1
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Chatterjee S, Xiao L, Zhong W, Feng S, Kool ET. Selective Arylation of RNA 2'-OH Groups via S NAr Reaction with Trialkylammonium Heterocycles. Angew Chem Int Ed Engl 2024; 63:e202403496. [PMID: 38625814 DOI: 10.1002/anie.202403496] [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: 02/19/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/18/2024]
Abstract
Small-molecule reactions at the 2'-OH groups of RNA enable useful applications for transcriptome technology and biology. To date, all reactions have involved carbonyl acylation and mechanistically related sulfonylation, limiting the types of modifications and properties that can be achieved. Here we report that electron-deficient heteroaryl species selectively react with 2'-OH groups of RNA in water via SNAr chemistry. In particular, trialkyl-ammonium (TAA)-activated aromatic heterocycles, prepared in one step from aryl chloride precursors, give high conversions to aryl ether adducts with RNAs in aqueous buffer in ~2-3 h. Remarkably, a TAA triazine previously used only for reaction with carboxylic acids, shows unprecedented selectivity for RNA over water, reacting rapidly with 2'-OH groups while exhibiting a half-life in water of >10 days. We further show that a triazine aryl species can be used as a probe at trace-level yields to map RNA structure in vitro. Finally, we prepare a number of functionalized trialkylammonium triazine reagents and show that they can be used to covalently label RNA efficiently for use in vitro and in living cells. This direct arylation chemistry offers a simple and distinct structural scaffold for post-synthetic RNA modification, with potential utility in multiple applications in transcriptome research.
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Affiliation(s)
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Wenrui Zhong
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Sheng Feng
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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2
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Liu P, Lin Y, Zhuo X, Zeng J, Chen B, Zou Z, Liu G, Xiong E, Yang R. Universal crRNA Acylation Strategy for Robust Photo-Initiated One-Pot CRISPR-Cas12a Nucleic Acid Diagnostics. Angew Chem Int Ed Engl 2024; 63:e202401486. [PMID: 38563640 DOI: 10.1002/anie.202401486] [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: 01/22/2024] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 04/04/2024]
Abstract
Spatiotemporal regulation of clustered regularly interspaced short palindromic repeats (CRISPR) system is attractive for precise gene editing and accurate molecular diagnosis. Although many efforts have been made, versatile and efficient strategies to control CRISPR system are still desirable. Here, we proposed a universal and accessible acylation strategy to regulate the CRISPR-Cas12a system by efficient acylation of 2'-hydroxyls (2'-OH) on crRNA strand with photolabile agents (PLGs). The introduction of PLGs confers efficient suppression of crRNA function and rapid restoration of CRISPR-Cas12a reaction upon short light exposure regardless of crRNA sequences. Based on this strategy, we constructed a universal PhotO-Initiated CRISPR-Cas12a system for Robust One-pot Testing (POIROT) platform integrated with recombinase polymerase amplification (RPA), which showed two orders of magnitude more sensitive than the conventional one-step assay and comparable to the two-step assay. For clinical sample testing, POIROT achieved high-efficiency detection performance comparable to the gold-standard quantitative PCR (qPCR) in sensitivity and specificity, but faster than the qPCR method. Overall, we believe the proposed strategy will promote the development of many other universal photo-controlled CRISPR technologies for one-pot assay, and even expand applications in the fields of controllable CRISPR-based genomic editing, disease therapy, and cell imaging.
