901
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Fang L, Hung SSC, Yek J, El Wazan L, Nguyen T, Khan S, Lim SY, Hewitt AW, Wong RCB. A Simple Cloning-free Method to Efficiently Induce Gene Expression Using CRISPR/Cas9. MOLECULAR THERAPY-NUCLEIC ACIDS 2018; 14:184-191. [PMID: 30594894 PMCID: PMC6307107 DOI: 10.1016/j.omtn.2018.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/15/2018] [Accepted: 11/15/2018] [Indexed: 12/13/2022]
Abstract
Gain-of-function studies often require the tedious cloning of transgene cDNA into vectors for overexpression beyond the physiological expression levels. The rapid development of CRISPR/Cas technology presents promising opportunities to address these issues. Here, we report a simple, cloning-free method to induce gene expression at an endogenous locus using CRISPR/Cas9 activators. Our strategy utilizes synthesized sgRNA expression cassettes to direct a nuclease-null Cas9 complex fused with transcriptional activators (VP64, p65, and Rta) for site-specific induction of endogenous genes. This strategy allows rapid initiation of gain-of-function studies in the same day. Using this approach, we tested two CRISPR activation systems, dSpCas9VPR and dSaCas9VPR, for induction of multiple genes in human and rat cells. Our results showed that both CRISPR activators allow efficient induction of six different neural development genes (CRX, RORB, RAX, OTX2, ASCL1, and NEUROD1) in human cells, whereas the rat cells exhibit more variable and less-efficient levels of gene induction, as observed in three different genes (Ascl1, Neurod1, Nrl). Altogether, this study provides a simple method to efficiently activate endogenous gene expression using CRISPR/Cas9 activators, which can be applied as a rapid workflow to initiate gain-of-function studies for a range of molecular- and cell-biology disciplines.
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Affiliation(s)
- Lyujie Fang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia; Jinan University, Guangzhou, China
| | - Sandy S C Hung
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Jennifer Yek
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Layal El Wazan
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Tu Nguyen
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia
| | - Shahnaz Khan
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia
| | - Shiang Y Lim
- O'Brien Institute Department, St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Alex W Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Raymond C B Wong
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, VIC, Australia; Shenzhen Eye Hospital, School of Medicine, Shenzhen University, Shenzhen, China.
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902
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Duan J, Lu G, Hong Y, Hu Q, Mai X, Guo J, Si X, Wang F, Zhang Y. Live imaging and tracking of genome regions in CRISPR/dCas9 knock-in mice. Genome Biol 2018; 19:192. [PMID: 30409154 PMCID: PMC6225728 DOI: 10.1186/s13059-018-1530-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 09/09/2018] [Indexed: 12/23/2022] Open
Abstract
CRISPR/dCas9 is a versatile tool that can be used to recruit various effectors and fluorescent molecules to defined genome regions where it can modulate genetic and epigenetic markers, or track the chromatin dynamics in live cells. In vivo applications of CRISPR/dCas9 in animals have been challenged by delivery issues. We generate and characterize a mouse strain with dCas9-EGFP ubiquitously expressed in various tissues. Studying telomere dynamics in these animals reveals surprising results different from those observed in cultured cell lines. The CRISPR/dCas9 knock-in mice provide an important and versatile tool to mechanistically study genome functions in live animals.
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Affiliation(s)
- Jinzhi Duan
- Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Guangqing Lu
- Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Yu Hong
- Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, 100871, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Qingtao Hu
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xueying Mai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Jing Guo
- Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Xiaofang Si
- Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Fengchao Wang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yu Zhang
- Graduate Program, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Peking University, Beijing, 100871, China. .,National Institute of Biological Sciences, Beijing, 102206, China. .,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China.
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903
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Predictable and precise template-free CRISPR editing of pathogenic variants. Nature 2018; 563:646-651. [PMID: 30405244 DOI: 10.1038/s41586-018-0686-x] [Citation(s) in RCA: 339] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022]
Abstract
Following Cas9 cleavage, DNA repair without a donor template is generally considered stochastic, heterogeneous and impractical beyond gene disruption. Here, we show that template-free Cas9 editing is predictable and capable of precise repair to a predicted genotype, enabling correction of disease-associated mutations in humans. We constructed a library of 2,000 Cas9 guide RNAs paired with DNA target sites and trained inDelphi, a machine learning model that predicts genotypes and frequencies of 1- to 60-base-pair deletions and 1-base-pair insertions with high accuracy (r = 0.87) in five human and mouse cell lines. inDelphi predicts that 5-11% of Cas9 guide RNAs targeting the human genome are 'precise-50', yielding a single genotype comprising greater than or equal to 50% of all major editing products. We experimentally confirmed precise-50 insertions and deletions in 195 human disease-relevant alleles, including correction in primary patient-derived fibroblasts of pathogenic alleles to wild-type genotype for Hermansky-Pudlak syndrome and Menkes disease. This study establishes an approach for precise, template-free genome editing.
