.pmbts.2017.03.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over the past two decades, new technologies enabling targeted modification of plant genomes have been developed. Among these are zinc-finger nucleases (ZFNs) which are composed of engineered zinc-finger DNA-binding domains fused with a nuclease, generally the FokI nuclease. The zinc-finger domains are composed of a series of four to six 30 amino acid domains that can bind to trinucleotide sequences giving the entire DNA-binding domain specificity to 12-18 nucleotides. Since the FokI nuclease functions as a dimer, pairs of zinc-finger domains are designed to bind upstream and downstream of the cut site which increases the specificity of the complete ZFN to 24-36 nucleotides. The ability of these engineered nucleases to create targeted double-stranded breaks at designated locations throughout the genome has enabled precise deletion, addition, and editing of genes. These techniques are being used to create new genetic variation by deleting or editing endogenous gene sequences and enhancing the efficiency of transgenic product development through targeted insertion of transgenes to specific genomic locations and to sequentially add and/or delete transgenes from existing transgenic events.
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13
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Abstract
When constructing transgenic cell lines via plasmid DNA integration, precise targeting to a desired genomic location is advantageous. It is also often advantageous to remove the bacterial backbone, since bacterial elements can lead to the epigenetic silencing of neighboring DNA. The least cumbersome method to remove the plasmid backbone is recombinase-mediated cassette exchange (RMCE). RMCE is accomplished by arranging recombinase sites in the genome and in a donor plasmid such that a recombinase can both integrate the donor plasmid and excise its bacterial backbone. When a single recombinase is used for RMCE, recombination between undesired pairings of the sites can lead to a significant number of unwanted cell lines. To reduce the frequency with which these side products occur, several variants of RMCE that increase desired outcomes have been developed. Nevertheless, an important feature lacking from these improved RMCE methods is that none have fully utilized the recombinases that have been demonstrated to be the most robust and stringent at performing genomic integration in plants and animals, i.e., the phiC31 and Bxb1 phage integrases. To address this need, we have developed an RMCE protocol using these two serine integrases that we call dual integrase cassette exchange (DICE). Our DICE system provides a means to achieve high-precision DNA integration at a desired location and is especially well suited for repeated recombination into the same locus. In this chapter, we provide our most current protocols for using DICE in feeder-free human-induced pluripotent stem cells .
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Affiliation(s)
- Alfonso P Farruggio
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA
| | - Mital S Bhakta
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA
| | - Michele P Calos
- Department of Genetics, Stanford University School of Medicine, 300 Pasteur Drive, Alway Building, M316, Stanford, CA, 94305-5120, USA.
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Gaj T, Sirk SJ, Shui SL, Liu J. Genome-Editing Technologies: Principles and Applications. Cold Spring Harb Perspect Biol 2016; 8:a023754. [PMID: 27908936 PMCID: PMC5131771 DOI: 10.1101/cshperspect.a023754] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Targeted nucleases have provided researchers with the ability to manipulate virtually any genomic sequence, enabling the facile creation of isogenic cell lines and animal models for the study of human disease, and promoting exciting new possibilities for human gene therapy. Here we review three foundational technologies-clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs). We discuss the engineering advances that facilitated their development and highlight several achievements in genome engineering that were made possible by these tools. We also consider artificial transcription factors, illustrating how this technology can complement targeted nucleases for synthetic biology and gene therapy.
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Affiliation(s)
- Thomas Gaj
- Department of Bioengineering, University of California, Berkeley, California 94720
| | - Shannon J Sirk
- Department of Chemical Engineering, Stanford University, Stanford, California 94305
| | - Sai-Lan Shui
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
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15
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Chaikind B, Bessen JL, Thompson DB, Hu JH, Liu DR. A programmable Cas9-serine recombinase fusion protein that operates on DNA sequences in mammalian cells. Nucleic Acids Res 2016; 44:9758-9770. [PMID: 27515511 PMCID: PMC5175349 DOI: 10.1093/nar/gkw707] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 08/01/2016] [Accepted: 08/02/2016] [Indexed: 02/07/2023] Open
Abstract
We describe the development of ‘recCas9’, an RNA-programmed small serine recombinase that functions in mammalian cells. We fused a catalytically inactive dCas9 to the catalytic domain of Gin recombinase using an optimized fusion architecture. The resulting recCas9 system recombines DNA sites containing a minimal recombinase core site flanked by guide RNA-specified sequences. We show that these recombinases can operate on DNA sites in mammalian cells identical to genomic loci naturally found in the human genome in a manner that is dependent on the guide RNA sequences. DNA sequencing reveals that recCas9 catalyzes guide RNA-dependent recombination in human cells with an efficiency as high as 32% on plasmid substrates. Finally, we demonstrate that recCas9 expressed in human cells can catalyze in situ deletion between two genomic sites. Because recCas9 directly catalyzes recombination, it generates virtually no detectable indels or other stochastic DNA modification products. This work represents a step toward programmable, scarless genome editing in unmodified cells that is independent of endogenous cellular machinery or cell state. Current and future generations of recCas9 may facilitate targeted agricultural breeding, or the study and treatment of human genetic diseases.