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Affiliation(s)
- Pengfei Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Yating Lin
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Xiaohua Zhuo
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Jiayu Zeng
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Bolin Chen
- The Second Department of Thoracic Oncology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, 410013, Changsha, P. R. China
| | - Zhen Zou
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Guhuan Liu
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Erhu Xiong
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
| | - Ronghua Yang
- Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research, Ministry of Education, College of Chemistry and Chemical Engineering, Hunan Normal University, 410081, Changsha, P. R. China
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3
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Shioi R, Chatterjee S, Xiao L, Zhong W, Kool ET. Second-Generation Chiral Amino Acid Derivatives Afford High Stereoselectivity and Stability in Aqueous RNA Acylation. J Org Chem 2024. [PMID: 38809698 DOI: 10.1021/acs.joc.4c00686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Activated acyl species have proven versatile in the esterification of 2'-OH groups in RNA, enabling structure mapping, caging, profiling, and labeling of the biopolymer. Nearly all reagents developed for this reaction have been achiral; however, a recent study reported that simple chiral amino acid acylimidazole derivatives could yield diastereoselective reactions at RNA 2'-OH in water, enabling up to 4:1 selectivity in screening. Here, we investigated the effect of steric bulk on the stereoselectivity of RNA reaction and on the stability of adducts with a library of 36 chiral acylimidazole scaffolds with increasing steric demand. The results document the highest stereoselectivity yet achieved in RNA acylation reactions, with as high as >99:1 diastereoselectivity at >70% conversion. Also notably, the bulky adducts were found to have markedly improved stability on RNA.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Sayantan Chatterjee
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Wenrui Zhong
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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4
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Guo J, Chen S, Onishi Y, Shi Q, Song Y, Mei H, Chen L, Kool ET, Zhu RY. RNA Control via Redox-Responsive Acylation. Angew Chem Int Ed Engl 2024; 63:e202402178. [PMID: 38480851 DOI: 10.1002/anie.202402178] [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: 02/05/2024] [Indexed: 04/05/2024]
Abstract
Incorporating stimuli-responsive components into RNA constructs provides precise spatiotemporal control over RNA structures and functions. Despite considerable advancements, the utilization of redox-responsive stimuli for the activation of caged RNAs remains scarce. In this context, we present a novel strategy that leverages post-synthetic acylation coupled with redox-responsive chemistry to exert control over RNA. To achieve this, we design and synthesize a series of acylating reagents specifically tailored for introducing disulfide-containing acyl adducts into the 2'-OH groups of RNA ("cloaking"). Our data reveal that these acyl moieties can be readily appended, effectively blocking RNA catalytic activity and folding. We also demonstrate the traceless release and reactivation of caged RNAs ("uncloaking") through reducing stimuli. By employing this strategy, RNA exhibits rapid cellular uptake, effective distribution and activation in the cytosol without lysosomal entrapment. We anticipate that our methodology will be accessible to laboratories engaged in RNA biology and holds promise as a versatile platform for RNA-based applications.
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Affiliation(s)
- Junsong Guo
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Siqin Chen
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Yoshiyuki Onishi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Qi Shi
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
| | - Yangyang Song
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Hui Mei
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Leilei Chen
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Ru-Yi Zhu
- Department of Chemistry, National University of Singapore, 4 Science Drive 2, Singapore, 117544, Singapore
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5
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Li T, Cheng C, Liu J. Chemical and Enzyme-Mediated Chemical Reactions for Studying Nucleic Acids and Their Modifications. Chembiochem 2024:e202400220. [PMID: 38742371 DOI: 10.1002/cbic.202400220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024]
Abstract
Nucleic acids are genetic information-carrying molecules inside cells. Apart from basic nucleotide building blocks, there exist various naturally occurring chemical modifications on nucleobase and ribose moieties, which greatly increase the encoding complexity of nuclei acids, contribute to the alteration of nucleic acid structures, and play versatile regulation roles in gene expression. To study the functions of certain nucleic acids in various biological contexts, robust tools to specifically label and identify these macromolecules and their modifications, and to illuminate their structures are highly necessary. In this review, we summarize recent technique advances of using chemical and enzyme-mediated chemical reactions to study nucleic acids and their modifications and structures. By highlighting the chemical principles of these techniques, we aim to present a perspective on the advancement of the field as well as to offer insights into developing specific chemical reactions and precise enzyme catalysis utilized for nucleic acids and their modifications.
