1
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Aqib RM, Umer A, Li J, Liu J, Ding B. Light Responsive DNA Nanomaterials and Their Biomedical Applications. Chem Asian J 2024; 19:e202400226. [PMID: 38514391 DOI: 10.1002/asia.202400226] [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: 02/29/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 03/23/2024]
Abstract
DNA nanomaterials have been widely employed for various biomedical applications. With rapid development of chemical modification of nucleic acid, serials of stimuli-responsive elements are included in the multifunctional DNA nanomaterials. In this review, we summarize the recent advances in light responsive DNA nanomaterials based on photocleavage/photodecage, photoisomerization, and photocrosslinking for efficient bioimaging (including imaging of small molecule, microRNA, and protein) and drug delivery (including delivery of small molecule, nucleic acid, and gene editing system). We also discuss the remaining challenges and future perspectives of the light responsive DNA nanomaterials in biomedical applications.
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Affiliation(s)
- Raja Muhammad Aqib
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Arsalan Umer
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jialin Li
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Jianbing Liu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baoquan Ding
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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2
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Liu R, Jiang D, Yun Y, Feng Z, Zheng F, Xiang Y, Fan H, Zhang J. Photoactivatable Engineering of CRISPR/Cas9-Inducible DNAzyme Probe for In Situ Imaging of Nuclear Zinc Ions. Angew Chem Int Ed Engl 2024; 63:e202315536. [PMID: 38253802 DOI: 10.1002/anie.202315536] [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: 10/15/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
DNAzyme-based fluorescent probes for imaging metal ions in living cells have received much attention recently. However, employing in situ metal ions imaging within subcellular organelles, such as nucleus, remains a significant challenge. We developed a three-stranded DNAzyme probe (TSDP) that contained a 20-base-pair (20-bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure. With this design, the CRISPR/Cas9-inducible imaging of nuclear Zn2+ is demonstrated in living cells. Moreover, the superiority of CRISPR-DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn2+ in both HeLa cells and mice. Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal-associated biology.
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Affiliation(s)
- Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Difei Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Changhui Rd. 666, Zhenjiang, Jiangsu, 212003, China
| | - Yangfang Yun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Zhe Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Fenfen Zheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Changhui Rd. 666, Zhenjiang, Jiangsu, 212003, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing, 100084, China
| | - Huanhuan Fan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, China
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3
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Devarajan A. Optically Controlled CRISPR-Cas9 and Cre Recombinase for Spatiotemporal Gene Editing: A Review. ACS Synth Biol 2024; 13:25-44. [PMID: 38134336 DOI: 10.1021/acssynbio.3c00596] [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: 12/24/2023]
Abstract
CRISPR-Cas9 and Cre recombinase, two tools extensively used for genome interrogation, have catalyzed key breakthroughs in our understanding of complex biological processes and diseases. However, the immense complexity of biological systems and off-target effects hinder clinical applications, necessitating the development of platforms to control gene editing over spatial and temporal dimensions. Among the strategies developed for inducible control, light is particularly attractive as it is noninvasive and affords high spatiotemporal resolution. The principles for optical control of Cas9 and Cre recombinase are broadly similar and involve photocaged enzymes and small molecules, engineered split- and single-chain constructs, light-induced expression, and delivery by light-responsive nanocarriers. Few systems enable spatiotemporal control with a high dynamic range without loss of wild-type editing efficiencies. Such systems posit the promise of light-activatable systems in the clinic. While the prospect of clinical applications is palpably exciting, optimization and extensive preclinical validation are warranted. Judicious integration of optically activated CRISPR and Cre, tailored for the desired application, may help to bridge the "bench-to-bedside" gap in therapeutic gene editing.
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Affiliation(s)
- Archit Devarajan
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhauri, Bhopal, Madhya Pradesh, India - 462066
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4
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Chowdhry R, Lu SZ, Lee S, Godhulayyagari S, Ebrahimi SB, Samanta D. Enhancing CRISPR/Cas systems with nanotechnology. Trends Biotechnol 2023; 41:1549-1564. [PMID: 37451945 DOI: 10.1016/j.tibtech.2023.06.005] [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: 04/18/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
CRISPR/Cas systems have revolutionized biology and medicine, and have led to new paradigms in disease diagnostics and therapeutics. However, these complexes suffer from key limitations regarding barriers to cellular entry, stability in biological environments, and off-target effects. Integrating nanotechnology with CRISPR/Cas systems has emerged as a promising strategy to overcome these challenges and has further unlocked structures that accumulate preferentially in tissues of interest, have tunable pharmacological properties, and are activated in response to desired stimuli. Nanomaterials can also enhance CRISPR/Cas-mediated detection platforms by enabling faster, more sensitive, and convenient readouts. We highlight recent advances in this rapidly growing field. We also outline areas that need further development to fully realize the potential of CRISPR technologies.