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Affiliation(s)
- Brian Chaikind
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
| | - Jeffrey L Bessen
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
| | - David B Thompson
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - Johnny H Hu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA 02138, USA
| | - David R Liu
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA 02138, USA .,Howard Hughes Medical institute, Harvard University, Cambridge, MA 02138 USA
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Perdigão P, Gaj T, Santa-Marta M, Barbas CF, Goncalves J. Reactivation of Latent HIV-1 Expression by Engineered TALE Transcription Factors. PLoS One 2016; 11:e0150037. [PMID: 26933881 PMCID: PMC4774903 DOI: 10.1371/journal.pone.0150037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/08/2016] [Indexed: 11/22/2022] Open
Abstract
The presence of replication-competent HIV-1 -which resides mainly in resting CD4+ T cells--is a major hurdle to its eradication. While pharmacological approaches have been useful for inducing the expression of this latent population of virus, they have been unable to purge HIV-1 from all its reservoirs. Additionally, many of these strategies have been associated with adverse effects, underscoring the need for alternative approaches capable of reactivating viral expression. Here we show that engineered transcriptional modulators based on customizable transcription activator-like effector (TALE) proteins can induce gene expression from the HIV-1 long terminal repeat promoter, and that combinations of TALE transcription factors can synergistically reactivate latent viral expression in cell line models of HIV-1 latency. We further show that complementing TALE transcription factors with Vorinostat, a histone deacetylase inhibitor, enhances HIV-1 expression in latency models. Collectively, these findings demonstrate that TALE transcription factors are a potentially effective alternative to current pharmacological routes for reactivating latent virus and that combining synthetic transcriptional activators with histone deacetylase inhibitors could lead to the development of improved therapies for latent HIV-1 infection.
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Affiliation(s)
- Pedro Perdigão
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Thomas Gaj
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Mariana Santa-Marta
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Carlos F. Barbas
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, United States of America
- Departments of Chemistry, The Scripps Research Institute, La Jolla, California, United States of America
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California, United States of America
| | - Joao Goncalves
- Research Institute for Medicines (iMed ULisboa), Faculdadede Farmácia, Universidade de Lisboa, Lisboa, Portugal
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Formation of functional super-helical assemblies by constrained single heptad repeat. Nat Commun 2015; 6:8615. [PMID: 26468599 PMCID: PMC4634320 DOI: 10.1038/ncomms9615] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 09/10/2015] [Indexed: 12/18/2022] Open
Abstract
Inspired by the key role of super-helical motifs in molecular self-organization, several tandem heptad repeat peptides were used as building blocks to form well-ordered supramolecular nano-assemblies. However, the need for stable helical structures limits the length of the smallest described units to three heptad repeats. Here we describe the first-ever self-assembling single heptad repeat module, based on the ability of the non-coded α-aminoisobutyric acid to stabilize very short peptides in helical conformation. A conformationally constrained peptide comprised of aromatic, but not aliphatic, residues, at the first and fourth positions formed helical fibrillar assemblies. Single crystal X-ray analysis of the peptide demonstrates super-helical packing in which phenylalanine residues formed an ‘aromatic zipper' arrangement at the molecular interface. The modification of the minimal building block with positively charged residues results in tight DNA binding ascribed to the combined factors of helicity, hydrophobicity and charge. The design of these peptides defines a new direction for assembly of super-helical nanostructures by minimal molecular elements. Advances in bionanotechnology demand an increased portfolio of assemblies beyond those currently available. Here, the authors design a crystallographically characterized super-helical sequence composed of single heptad repeats which, through derivatisation, offers vast potential applications.
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18
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Redesigning Recombinase Specificity for Safe Harbor Sites in the Human Genome. PLoS One 2015; 10:e0139123. [PMID: 26414179 PMCID: PMC4587366 DOI: 10.1371/journal.pone.0139123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/09/2015] [Indexed: 11/19/2022] Open
Abstract
Site-specific recombinases (SSRs) are valuable tools for genetic engineering due to their ability to manipulate DNA in a highly specific manner. Engineered zinc-finger and TAL effector recombinases, in particular, are two classes of SSRs composed of custom-designed DNA-binding domains fused to a catalytic domain derived from the resolvase/invertase family of serine recombinases. While TAL effector and zinc-finger proteins can be assembled to recognize a wide range of possible DNA sequences, recombinase catalytic specificity has been constrained by inherent base requirements present within each enzyme. In order to further expand the targeted recombinase repertoire, we used a genetic screen to isolate enhanced mutants of the Bin and Tn21 recombinases that recognize target sites outside the scope of other engineered recombinases. We determined the specific base requirements for recombination by these enzymes and demonstrate their potential for genome engineering by selecting for variants capable of specifically recombining target sites present in the human CCR5 gene and the AAVS1 safe harbor locus. Taken together, these findings demonstrate that complementing functional characterization with protein engineering is a potentially powerful approach for generating recombinases with expanded targeting capabilities.