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Affiliation(s)
- Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Chongguang Cheng
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- Life Sciences Institute, Zhejiang University, Yuhangtang Road 866, Hangzhou, 310058, Zhejiang Province, China
- State Key Laboratory of Transvascular Implantation Devices, Hangzhou, 310009, Zhejiang Province, China
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6
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Bardhan A, Brown W, Albright S, Tsang M, Davidson LA, Deiters A. Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function. Angew Chem Int Ed Engl 2024; 63:e202318773. [PMID: 38411401 DOI: 10.1002/anie.202318773] [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: 12/06/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Savannah Albright
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Tsang
- Department of Cell Biology, Center for Integrative Organ Systems., University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Lance A Davidson
- Department of Bioengineering, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
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7
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Xiao L, Fang L, Kool ET. 2'-OH as a universal handle for studying intracellular RNAs. Cell Chem Biol 2024; 31:110-124. [PMID: 37992716 PMCID: PMC10841764 DOI: 10.1016/j.chembiol.2023.10.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/28/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023]
Abstract
RNA plays pivotal roles in most cellular processes, serving as both the traditional carrier of genetic information and as a key regulator of cellular functions. The advent of chemical technologies has contributed critically to the analysis of cellular RNA structures, functions, and interactions. Many of these methods and molecules involve the utilization of chemically reactive handles in RNAs, either introduced externally or inherent within the polymer itself. Among these handles, the 2'-hydroxyl (2'-OH) group has emerged as an exceptionally well-suited and general chemical moiety for the modification and profiling of RNAs in intracellular studies. In this review, we provide an overview of the recent advancements in intracellular applications of acylation at the 2'-OH group of RNA. We outline progress made in probing RNA structure and interactomes, controlling RNA function, RNA imaging, and analyzing RNA-small molecule interactions, all achieved in living cells through this simple chemical handle on the biopolymer.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA.
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8
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Shioi R, Xiao L, Fang L, Kool ET. Efficient post-synthesis incorporation and conjugation of reactive ketones in RNA via 2'-acylation. Chem Commun (Camb) 2023; 60:232-235. [PMID: 38054242 PMCID: PMC10745195 DOI: 10.1039/d3cc05123d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Despite the broad utility of ketones in bioconjugation, few methods exist to introduce them into RNA. Here we develop highly reactive 2'-OH acylating reagents containing strained-ring ketones, and employ them as versatile labeling handles for RNA.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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9
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Shioi R, Xiao L, Chatterjee S, Kool ET. Stereoselective RNA reaction with chiral 2'-OH acylating agents. Chem Sci 2023; 14:13235-13243. [PMID: 38023505 PMCID: PMC10664579 DOI: 10.1039/d3sc03067a] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023] Open
Abstract
The reactivity of RNA 2'-OH groups with acylating agents has recently been investigated for high-yield conjugation of RNA strands. To date, only achiral molecules have been studied for this reaction, despite the complex chiral structure of RNA. Here we prepare a set of chiral acylimidazoles and study their stereoselectivity in RNA reactions. Reactions performed with unfolded and folded RNAs reveal that positional selectivity and reactivity vary widely with local RNA macro-chirality. We further document remarkable effects of chirality on reagent reactivity, identifying an asymmetric reagent with 1000-fold greater reactivity than prior achiral reagents. In addition, we identify a chiral compound with higher RNA structural selectivity than any previously reported RNA-mapping species. Further, azide-containing homologs of a chiral dimethylalanine reagent were synthesized and applied to local RNA labeling, displaying 92% yield and 16 : 1 diastereoselectivity. The results establish that reagent stereochemistry and chiral RNA structure are critical elements of small molecule-RNA reactions, and demonstrate new chemical strategies for selective RNA modification and probing.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | - Lu Xiao
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | | | - Eric T Kool
- Department of Chemistry, Stanford University Stanford CA 94305 USA
- Sarafan ChEM-H, Stanford University Stanford CA 94305 USA
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10
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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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11
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Fang L, Xiao L, Jun YW, Onishi Y, Kool ET. Reversible 2'-OH acylation enhances RNA stability. Nat Chem 2023; 15:1296-1305. [PMID: 37365334 DOI: 10.1038/s41557-023-01246-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/19/2023] [Indexed: 06/28/2023]
Abstract
The presence of a hydroxyl group at the 2'-position in its ribose makes RNA susceptible to hydrolysis. Stabilization of RNAs for storage, transport and biological application thus remains a serious challenge, particularly for larger RNAs that are not accessible by chemical synthesis. Here we present reversible 2'-OH acylation as a general strategy to preserve RNA of any length or origin. High-yield polyacylation of 2'-hydroxyls ('cloaking') by readily accessible acylimidazole reagents effectively shields RNAs from both thermal and enzymatic degradation. Subsequent treatment with water-soluble nucleophilic reagents removes acylation adducts quantitatively ('uncloaking') and recovers a remarkably broad range of RNA functions, including reverse transcription, translation and gene editing. Furthermore, we show that certain α-dimethylamino- and α-alkoxy- acyl adducts are spontaneously removed in human cells, restoring messenger RNA translation with extended functional half-lives. These findings support the potential of reversible 2'-acylation as a simple and general molecular solution for enhancing RNA stability and provide mechanistic insights for stabilizing RNA regardless of length or origin.