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Affiliation(s)
- Rupali Chowdhry
- Department of Public Health, The University of Texas at Austin, Austin, TX 78712, USA
| | - Steven Z Lu
- Department of Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Seungheon Lee
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | | | - Sasha B Ebrahimi
- Drug Product Development - Steriles, GlaxoSmithKline, Collegeville, PA 19426, USA
| | - Devleena Samanta
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
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5
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Zhao J, Hu H, Zhou H, Zhang J, Wang L, Wang R. Reactive oxygen signaling molecule inducible regulation of CRISPR-Cas9 gene editing. Cell Biol Toxicol 2023; 39:2421-2429. [PMID: 35644856 DOI: 10.1007/s10565-022-09723-3] [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: 12/09/2021] [Accepted: 05/11/2022] [Indexed: 11/02/2022]
Abstract
We report development of a controllable gene editing tool that boronated gRNA, simply generated in situ, could regulate binding of gRNA molecules with either Cas9 endonuclease or target genes, thus serving as a modulator that can control CRISPR-Cas9 gene editing. Subsequent treatment with H2O2 facilitates the restoration of gene editing ability of the boronated gRNA to the level of using untreated gRNA. This is one of the few cases using small molecule to regulate CRISPR-Cas9 gene editing, which is a complement to the light approach, displaying great application potential. We develop a controllable gene editing tools based on the CRISPR-Cas9 gene editing system. This tool can be regulated by oxidative small molecule, i.e., H2O2. Compared with the light method, the application scope of our CRISPR-Cas9 systems have been widened with the small-molecule-triggered approaches, preventing the potential damage of cells or organism caused by UV light. In addition, the gain-of-function tools are expanding the gene code expansion for mechanistic studies of target enzymes since it provides a positive route to evaluate the activity of a given enzyme in dynamic and inversible regulation of targeting cellular processes.
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Affiliation(s)
- Jizhong Zhao
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hongmei Hu
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Hongling Zhou
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jingwen Zhang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Li Wang
- Wuhan No.1 Hospital, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Rui Wang
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
- Shenzhen Huazhong University of Science and Technology Research Institute, Shenzhen, Guangdong, 518057, China.
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6
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Zhang Y, Feng D, Mu G, Wang Q, Wang J, Luo Y, Tang X. Light-triggered site-directed RNA editing by endogenous ADAR1 with photolabile guide RNA. Cell Chem Biol 2023:S2451-9456(23)00149-6. [PMID: 37295425 DOI: 10.1016/j.chembiol.2023.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 03/21/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
RNA A-to-I editing is a post-transcriptional modification pervasively occurring in cells. Artificial intervention of A-to-I editing at specific sites of RNA could also be achieved with guide RNA and exogenous ADAR enzymes. In contrast to previous fused SNAP-ADAR enzymes for light-driven RNA A-to-I editing, we developed photo-caged antisense guide RNA oligonucleotides with simple 3'-terminal cholesterol modification, and successfully achieved light-triggered site-specific RNA A-to-I editing for the first time utilizing endogenous ADAR enzymes. Our caged A-to-I editing system effectively implemented light-dependent point mutation of mRNA transcripts of both exogenous and endogenous genes in living cells and 3D tumorspheres, as well as spatial regulation of EGFP expression, which provides a new approach for precise manipulation of RNA editing.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Di Feng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Guanqun Mu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Yun Luo
- Shanghai Primerna Biotechnology Co. Ltd, Shanghai 201600, China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing 210023, Jiangsu, China.
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7
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Lei H, Zeng T, Ye X, Fan R, Xiong W, Tian T, Zhou X. Chemical Control of CRISPR Gene Editing via Conditional Diacylation Crosslinking of Guide RNAs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206433. [PMID: 36737854 PMCID: PMC10074079 DOI: 10.1002/advs.202206433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Conditional control of RNA structure and function has emerged as an effective toolkit. Here, a strategy based on a one-step introduction of diacylation linkers and azide groups on the 2'-OH of RNA is advance. Selected from eight phosphine reagents, it is found that 2-(diphenylphosphino)ethylamine has excellent performance in reducing azides via a Staudinger reduction to obtain the original RNA. It is demonstrated that the enzymatic activities of Cas13 and Cas9 can be regulated by chemically modified guide RNAs, and further achieved ligand-induced gene editing in living cells by a controllable CRISPR/Cas9 system.
