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Aman R, Syed MM, Saleh A, Melliti F, Gundra S, Wang Q, Marsic T, Mahas A, Mahfouz M. Peptide nucleic acid-assisted generation of targeted double-stranded DNA breaks with T7 endonuclease I. Nucleic Acids Res 2024; 52:3469-3482. [PMID: 38421613 PMCID: PMC11014363 DOI: 10.1093/nar/gkae148] [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: 11/01/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024] Open
Abstract
Gene-editing technologies have revolutionized biotechnology, but current gene editors suffer from several limitations. Here, we harnessed the power of gamma-modified peptide nucleic acids (γPNAs) to facilitate targeted, specific DNA invasion and used T7 endonuclease I (T7EI) to recognize and cleave the γPNA-invaded DNA. Our data show that T7EI can specifically target PNA-invaded linear and circular DNA to introduce double-strand breaks (DSBs). Our PNA-Guided T7EI (PG-T7EI) technology demonstrates that T7EI can be used as a programmable nuclease capable of generating single or multiple specific DSBs in vitro under a broad range of conditions and could be potentially applied for large-scale genomic manipulation. With no protospacer adjacent motif (PAM) constraints and featuring a compact protein size, our PG-T7EI system will facilitate and expand DNA manipulations both in vitro and in vivo, including cloning, large-fragment DNA assembly, and gene editing, with exciting applications in biotechnology, medicine, agriculture, and synthetic biology.
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Affiliation(s)
- Rashid Aman
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Muntjeeb M Syed
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Saleh
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Firdaws Melliti
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Sivakrishna Rao Gundra
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Qiaochu Wang
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Tin Marsic
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Ahmed Mahas
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
- Department of Genetics, Harvard University, Boston, MA 02115, USA
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
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Johnson LA, Mart RJ, Allemann RK. A Photoresponsive Homing Endonuclease for Programmed DNA Cleavage. ACS Synth Biol 2024; 13:195-205. [PMID: 38061193 PMCID: PMC10804406 DOI: 10.1021/acssynbio.3c00425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 01/23/2024]
Abstract
Homing endonucleases are used in a wide range of biotechnological applications including gene editing, in gene drive systems, and for the modification of DNA structures, arrays, and prodrugs. However, controlling nuclease activity and sequence specificity remain key challenges when developing new tools. Here a photoresponsive homing endonuclease was engineered for optical control of DNA cleavage by partitioning DNA binding and nuclease domains of the monomeric homing endonuclease I-TevI into independent polypeptide chains. Use of the Aureochrome1a light-oxygen-voltage domain delivered control of dimerization with light. Illumination reduced the concentration needed to achieve 50% cleavage of the homing target site by 6-fold when compared to the dark state, resulting in an up to 9-fold difference in final yields between cleavage products. I-TevI nucleases with and without a native I-TevI zinc finger motif displayed different nuclease activity and sequence preference impacting the promiscuity of the nuclease domain. By harnessing an alternative DNA binding domain, target preference was reprogrammed only when the nuclease lacked the I-TevI zinc finger motif. This work establishes a first-generation photoresponsive platform for spatiotemporal activation of DNA cleavage.
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Affiliation(s)
- Luke A. Johnson
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
| | | | - Rudolf K. Allemann
- School of Chemistry, Cardiff
University, Main Building, Park Place, CF10 3AT, Cardiff, U.K.
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Mechikoff MA, Lee KZ, Solomon KV. Positive Selection Screens for Programmable Endonuclease Activity Using I-SceI. Methods Mol Biol 2024; 2760:253-265. [PMID: 38468093 DOI: 10.1007/978-1-0716-3658-9_15] [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] [Indexed: 03/13/2024]
Abstract
Positive selection screens are high-throughput assays to characterize novel enzymes from environmental samples and enrich for more powerful variants from libraries in applications such as biodiversity mining and directed evolution. However, overly stringent selection can limit the power of these screens due to a high false-negative rate. To create a more flexible and less restrictive screen for novel programmable DNA endonucleases, we developed a novel I-SceI-based platform. In this system, mutant E. coli genomes are cleaved upon induction of I-SceI to inhibit cell growth. Growth is rescued in an activity-dependent manner by plasmid curing or cleavage of the I-SceI expression plasmid via endonuclease candidates. More active candidates more readily proliferate and overtake growth of less active variants leading to enrichment. While demonstrated here with Cas9, this protocol can be readily adapted to any programmable DNA endonuclease and used to characterize single candidates or to enrich more powerful variants from pooled candidates or libraries.
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Affiliation(s)
| | - Kok Zhi Lee
- Department of Energy, Environmental & Chemical Engineering, Washington University at St. Louis, St. Louis, MO, USA
| | - Kevin V Solomon
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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4
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Graver BA, Chakravarty N, Solomon KV. Prokaryotic Argonautes for in vivo biotechnology and molecular diagnostics. Trends Biotechnol 2024; 42:61-73. [PMID: 37451948 DOI: 10.1016/j.tibtech.2023.06.010] [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: 04/20/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
Prokaryotic Argonautes (pAgos) are an emerging class of programmable endonucleases that are believed to be more flexible than existing CRISPR-Cas systems and have significant potential for biotechnology. Current applications of pAgos include a myriad of molecular diagnostics and in vitro DNA assembly tools. However, efforts have historically been centered on thermophilic pAgo variants. To enable in vivo biotechnological applications such as gene editing, focus has shifted to pAgos from mesophilic organisms. We discuss what is known of pAgos, how they are being developed for various applications, and strategies to overcome current challenges to in vivo applications in prokaryotes and eukaryotes.
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Affiliation(s)
- Brett A Graver
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Namrata Chakravarty
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA
| | - Kevin V Solomon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716, USA.
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5
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Lu Y, Happi Mbakam C, Song B, Bendavid E, Tremblay JP. Improvements of nuclease and nickase gene modification techniques for the treatment of genetic diseases. Front Genome Ed 2022; 4:892769. [PMID: 35958050 PMCID: PMC9360573 DOI: 10.3389/fgeed.2022.892769] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/08/2022] [Indexed: 12/20/2022] Open
Abstract
Advancements in genome editing make possible to exploit the functions of enzymes for efficient DNA modifications with tremendous potential to treat human genetic diseases. Several nuclease genome editing strategies including Meganucleases (MNs), Zinc Finger Nucleases (ZFNs), Transcription Activator-like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR associated proteins (CRISPR-Cas) have been developed for the correction of genetic mutations. CRISPR-Cas has further been engineered to create nickase genome editing tools including Base editors and Prime editors with much precision and efficacy. In this review, we summarized recent improvements in nuclease and nickase genome editing approaches for the treatment of genetic diseases. We also highlighted some limitations for the translation of these approaches into clinical applications.
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Affiliation(s)
- Yaoyao Lu
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Cedric Happi Mbakam
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Bo Song
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Eli Bendavid
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
| | - Jacques-P. Tremblay
- CHU de Québec Research Center, Laval University, Quebec City, QC, Canada
- Department of Molecular Medicine, Laval University, Quebec City, QC, Canada
- *Correspondence: Jacques-P. Tremblay,
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