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Affiliation(s)
- Linglan Fang
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | | | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, USA.
- Sarafan ChEM-H Institute, Stanford University, Stanford, CA, USA.
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12
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Hu Z, Sun A, Yang J, Naz G, Sun G, Li Z, Gogo Liu JJ, Zhang S, Zhang X. Regulation of the CRISPR-Cas12a system by methylation and demethylation of guide RNA. Chem Sci 2023; 14:5945-5955. [PMID: 37293662 PMCID: PMC10246701 DOI: 10.1039/d3sc00629h] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Chemical modifications of CRISPR-Cas nucleases help decrease off-target editing and expand the biomedical applications of CRISPR-based gene manipulation tools. Here, we found that epigenetic modifications of guide RNA, such as m6A and m1A methylation, can effectively inhibit both the cis- and trans-DNA cleavage activities of CRISPR-Cas12a. The underlying mechanism is that methylations destabilize the secondary and tertiary structure of gRNA which prevents the assembly of the Cas12a-gRNA nuclease complex, leading to decreased DNA targeting ability. A minimum of three adenine methylated nucleotides are required to completely inhibit the nuclease activity. We also demonstrate that these effects are reversible through the demethylation of gRNA by demethylases. This strategy has been used in the regulation of gene expression, demethylase imaging in living cells and controllable gene editing. The results demonstrate that the methylation-deactivated and demethylase-activated strategy is a promising tool for regulation of the CRISPR-Cas12a system.
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Affiliation(s)
- Zhian Hu
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Ao Sun
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
| | - Jinlei Yang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Gul Naz
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Gongwei Sun
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Zhengping Li
- Beijing Key Laboratory for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing 30 Xueyuan Road, Haidian District Beijing 100083 P. R. China
| | - Jun-Jie Gogo Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University Beijing 100084 P. R. China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University Beijing 100084 P. R. China
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13
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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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14
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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: 0] [Impact Index Per Article: 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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15
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Dorn RS, Prescher JA. Bioorthogonal Phosphines: Then and Now. Isr J Chem 2022. [DOI: 10.1002/ijch.202200070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert S. Dorn
- Departments of Chemistry University of California Irvine California 92697 United States
| | - Jennifer A. Prescher
- Departments of Chemistry University of California Irvine California 92697 United States
- Molecular Biology & Biochemistry University of California Irvine California 92697 United States
- Pharmaceutical Sciences University of California Irvine California 92697 United States
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16
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Shin S, Jang S, Lim D. Small Molecules for Enhancing the Precision and Safety of Genome Editing. Molecules 2022; 27:6266. [PMID: 36234804 PMCID: PMC9573751 DOI: 10.3390/molecules27196266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/17/2022] [Accepted: 09/20/2022] [Indexed: 11/24/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based genome-editing technologies have revolutionized biology, biotechnology, and medicine, and have spurred the development of new therapeutic modalities. However, there remain several barriers to the safe use of CRISPR technologies, such as unintended off-target DNA cleavages. Small molecules are important resources to solve these problems, given their facile delivery and fast action to enable temporal control of the CRISPR systems. Here, we provide a comprehensive overview of small molecules that can precisely modulate CRISPR-associated (Cas) nucleases and guide RNAs (gRNAs). We also discuss the small-molecule control of emerging genome editors (e.g., base editors) and anti-CRISPR proteins. These molecules could be used for the precise investigation of biological systems and the development of safer therapeutic modalities.