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Affiliation(s)
- Huajun Lei
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Tianying Zeng
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Xiaofang Ye
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Ruochen Fan
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Wei Xiong
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Tian Tian
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
| | - Xiang Zhou
- College of Chemistry and Molecular SciencesKey Laboratory of Biomedical Polymers of Ministry of EducationThe Institute of Molecular MedicineWuhan University People's HospitalHubei Province Key Laboratory of Allergy and ImmunologyWuhan UniversityWuhanHubei430072China
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8
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Sun YJ, Chen WD, Liu J, Li JJ, Zhang Y, Cai WQ, Liu L, Tang XJ, Hou J, Wang M, Cheng L. A Conformational Restriction Strategy for the Control of CRISPR/Cas Gene Editing with Photoactivatable Guide RNAs. Angew Chem Int Ed Engl 2023; 62:e202212413. [PMID: 36453982 DOI: 10.1002/anie.202212413] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/05/2022]
Abstract
The CRISPR/Cas system is one of the most powerful tools for gene editing. However, approaches for precise control of genome editing and regulatory events are still desirable. Here, we report the spatiotemporal and efficient control of CRISPR/Cas9- and Cas12a-mediated editing with conformationally restricted guide RNAs (gRNAs). This approach relied on only two or three pre-installed photo-labile substituents followed by an intramolecular cyclization, representing a robust synthetic method in comparison to the heavily modified linear gRNAs that often require extensive screening and time-consuming optimization. This tactic could direct the precise cleavage of the genes encoding green fluorescent protein (GFP) and the vascular endothelial growth factor A (VEGFA) protein within a predefined cutting region without notable editing leakage in live cells. We also achieved light-mediated myostatin (MSTN) gene editing in embryos, wherein a new bow-knot-type gRNA was constructed with excellent OFF/ON switch efficiency. Overall, our work provides a significant new strategy in CRISPR/Cas editing with modified circular gRNAs to precisely manipulate where and when genes are edited.
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Affiliation(s)
- Ying-Jie Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Wen-Da Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ji Liu
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun-Jin Li
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Wei-Qi Cai
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin-Jing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Jian Hou
- State Key Laboratory of Agrobiotechnology and College of Biological Science, China Agricultural University, Beijing, 100193, China
| | - Ming Wang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, 310024, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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9
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Cai W, Liu J, Chen X, Mao L, Wang M. Orthogonal Chemical Activation of Enzyme-Inducible CRISPR/Cas9 for Cell-Selective Genome Editing. J Am Chem Soc 2022; 144:22272-22280. [PMID: 36367552 DOI: 10.1021/jacs.2c10545] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The precision and therapeutic potential of CRISPR/Cas9 genome editing are greatly challenged by the less control over Cas9-mediated DNA cleavage. Herein, we introduce a conditional and cell-selective genome editing system controlled by disease-associated enzymes, termed enzyme-inducible CRISPR (eiCRISPR). eiCRISPR comprises Cas9 protein, a self-blocked inactive single-guide RNA (bsgRNA), and a chemically caged deoxyribozyme (DNAzyme) that activates bsgRNA and eiCRISPR in a controllable manner. We design chemical modifications of DNAzyme to suppress its ability to cleave the blocking region of bsgRNA, while the decaging of DNAzyme triggered by the tumor cell-overexpressed enzyme, for instance, NAD(P)H:quinone oxidoreductase (NQO1), restores the activity of bsgRNA and switches on eiCRISPR selectively for genome editing in cancer cells. Moreover, using a biodegradable lipid nanoparticle to deliver eiCRISPR in a tumor-bearing xenograft, we show that the in vivo activation of eiCRISPR enables the editing of human papillomavirus 18 E6 for potential cancer therapy. The strategy of postsynthetic and site-specific modification of DNAzyme is compatible with endogenous chemistries for regulating eiCRISPR for cell-selective genome editing and targeted gene therapy.