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904
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Lin G, Li L, Panwar N, Wang J, Tjin SC, Wang X, Yong KT. Non-viral gene therapy using multifunctional nanoparticles: Status, challenges, and opportunities. Coord Chem Rev 2018. [DOI: 10.1016/j.ccr.2018.07.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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905
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Moris N, Edri S, Seyres D, Kulkarni R, Domingues AF, Balayo T, Frontini M, Pina C. Histone Acetyltransferase KAT2A Stabilizes Pluripotency with Control of Transcriptional Heterogeneity. Stem Cells 2018; 36:1828-1838. [PMID: 30270482 PMCID: PMC6334525 DOI: 10.1002/stem.2919] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 08/19/2018] [Accepted: 09/01/2018] [Indexed: 12/20/2022]
Abstract
Cell fate transitions in mammalian stem cell systems have often been associated with transcriptional heterogeneity; however, existing data have failed to establish a functional or mechanistic link between the two phenomena. Experiments in unicellular organisms support the notion that transcriptional heterogeneity can be used to facilitate adaptability to environmental changes and have identified conserved chromatin‐associated factors that modulate levels of transcriptional noise. Herein, we show destabilization of pluripotency‐associated gene regulatory networks through increased transcriptional heterogeneity of mouse embryonic stem cells in which paradigmatic histone acetyl‐transferase, and candidate noise modulator, Kat2a (yeast orthologue Gcn5), have been inhibited. Functionally, network destabilization associates with reduced pluripotency and accelerated mesendodermal differentiation, with increased probability of transitions into lineage commitment. Thus, we show evidence of a relationship between transcriptional heterogeneity and cell fate transitions through manipulation of the histone acetylation landscape of mouse embryonic stem cells, suggesting a general principle that could be exploited in other normal and malignant stem cell fate transitions. stem cells2018;36:1828–11
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Affiliation(s)
- Naomi Moris
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Shlomit Edri
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Denis Seyres
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,National Health Service Blood and Transplant, University of Cambridge, Cambridge, United Kingdom.,NIHR BioResource-Rare Diseases, University of Cambridge, Cambridge, United Kingdom
| | - Rashmi Kulkarni
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | | | - Tina Balayo
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom.,National Health Service Blood and Transplant, University of Cambridge, Cambridge, United Kingdom.,BHF Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Pina
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
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906
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A transportome-scale amiRNA-based screen identifies redundant roles of Arabidopsis ABCB6 and ABCB20 in auxin transport. Nat Commun 2018; 9:4204. [PMID: 30310073 PMCID: PMC6182007 DOI: 10.1038/s41467-018-06410-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 08/29/2018] [Indexed: 12/28/2022] Open
Abstract
Transport of signaling molecules is of major importance for regulating plant growth, development, and responses to the environment. A prime example is the spatial-distribution of auxin, which is regulated via transporters to govern developmental patterning. A critical limitation in our ability to identify transporters by forward genetic screens is their potential functional redundancy. Here, we overcome part of this functional redundancy via a transportome, multi-targeted forward-genetic screen using artificial-microRNAs (amiRNAs). We generate a library of 3000 plant lines expressing 1777 amiRNAs, designed to target closely homologous genes within subclades of transporter families and identify, genotype and quantitatively phenotype, 80 lines showing reproducible shoot growth phenotypes. Within this population, we discover and characterize a strong redundant role for the unstudied ABCB6 and ABCB20 genes in auxin transport and response. The unique multi-targeted lines generated in this study could serve as a genetic resource that is expected to reveal additional transporters. Characterizing plant membrane transporters via genetic methods is complicated by functional redundancy among multi-gene transporter families. Here Zhang et al. use an artificial microRNA-based screen to overcome this issue and show that ABCB6 and ABCB20 act redundantly to regulate auxin transport.