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Affiliation(s)
- Siyoon Shin
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Seeun Jang
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
| | - Donghyun Lim
- School of Biopharmaceutical and Medical Sciences, Sungshin University, Seoul 01133, Korea
- Department of Next-Generation Applied Science, Sungshin University, Seoul 01133, Korea
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17
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Ji H, Xiong W, Zhang K, Tian T, Zhou X. Hydrogen Peroxide-triggered Chemical Strategy for Controlling CRISPR systems. Chem Asian J 2022; 17:e202200214. [PMID: 35483968 DOI: 10.1002/asia.202200214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/04/2022] [Indexed: 11/09/2022]
Abstract
The function of the CRISPR system can be conditionally controlled through rationally guided RNA engineering such that the target sequences can be precisely selected and manipulated. In particular, gRNA, as an important component of the CRISPR system, provides a unique tool for multifunctional control of the system based on the structure of the RNA itself. Therefore, we introduced here a protective group on the 2'-OH position of RNA to inhibit RNA-guided nucleic acid cleavage. Next, the modified gRNA can restore its original function under the chemical stimulation of hydrogen peroxide to realize the control of the CRISPR system. The experiment result demonstrated that the operating mechanism of this strategy may be based on chemical modifications that reduce the number of complementary base pairs between RNAs and targets, and the RNA-protein interaction. This further enriches the toolbox of conditional control of CRISPR function and has broad potential for gene editing in living cells and disease treatment using endogenous hydrogen peroxide.
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Affiliation(s)
- Huimin Ji
- The Institute of Molecular Medicine, Wuhan University People's Hospital, 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, 430072, Wuhan, Hubei, P. R. China
| | - Wei Xiong
- The Institute of Molecular Medicine, Wuhan University People's Hospital, 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, 430072, Wuhan, Hubei, P. R. China
| | - Kaisong Zhang
- The Institute of Molecular Medicine, Wuhan University People's Hospital, 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, 430072, Wuhan, Hubei, P. R. China
| | - Tian Tian
- The Institute of Molecular Medicine, Wuhan University People's Hospital, 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, 430072, Wuhan, Hubei, P. R. China
| | - Xiang Zhou
- The Institute of Molecular Medicine, Wuhan University People's Hospital, 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, 430072, Wuhan, Hubei, P. R. China
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18
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Xie S, Xu B, Tang R, Chen S, Lei C, Nie Z. Kinetics Accelerated CRISPR-Cas12a Enabling Live-Cell Monitoring of Mn 2+ Homeostasis. Anal Chem 2022; 94:10159-10167. [PMID: 35786883 DOI: 10.1021/acs.analchem.2c01461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The CRISPR/Cas12a system has been repurposed as a versatile nuclei acid bio-imaging tool, but its utility in sensing non-nucleic acid analytes in living cells has been less exploited. Herein, we demonstrated the ability of Mn2+ to accelerate cleavage kinetics of Cas12a and deployed for live-cell Mn2+ sensing by leveraging the accelerated trans-cleavage for signal reporting. In this work, we found that Mn2+ could significantly boost both the cis-cleavage and trans-cleavage activities of Cas12a. On the basis of this phenomenon, we harnessed CRISPR-Cas12a as a direct sensing system for Mn2+, which achieved robust Mn2+ detection in the concentration range of 0.5-700 μM within 15 min in complex biological samples. Furthermore, we also demonstrated the versatility of this system to sense Mn2+ in the cytoplasm of living cells. With the usage of a conditional guide RNA, this Cas12a-based sensing method was applied to study the cytotoxicity of Mn2+ in living nerve cells, offering a valuable tool to reveal the cellular response of nerve cells to Mn2+ disorder and homeostasis.
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Affiliation(s)
- Shiyi Xie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Benfeng Xu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Rui Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Siyu Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Chunyang Lei
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha 410082, People's Republic of China
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19
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Liu X, Xiong W, Qi Q, Zhang Y, Ji H, Cui S, An J, Sun X, Yin H, Tian T, Zhou X. Rational guide RNA engineering for small-molecule control of CRISPR/Cas9 and gene editing. Nucleic Acids Res 2022; 50:4769-4783. [PMID: 35446403 PMCID: PMC9071477 DOI: 10.1093/nar/gkac255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/30/2022] [Accepted: 04/10/2022] [Indexed: 12/24/2022] Open
Abstract
It is important to control CRISPR/Cas9 when sufficient editing is obtained. In the current study, rational engineering of guide RNAs (gRNAs) is performed to develop small-molecule-responsive CRISPR/Cas9. For our purpose, the sequence of gRNAs are modified to introduce ligand binding sites based on the rational design of ligand-RNA pairs. Using short target sequences, we demonstrate that the engineered RNA provides an excellent scaffold for binding small molecule ligands. Although the 'stem-loop 1' variants of gRNA induced variable cleavage activity for different target sequences, all 'stem-loop 3' variants are well tolerated for CRISPR/Cas9. We further demonstrate that this specific ligand-RNA interaction can be utilized for functional control of CRISPR/Cas9 in vitro and in human cells. Moreover, chemogenetic control of gene editing in human cells transfected with all-in-one plasmids encoding Cas9 and designer gRNAs is demonstrated. The strategy may become a general approach for generating switchable RNA or DNA for controlling other biological processes.