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Affiliation(s)
- Weiqi Cai
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Liu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xianghan Chen
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lanqun Mao
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ming Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Design and synthesis of DNA hydrogel based on EXPAR and CRISPR/Cas14a for ultrasensitive detection of creatine kinase MB. Biosens Bioelectron 2022; 218:114792. [DOI: 10.1016/j.bios.2022.114792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/06/2022] [Indexed: 11/20/2022]
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11
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Yang Y, Li D, Wan F, Chen B, Wu G, Li F, Ren Y, Liang P, Wan J, Songyang Z. Identification and Analysis of Small Molecule Inhibitors of CRISPR-Cas9 in Human Cells. Cells 2022; 11:3574. [PMID: 36429003 PMCID: PMC9688475 DOI: 10.3390/cells11223574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Genome editing tools based on CRISPR-Cas systems can repair genetic mutations in situ; however, off-target effects and DNA damage lesions that result from genome editing remain major roadblocks to its full clinical implementation. Protein and chemical inhibitors of CRISPR-Cas systems may reduce off-target effects and DNA damage. Here we describe the identification of several lead chemical inhibitors that could specifically inhibit the activity of Streptococcus pyogenes Cas9 (SpCas9). In addition, we obtained derivatives of lead inhibitors that could penetrate the cell membrane and inhibit SpCas9 in cellulo. Two of these compounds, SP2 and SP24, were able to improve the specificity of SpCas9 in cellulo at low-micromolar concentration. Furthermore, microscale thermophoresis (MST) assays showed that SP24 might inhibit SpCas9 activity by interacting with both the SpCas9 protein and the SpCas9-gRNA ribonucleoprotein complex. Taken together, SP24 is a novel chemical inhibitor of SpCas9 which has the potential to enhance therapies that utilize SpCas9.
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Affiliation(s)
- Yue Yang
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Donghua Li
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Fen Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Bohong Chen
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Guanglan Wu
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Feng Li
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yanliang Ren
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Puping Liang
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Jian Wan
- International Cooperation Base of Pesticide and Green Synthesis (Hubei), Key Laboratory of Pesticide & Chemical Biology (CCNU), Ministry of Education, Department of Chemistry, Central China Normal University, Wuhan 430079, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation and Guangzhou Key Laboratory of Healthy Aging Research, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
- Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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12
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Chen L, Liu Y, Guo W, Liu Z. Light responsive nucleic acid for biomedical application. EXPLORATION 2022; 2:20210099. [PMCID: PMC10190984 DOI: 10.1002/exp.20210099] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/03/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Liwei Chen
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University Changsha Hunan Province P. R. China
| | - Weisheng Guo
- Department of Minimally Invasive Interventional Radiology Guangdong Provincial Key Laboratory of Molecular Target & Clinical Pharmacology, the NMPA and State Key Laboratory of Respiratory Disease School of Pharmaceutical Sciences & The Second Affiliated Hospital Guangzhou Medical University Guangzhou Guangdong Province P. R. China
| | - Zhenbao Liu
- Department of Pharmaceutics Xiangya School of Pharmaceutical Sciences Central South University Changsha Hunan Province P. R. China
- Molecular Imaging Research Center of Central South University Changsha Hunan Province P. R. China
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13
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Feng Z, Ducos B, Scerbo P, Aujard I, Jullien L, Bensimon D. The Development and Application of Opto-Chemical Tools in the Zebrafish. Molecules 2022; 27:molecules27196231. [PMID: 36234767 PMCID: PMC9572478 DOI: 10.3390/molecules27196231] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
The zebrafish is one of the most widely adopted animal models in both basic and translational research. This popularity of the zebrafish results from several advantages such as a high degree of similarity to the human genome, the ease of genetic and chemical perturbations, external fertilization with high fecundity, transparent and fast-developing embryos, and relatively low cost-effective maintenance. In particular, body translucency is a unique feature of zebrafish that is not adequately obtained with other vertebrate organisms. The animal’s distinctive optical clarity and small size therefore make it a successful model for optical modulation and observation. Furthermore, the convenience of microinjection and high embryonic permeability readily allow for efficient delivery of large and small molecules into live animals. Finally, the numerous number of siblings obtained from a single pair of animals offers large replicates and improved statistical analysis of the results. In this review, we describe the development of opto-chemical tools based on various strategies that control biological activities with unprecedented spatiotemporal resolution. We also discuss the reported applications of these tools in zebrafish and highlight the current challenges and future possibilities of opto-chemical approaches, particularly at the single cell level.