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907
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Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol 2018; 3:135-149. [PMID: 30345399 PMCID: PMC6190536 DOI: 10.1016/j.synbio.2018.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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908
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Quantitative assessment of HR and NHEJ activities via CRISPR/Cas9-induced oligodeoxynucleotide-mediated DSB repair. DNA Repair (Amst) 2018; 70:67-71. [PMID: 30212742 DOI: 10.1016/j.dnarep.2018.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/01/2018] [Accepted: 09/04/2018] [Indexed: 11/22/2022]
Abstract
Homologous recombination (HR) and non-homologous end joining (NHEJ) are the two major mechanisms for the repair of DNA double-strand breaks (DSBs) in eukaryotic cells. Previously, we designed an assay for detecting NHEJ activity by using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system, however, this approach cannot be used to predict the activity of HR repair. Hence, we developed a novel method that is capable of quantitatively measuring both HR and NHEJ activities via CRISPR/Cas9-induced oligodeoxynucleotide (ODN)-mediated DSB repair. In the present experimental procedures, the CRISPR/Cas9 plasmid was cotransfected with single-stranded ODN (ssODN) or blunt-ended double-stranded ODN (dsODN), both of which harbored a unique marker sequence. After the induction of site-specific DSBs by CRISPR/Cas9 system, the ssODN, functioned as the donor template for HR repair, could insert the marker sequence into the DSB sites, while the dsODN was embedded in the DSB sites through NHEJ pathway. Next, by means of PCR analysis using a specific primer for the marker sequence and the primers that flank the DSB sites, the relative amount of integrated marker sequence in the genomic DNA could be quantitatively determined. The correlation between the marker sequence abundance and the HR and NHEJ activities was confirmed by using the selective HR and NHEJ inhibitors. This accessible and rapid quantitative assay for HR and NHEJ activities might be useful for the future research of the DSB repair mechanisms.
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909
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De Majo F, De Windt LJ. RNA therapeutics for heart disease. Biochem Pharmacol 2018; 155:468-478. [DOI: 10.1016/j.bcp.2018.07.037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022]
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910
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Devkota S. The road less traveled: strategies to enhance the frequency of homology-directed repair (HDR) for increased efficiency of CRISPR/Cas-mediated transgenesis. BMB Rep 2018; 51:437-443. [PMID: 30103848 PMCID: PMC6177507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2018] [Indexed: 09/29/2023] Open
Abstract
Non-homologous end joining (NHEJ), and to a lesser extent, the error-free pathway known as homology-directed repair (HDR) are cellular mechanisms for recovery from double-strand DNA breaks (DSB) induced by RNA-guided programmable nuclease CRISPR/Cas. Since NHEJ is equivalent to using a duck tape to stick two pieces of metals together, the outcome of this repair mechanism is prone to error. Any out-of-frame mutations or premature stop codons resulting from NHEJ repair mechanism are extremely handy for loss-of-function studies. Substitution of a mutation on the genome with the correct exogenous repair DNA requires coordination via an error-free HDR, for targeted transgenesis. However, several practical limitations exist in harnessing the potential of HDR to replace a faulty mutation for therapeutic purposes in all cell types and more so in somatic cells. In germ cells after the DSB, copying occurs from the homologous chromosome, which increases the chances of incorporation of exogenous DNA with some degree of homology into the genome compared with somatic cells where copying from the identical sister chromatid is always preferred. This review summarizes several strategies that have been implemented to increase the frequency of HDR with a focus on somatic cells. It also highlights the limitations of this technology in gene therapy and suggests specific solutions to circumvent those barriers. [BMB Reports 2018; 51(9): 437-443].
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Affiliation(s)
- Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093,
USA
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911
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Zhang K, Deng R, Teng X, Li Y, Sun Y, Ren X, Li J. Direct Visualization of Single-Nucleotide Variation in mtDNA Using a CRISPR/Cas9-Mediated Proximity Ligation Assay. J Am Chem Soc 2018; 140:11293-11301. [PMID: 30125486 DOI: 10.1021/jacs.8b05309] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The accumulation of mitochondrial DNA (mtDNA) mutations in cells is strongly related to aging-associated diseases. Imaging of single-nucleotide variation (SNV) in mtDNA is crucial for understanding the heteroplasmy of mtDNAs that harbor pathogenic changes. Herein, we designed a CRISPR/Cas9-mediated proximity ligation assay (CasPLA) for direct visualization of the ND4 and ND5 genes in the mtDNAs of single cells. Taking advantage of the high specificity of CRISPR/Cas9, CasPLA can be used to image SNV in the ND4 gene at single-molecule resolution. Using CasPLA, we observed a mtDNA-transferring process between different cells through a tunneling nanotube, which may account for the spreading of mtDNA heteroplasmy. Moreover, we demonstrated that CasPLA strategy can be applied for imaging of single copy genomic loci ( KRAS gene) in the nuclear genome. Our results establish CasPLA as a tool to study SNV in situ in single cells for basic research and genetic diagnosis.
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Affiliation(s)
- Kaixiang Zhang
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Yupeng Sun
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Xiaojun Ren
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Beijing Key Laboratory for Microanalytical Methods and Instrumentation , Tsinghua University , Beijing 100084 , China
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912
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Bacterial nanotechnology. NATURE NANOTECHNOLOGY 2018; 13:435. [PMID: 29875502 DOI: 10.1038/s41565-018-0177-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
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