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Affiliation(s)
- 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
| | - 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
| | - 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
| | - Huimin Ji
- 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
| | - Jing An
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, Hubei, China
| | - Xiaoming Sun
- Department of Human Anatomy, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Hao Yin
- Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan 430071, 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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20
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Xiong W, Liu X, Qi Q, Ji H, Liu F, Zhong C, Liu S, Tian T, Zhou X. Supramolecular CRISPR-OFF switches with host-guest chemistry. Nucleic Acids Res 2022; 50:1241-1255. [PMID: 35100423 PMCID: PMC8860601 DOI: 10.1093/nar/gkac008] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 12/26/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeat) technology is a powerful tool in biology and medicine. However, the safety and application of this technology is hampered by excessive activity of CRISPR machinery. It is particularly important to develop methods for switching off CRISPR activity in human cells. The current study demonstrates the concept of supramolecular CRISPR-OFF switches by employing host-guest chemistry. We demonstrate that the CRISPR systems show considerable tolerance to adamantoylation on guide RNAs (gRNAs), whereas supramolecular complexation tremendously affects the function of adamantoyl gRNAs. Host-guest chemistry is demonstrated to be novel and effective tools to reduce unwanted excessive activities of CRISPR complexes in human cells. This work indicates considerable potential of supramolecular strategy for controlling and enhancing CRISPR systems.
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Affiliation(s)
- 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
| | - 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
| | - Huimin Ji
- 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
| | - Fengbo Liu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, Hubei, China
| | - Cheng Zhong
- 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
| | - Simin Liu
- School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, 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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21
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Liu X, Kang X, Lei C, Ren W, Liu C. Programming the trans-cleavage Activity of CRISPR-Cas13a by Single-Strand DNA Blocker and Its Biosensing Application. Anal Chem 2022; 94:3987-3996. [PMID: 35193353 DOI: 10.1021/acs.analchem.1c05124] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The precise and controllable programming of the trans-cleavage activity of the CRISPR-Cas13a systems is significant but challenging for fabricating high-performance biosensing systems toward various kinds of biomolecule targets. In this work, we have demonstrated that under a critical low Mg2+ concentration, a simple and short single-stranded DNA (ssDNA) probe free of any modification can efficiently prevent the assembly of crRNA and LwaCas13a only by partially binding with the crRNA repeat region, thereby blocking the trans-cleavage activity of the LwaCas13a system. Furthermore, we have demonstrated that the blocked trans-cleavage activity of the LwaCas13a system can be recovered by various kinds of biologically important substances as long as they could specifically release the blocker DNA from the crRNA in a target-responsive manner, providing a facile route for the quantification of diverse biomarkers such as enzymes, antigens/proteins, and exosomes. To the best of our knowledge, this is reported for the first time that a simple ssDNA can be employed as the switch element to control the crRNA structure and regulate the trans-cleavage activity of Cas13a, which has enriched the CRISPR-Cas13a sensing toolbox and will greatly expand its application scope.
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Affiliation(s)
- Xiaoling Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Xinyue Kang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Chao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi, P. R. China
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22
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Zhao J, Hu H, Zhang J, Li Y, Wang L, Zhou H, Wang R. Endogenous hydrogen peroxide can efficiently regulate CRISPR-Cas9 based gene editing. NEW J CHEM 2022. [DOI: 10.1039/d1nj04203c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report controllable gene editing tools for the CRISPR-Cas9 system via genetic code expansion triggered by oxidative small molecule H2O2.