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Affiliation(s)
- Zhiping Feng
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
- Correspondence: (Z.F.); (D.B.)
| | - Bertrand Ducos
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- High Throughput qPCR Core Facility, Ecole Normale Supérieure, Paris Sciences Letters University, 46 Rue d’Ulm, 75005 Paris, France
| | - Pierluigi Scerbo
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Inovarion, 75005 Paris, France
| | - Isabelle Aujard
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - Ludovic Jullien
- Laboratoire PASTEUR, Département de Chimie, Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
| | - David Bensimon
- Laboratoire de Physique de l’Ecole Normale Supérieure, Paris Sciences Letters University, Sorbonne Université, Université de Paris, Centre National de la Recherche Scientifique, 24 Rue Lhomond, 75005 Paris, France
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
- Correspondence: (Z.F.); (D.B.)
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Photocontrolled crRNA activation enables robust CRISPR-Cas12a diagnostics. Proc Natl Acad Sci U S A 2022; 119:e2202034119. [PMID: 35727982 DOI: 10.1073/pnas.2202034119] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
CRISPR diagnostics based on nucleic acid amplification faces barriers to its commercial use, such as contamination risks and insufficient sensitivity. Here, we propose a robust solution involving optochemical control of CRISPR RNA (crRNA) activation in CRISPR detection. Based on this strategy, recombinase polymerase amplification (RPA) and CRISPR-Cas12a detection systems can be integrated into a completely closed test tube. crRNA can be designed to be temporarily inactivated so that RPA is not affected by Cas12a cleavage. After the RPA reaction is completed, the CRISPR-Cas12a detection system is activated under rapid light irradiation. This photocontrolled, fully closed CRISPR diagnostic system avoids contamination risks and exhibits a more than two orders of magnitude improvement in sensitivity compared with the conventional one-pot assay. This photocontrolled CRISPR method was applied to the clinical detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA, achieving detection sensitivity and specificity comparable to those of PCR. Furthermore, a compact and automatic photocontrolled CRISPR detection device was constructed.
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15
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Ma L, Dong C, Yu M, Song X, Yu Y, Chen Y. Nanomedicine enables efficient CRISPR-Cas9 genome editing for disease treatment. Sci Bull (Beijing) 2022; 67:572-576. [PMID: 36546116 DOI: 10.1016/j.scib.2021.11.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Lifang Ma
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China; Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Caihong Dong
- Department of Ultrasound, Zhongshan Hospital, Fudan University, and Shanghai Institute of Medical Imaging, Shanghai 200032, China
| | - Meihua Yu
- Materdicine Laboratory, School of Life Sciences, Shanghai University, Shanghai 200444, China.
| | - Xinran Song
- Materdicine Laboratory, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yongchun Yu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China.
| | - Yu Chen
- Materdicine Laboratory, School of Life Sciences, Shanghai University, Shanghai 200444, China.
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16
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Hasanzadeh A, Noori H, Jahandideh A, Haeri Moghaddam N, Kamrani Mousavi SM, Nourizadeh H, Saeedi S, Karimi M, Hamblin MR. Smart Strategies for Precise Delivery of CRISPR/Cas9 in Genome Editing. ACS APPLIED BIO MATERIALS 2022; 5:413-437. [PMID: 35040621 DOI: 10.1021/acsabm.1c01112] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The emergence of CRISPR/Cas technology has enabled scientists to precisely edit genomic DNA sequences. This approach can be used to modulate gene expression for the treatment of genetic disorders and incurable diseases such as cancer. This potent genome-editing tool is based on a single guide RNA (sgRNA) strand that recognizes the targeted DNA, plus a Cas nuclease protein for binding and processing the target. CRISPR/Cas has great potential for editing many genes in different types of cells and organisms both in vitro and in vivo. Despite these remarkable advances, the risk of off-target effects has hindered the translation of CRISPR/Cas technology into clinical applications. To overcome this hurdle, researchers have devised gene regulatory systems that can be controlled in a spatiotemporal manner, by designing special sgRNA, Cas, and CRISPR/Cas delivery vehicles that are responsive to different stimuli, such as temperature, light, magnetic fields, ultrasound (US), pH, redox, and enzymatic activity. These systems can even respond to dual or multiple stimuli simultaneously, thereby providing superior spatial and temporal control over CRISPR/Cas gene editing. Herein, we summarize the latest advances on smart sgRNA, Cas, and CRISPR/Cas nanocarriers, categorized according to their stimulus type (physical, chemical, or biological).