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Nomura W. [Application and potential of genome engineering by artificial enzymes]. YAKUGAKU ZASSHI 2015; 135:405-14. [PMID: 25759050 DOI: 10.1248/yakushi.14-00240-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Artificial zinc finger proteins (ZFPs) consist of Cys2-His2-type modules composed of approximately 30 amino acids that adopt a ββα structure and coordinate a zinc ion. ZFPs recognizing specific DNA target sequences can substitute for the binding domains of various DNA-modifying enzymes to create designer nucleases, recombinases, and methylases with programmable sequence specificity. Enzymatic genome editing and modification can be applied to many fields of basic research and medicine. The recent development of new platforms using transcription activator-like effector (TALE) proteins or the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has expanded the range of possibilities for genome-editing technologies. These technologies empower investigators with the ability to efficiently knockout or regulate the functions of genes of interest. In this review, we discuss historical advancements in artificial ZFP applications and important issues that may influence the future of genome editing and engineering technologies. The development of artificial ZFPs has greatly increased the feasibility of manipulating endogenous gene functions through transcriptional control and gene modification. Advances in the ZFP, TALE, and CRISPR/Cas platforms have paved the way for the next generation of genome engineering approaches. Perspectives for the future of genome engineering are also discussed, including applications of targeting specific genomic alleles and studies in synthetic biology.
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Affiliation(s)
- Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University
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Gersbach CA, Gaj T, Barbas CF. Synthetic zinc finger proteins: the advent of targeted gene regulation and genome modification technologies. Acc Chem Res 2014; 47:2309-18. [PMID: 24877793 PMCID: PMC4139171 DOI: 10.1021/ar500039w] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
![]()
The understanding
of gene regulation and the structure and function
of the human genome increased dramatically at the end of the 20th
century. Yet the technologies for manipulating the genome have been
slower to develop. For instance, the field of gene therapy has been
focused on correcting genetic diseases and augmenting tissue repair
for more than 40 years. However, with the exception of a few very
low efficiency approaches, conventional genetic engineering methods
have only been able to add auxiliary genes to cells. This has been
a substantial obstacle to the clinical success of gene therapies and
has also led to severe unintended consequences in several cases. Therefore,
technologies that facilitate the precise modification of cellular
genomes have diverse and significant implications in many facets of
research and are essential for translating the products of the Genomic
Revolution into tangible benefits for medicine and biotechnology.
To address this need, in the 1990s, we embarked on a mission to develop
technologies for engineering protein–DNA interactions with
the aim of creating custom tools capable of targeting any DNA sequence.
Our goal has been to allow researchers to reach into genomes to specifically
regulate, knock out, or replace any gene. To realize these goals,
we initially focused on understanding and manipulating zinc finger
proteins. In particular, we sought to create a simple and straightforward
method that enables unspecialized laboratories to engineer custom
DNA-modifying proteins using only defined modular components, a web-based
utility, and standard recombinant DNA technology. Two significant
challenges we faced were (i) the development of zinc finger domains
that target sequences not recognized by naturally occurring zinc finger
proteins and (ii) determining how individual zinc finger domains could
be tethered together as polydactyl proteins to recognize unique locations
within complex genomes. We and others have since used this modular
assembly method to engineer artificial proteins and enzymes that activate,
repress, or create defined changes to user-specified genes in human
cells, plants, and other organisms. We have also engineered novel
methods for externally controlling protein activity and delivery,
as well as developed new strategies for the directed evolution of
protein and enzyme function. This Account summarizes our work in these
areas and highlights independent studies that have successfully used
the modular assembly approach to create proteins with novel function.
We also discuss emerging alternative methods for genomic targeting,
including transcription activator-like effectors (TALEs) and CRISPR/Cas
systems, and how they complement the synthetic zinc finger protein
technology.
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Affiliation(s)
- Charles A. Gersbach
- Department
of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Thomas Gaj
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The
Skaggs Institute for Chemical Biology and the Departments of Chemistry
and Cell and Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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Gaj T, Liu J, Anderson KE, Sirk SJ, Barbas CF. Protein delivery using Cys2-His2 zinc-finger domains. ACS Chem Biol 2014; 9:1662-7. [PMID: 24936957 DOI: 10.1021/cb500282g] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The development of new methods for delivering proteins into cells is a central challenge for advancing both basic research and therapeutic applications. We previously reported that zinc-finger nuclease proteins are intrinsically cell-permeable due to the cell-penetrating activity of the Cys2-His2 zinc-finger domain. Here, we demonstrate that genetically fused zinc-finger motifs can transport proteins and enzymes into a wide range of primary and transformed mammalian cell types. We show that zinc-finger domains mediate protein uptake at efficiencies that exceed conventional protein transduction systems and do so without compromising enzyme activity. In addition, we demonstrate that zinc-finger proteins enter cells primarily through macropinocytosis and facilitate high levels of cytosolic delivery. These findings establish zinc-finger proteins as not only useful tools for targeted genome engineering but also effective reagents for protein delivery.
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Affiliation(s)
- Thomas Gaj
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jia Liu
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kimberly E. Anderson
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Shannon J. Sirk
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carlos F. Barbas
- The Skaggs
Institute for
Chemical Biology and the Departments of Chemistry and Cell and Molecular
Biology, The Scripps Research Institute, La Jolla, California 92037, United States
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