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Affiliation(s)
- Akbar Hasanzadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Hamid Noori
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Atefeh Jahandideh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Niloofar Haeri Moghaddam
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Seyede Mahtab Kamrani Mousavi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Helena Nourizadeh
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Sara Saeedi
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
| | - Mahdi Karimi
- Cellular and Molecular Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Department of Medical Nanotechnology, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Advanced Nanobiotechnology and Nanomedicine Research Group (ANNRG), Iran University of Medical Sciences, Tehran 1449614535, Iran
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
- Research Center for Science and Technology in Medicine, Tehran University of Medical Sciences, Tehran 141556559, Iran
- Applied Biotechnology Research Centre, Tehran Medical Science, Islamic Azad University, Tehran 1584743311, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
- Radiation Biology Research Center, Iran University of Medical Sciences, Tehran 1449614535, Iran
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17
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Qi Q, Zhang Y, Xiong W, Liu X, Cui S, Ye X, Zhang K, Tian T, Xiang Zhou. Norbornene-tetrazine ligation chemistry for controlling RNA-guided CRISPR systems. Chem Sci 2022; 13:12577-12587. [DOI: 10.1039/d2sc02635j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 10/05/2022] [Indexed: 11/21/2022] Open
Abstract
Here, norbornene-tetrazine ligation chemistry is harnessed to control RNA-guided CRISPR systems in vitro and in human cells.
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Affiliation(s)
- Qianqian Qi
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Yutong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xingyu Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Shuangyu Cui
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiaofang Ye
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Kaisong Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Tian Tian
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
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18
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Darrah KE, Deiters A. Translational control of gene function through optically regulated nucleic acids. Chem Soc Rev 2021; 50:13253-13267. [PMID: 34739027 DOI: 10.1039/d1cs00257k] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Translation of mRNA into protein is one of the most fundamental processes within biological systems. Gene expression is tightly regulated both in space and time, often involving complex signaling or gene regulatory networks, as most prominently observed in embryo development. Thus, studies of gene function require tools with a matching level of external control. Light is an excellent conditional trigger as it is minimally invasive, can be easily tuned in wavelength and amplitude, and can be applied with excellent spatial and temporal resolution. To this end, modification of established oligonucleotide-based technologies with optical control elements, in the form of photocaging groups and photoswitches, has rendered these tools capable of navigating the dynamic regulatory pathways of mRNA translation in cellular and in vivo models. In this review, we discuss the different optochemical approaches used to generate photoresponsive nucleic acids that activate and deactivate gene expression and function at the translational level.
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Affiliation(s)
- Kristie E Darrah
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260, USA.
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19
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Photoactivatable nanoCRISPR/Cas9 System Based on crRNA Reversibly Immobilized on Carbon Nanoparticles. Int J Mol Sci 2021; 22:ijms222010919. [PMID: 34681578 PMCID: PMC8539621 DOI: 10.3390/ijms222010919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 11/23/2022] Open
Abstract
Here, we proposed a new approach to engineering a photoactivatable CRISPR/Cas9 gene-editing system. The novel nanoCRISPR/Cas9 system is based on the use of auxiliary photocleavable oligodeoxyribonucleotides (PC-DNAs) complementary to crRNA. PC-DNAs contained up to three UV-sensitive linkers made of 1-(2-nitrophenyl)-1,2-ethanediol inside the oligonucleotide chain. Immobilizing PC-DNAs on the surface of carbon nanoparticles through 3′-terminal pyrene residue provided sufficient blocking of crRNA (and corresponding Cas9 activity) before UV irradiation and allows for crRNA release after UV irradiation at 365 nm, which restores Cas9 activity. We optimized the length of blocking photocleavable oligonucleotide, number of linkers, time of irradiation, and the type of carbon nanoparticles. Based on the results, we consider the nanoCRISPR/Cas9 system involving carbon-encapsulated iron nanoparticles the most promising. It provides the greatest difference of functional activity before/after irradiation and can be used in prospective for magnetic field-controlled delivery of CRISPR system into the target cells or tissues and spatiotemporal gene editing induced by UV irradiation.
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20
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Lv W, Li T, Wang S, Wang H, Li X, Zhang S, Wang L, Xu Y, Wei W. The Application of the CRISPR/Cas9 System in the Treatment of Hepatitis B Liver Cancer. Technol Cancer Res Treat 2021; 20:15330338211045206. [PMID: 34605326 PMCID: PMC8493308 DOI: 10.1177/15330338211045206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was originally discovered in prokaryotes and functions as part of the adaptive immune system. The experimental research of many scholars, as well as scientific and technological advancements, has allowed prokaryote-derived CRISPR/Cas genome-editing systems to transform our ability to manipulate, detect, image, and annotate specific DNA and RNA sequences in the living cells of diverse species. Through modern genetic engineering editing technology and high-throughput gene sequencing, we can edit and splice covalently closed circular DNA to silence it, and correct the mutation and deletion of liver cancer genes to achieve precise in situ repair of defective genes and prohibit viral infection or replication. Such manipulations do not destroy the structure of the entire genome and facilitate the cure of diseases. In this review, we discussed the possibility that CRISPR/Cas could be used as a treatment for patients with liver cancer caused by hepatitis B virus infection, and reviewed the challenges incurred by this effective gene-editing technology.
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Affiliation(s)
- Wei Lv
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tao Li
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shanshan Wang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Huihui Wang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xuemei Li
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Shubing Zhang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lianzi Wang
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Wei Wei
- 36639The First Affiliated Hospital of Anhui Medical University, Hefei, China
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21
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Wu J, Peng H, Lu X, Lai M, Zhang H, Le XC. Binding-Mediated Formation of Ribonucleoprotein Corona for Efficient Delivery and Control of CRISPR/Cas9. Angew Chem Int Ed Engl 2021; 60:11104-11109. [PMID: 33354860 PMCID: PMC8252003 DOI: 10.1002/anie.202014162] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/27/2020] [Indexed: 01/26/2023]
Abstract
Protein coronae formed with nanoparticles confer several useful properties. However, the non-specific nature of protein corona formation makes it difficult to deliver specific proteins for therapeutic applications. Herein, we report on the construction of a new type of protein corona, termed binding-mediated protein corona. This new corona enables the efficient and controllable delivery of functional proteins, which is otherwise challenging for conventional protein coronae. We show the design and delivery of the ribonucleoprotein corona for the CRISPR/Cas9 system. Successful gene editing in human cell lines (Hela and HEK293) demonstrates the efficient delivery, high stability, low cytotoxicity, and well-controlled activity of the Cas9-guide RNA ribonucleoprotein. The binding-mediated protein corona strategy opens up new opportunities for therapeutic protein delivery.
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Affiliation(s)
- Jinjun Wu
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - Hanyong Peng
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - Xiufen Lu
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - Maode Lai
- Department of PathologyZhejiang University School of MedicineHangzhouZhejiang310058China
| | - Hongquan Zhang
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
| | - X. Chris Le
- Division of Analytical and Environmental ToxicologyDepartment of Laboratory Medicine and PathologyFaculty of Medicine and DentistryUniversity of AlbertaEdmontonAlbertaT6G 2G3Canada
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22
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Wu J, Peng H, Lu X, Lai M, Zhang H, Le XC. Binding‐Mediated Formation of Ribonucleoprotein Corona for Efficient Delivery and Control of CRISPR/Cas9. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jinjun Wu
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - Hanyong Peng
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - Xiufen Lu
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - Maode Lai
- Department of Pathology Zhejiang University School of Medicine Hangzhou Zhejiang 310058 China
| | - Hongquan Zhang
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
| | - X. Chris Le
- Division of Analytical and Environmental Toxicology Department of Laboratory Medicine and Pathology Faculty of Medicine and Dentistry University of Alberta Edmonton Alberta T6G 2G3 Canada
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23
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Akhmetova EA, Golyshev VM, Vokhtantcev IP, Meschaninova MI, Venyaminova AG, Novopashina DS. Photoactivatable CRISPR/Cas9 System. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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24
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Zhang Y, Wang Q, Wang J, Tang X. Chemical Modification and Transformation Strategies of Guide RNAs in CRISPR-Cas9 Gene Editing Systems. Chempluschem 2021; 86:587-600. [PMID: 33830675 DOI: 10.1002/cplu.202000785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 03/13/2021] [Indexed: 12/19/2022]
Abstract
The CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 (CRISPR-associated protein 9) is a most powerful tool and has been widely used in gene editing and gene regulation since its discovery. However, wild-type CRISPR-Cas9 suffers from off-target effects and low editing efficiency. To overcome these limitations, engineered Cas9 proteins have been extensively investigated. In addition to Cas9 protein engineering, chemically synthesized guide RNAs have been developed to improve the efficiency and specificity of genome editing as well as spatiotemporal controllability, which broadens the biological applications of CRISPR-Cas9 gene editing system and increases their potentials as therapeutics. In this review, we summarize the latest research advances in remodeling guide RNAs through length optimization, chemical modifications, and conditional control, as well as their powerful applications in gene editing tools and promising therapeutic agents.
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Affiliation(s)
- Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
| | - Qian Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
| | - Jing Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, No. 38, Xueyuan Rd., Beijing, 100191, P. R. China
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25
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Wu H, Wang F, Jiang JH. Inducible CRISPR-dCas9 Transcriptional Systems for Sensing and Genome Regulation. Chembiochem 2021; 22:1894-1900. [PMID: 33433941 DOI: 10.1002/cbic.202000723] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/11/2021] [Indexed: 12/21/2022]
Abstract
The clustered, regularly interspaced short palindromic repeats-associated protein 9 endonuclease (CRISPR-Cas9) and the nuclease-deactivated Cas9 (dCas9) systems have revolutionized our ability to precisely engineer and regulate genomes. Inducible CRISPR-dCas9-based transcriptional systems have been rapidly developed to conditionally control genetic manipulation. Current strategies mainly focus on conditional control of gRNA function and dCas9 protein using exogenous and endogenous triggers, including external light, small molecules, synthetic and intracellular oligonucleotides. These strategies have established novel platforms for the spatiotemporal regulation of genome activation and repression, epigenome editing, and so on. Herein, we summarize the recent progress in conditionally controlling CRISPR-dCas9 transcriptional systems through gRNA modulation and dCas9 protein engineering.
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Affiliation(s)
- Han Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
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26
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Brown W, Zhou W, Deiters A. Regulating CRISPR/Cas9 Function through Conditional Guide RNA Control. Chembiochem 2021; 22:63-72. [PMID: 32833316 PMCID: PMC7928076 DOI: 10.1002/cbic.202000423] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/21/2020] [Indexed: 12/26/2022]
Abstract
Conditional control of CRISPR/Cas9 has been developed by using a variety of different approaches, many focusing on manipulation of the Cas9 protein itself. However, more recent strategies for governing CRISPR/Cas9 function are based on guide RNA (gRNA) modifications. They include control of gRNAs by light, small molecules, proteins, and oligonucleotides. These designs have unique advantages compared to other approaches and have allowed precise regulation of gene editing and transcription. Here, we discuss strategies for conditional control of gRNA function and compare effectiveness of these methods.
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Affiliation(s)
| | | | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260 (USA)
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27
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Chen C, Jing N, Wang Z, Zhang Y, Chen W, Tang X. Multimerized self-assembled caged two-in-one siRNA nanoparticles for photomodulation of RNAi-induced gene silencing. Chem Sci 2020; 11:12289-12297. [PMID: 34094437 PMCID: PMC8162473 DOI: 10.1039/d0sc03562a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
We rationally designed and developed caged siRNA nanoparticles (Multi-Chol-siRNA) self-assembled with cholesterol-modified multimerized caged siRNAs for photomodulation of siRNA gene silencing activity. Strong resistance to serum nuclease and RNase A was observed for these cholesterol-modified caged siRNA nanoparticles due to the formation of nanostructures with high intensity of siRNA. These caged Multi-Chol-siRNA self-assembled nanoparticles were successfully used to achieve photochemical regulation of both exogenous GFP and endogenous Eg5 gene expressions with a GFP/RFP transient transfection system and Eg5-associated assays, respectively. Further, Two-in-One caged Multi-Chol-siGFP/siEg5 self-assembled nanoparticles simultaneously targeting GFP and Eg5 genes were also developed. The caged Multi-Chol-siRNA self-assembled nanoparticles have demonstrated the effectiveness of enhancing photomodulation of multiple RNAi-induced gene silencing activities in cells. Upon light irradiation, multimerized self-assembled caged Two-in-One siRNA nanoparticles (Multi-Chol-siRNA) were collapsed to release trapped siRNAs for multiple RNAi-induced gene silencing activity.![]()
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Affiliation(s)
- Changmai Chen
- School of Pharmacy, Fujian Medical University Fuzhou 350122 China.,State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Nannan Jing
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Zhongyu Wang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Yu Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
| | - Wei Chen
- School of Pharmacy, Fujian Medical University Fuzhou 350122 China
| | - Xinjing Tang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University Beijing 100191 China
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