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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, Hubei 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, Hubei 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, Hubei 430030, China
| | - Yuanyuan Li
- Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Li Wang
- Wuhan No. 1 Hospital, Huazhong University of Science and Technology, Wuhan, Hubei 430022, 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, Hubei 430030, 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, Hubei 430030, China
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23
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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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24
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation‐Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202112106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Lu Xiao
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Yong Woong Jun
- Department of Chemistry Stanford University Stanford CA 94305 USA
| | - Eric T. Kool
- Department of Chemistry Stanford University Stanford CA 94305 USA
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25
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Xiao L, Jun YW, Kool ET. DNA Tiling Enables Precise Acylation-Based Labeling and Control of mRNA. Angew Chem Int Ed Engl 2021; 60:26798-26805. [PMID: 34624169 PMCID: PMC8649056 DOI: 10.1002/anie.202112106] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/04/2021] [Indexed: 12/15/2022]
Abstract
Methods for the site-selective labeling of long, native RNAs are needed for studying mRNA biology and future therapies. Current approaches involve engineering RNA sequences, which may alter folding, or are limited to specific sequences or bases. Here, we describe a versatile strategy for mRNA conjugation via a novel DNA-tiling approach. The method, TRAIL, exploits a pool of "protector" oligodeoxynucleotides to hybridize and block the mRNA, combined with an "inducer" DNA that extrudes a reactive RNA loop for acylation at a predetermined site. Using TRAIL, an azido-acylimidazole reagent was employed for labeling and controlling RNA for multiple applications in vitro and in cells, including analysis of RNA-binding proteins, imaging mRNA in cells, and analysis and control of translation. The TRAIL approach offers an efficient and accessible way to label and manipulate RNAs of virtually any length or origin without altering native sequence.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
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26
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Park HS, Jash B, Xiao L, Jun YW, Kool ET. Control of RNA with quinone methide reversible acylating reagents. Org Biomol Chem 2021; 19:8367-8376. [PMID: 34528657 DOI: 10.1039/d1ob01713f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Caging RNA by polyacylation (cloaking) has been developed recently as a simple and rapid method to control the function of RNAs. Previous approaches for chemical reversal of acylation (uncloaking) made use of azide reduction followed by amine cyclization, requiring ∼2-4 h for the completion of cyclization. In new studies aimed at improving reversal rates and yields, we have designed novel acylating reagents that utilize quinone methide (QM) elimination for reversal. The QM de-acylation reactions were tested with two bioorthogonally cleavable motifs, azide and vinyl ether, and their acylation and reversal efficiencies were assessed with NMR and mass spectrometry on model small-molecule substrates as well as on RNAs. Successful reversal both with phosphines and strained alkenes was documented. Among the compounds tested, the azido-QM compound A-3 displayed excellent de-acylation efficiency, with t1/2 for de-acylation of less than an hour using a phosphine trigger. To test its function in RNA caging, A-3 was successfully applied to control EGFP mRNA translation in vitro and in HeLa cells. We expect that this molecular caging strategy can serve as a valuable tool for biological investigation and control of RNAs both in vitro and in cells.
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Affiliation(s)
- Hyun Shin Park
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Biswarup Jash
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Lu Xiao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Yong Woong Jun
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
| | - Eric T Kool
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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27
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Heiss TK, Dorn RS, Prescher JA. Bioorthogonal Reactions of Triarylphosphines and Related Analogues. Chem Rev 2021; 121:6802-6849. [PMID: 34101453 PMCID: PMC10064493 DOI: 10.1021/acs.chemrev.1c00014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Bioorthogonal phosphines were introduced in the context of the Staudinger ligation over 20 years ago. Since that time, phosphine probes have been used in myriad applications to tag azide-functionalized biomolecules. The Staudinger ligation also paved the way for the development of other phosphorus-based chemistries, many of which are widely employed in biological experiments. Several reviews have highlighted early achievements in the design and application of bioorthogonal phosphines. This review summarizes more recent advances in the field. We discuss innovations in classic Staudinger-like transformations that have enabled new biological pursuits. We also highlight relative newcomers to the bioorthogonal stage, including the cyclopropenone-phosphine ligation and the phospha-Michael reaction. The review concludes with chemoselective reactions involving phosphite and phosphonite ligations. For each transformation, we describe the overall mechanism and scope. We also showcase efforts to fine-tune the reagents for specific functions. We further describe recent applications of the chemistries in biological settings. Collectively, these examples underscore the versatility and breadth of bioorthogonal phosphine reagents.
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28
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Gu C, Xiao L, Shang J, Xu X, He L, Xiang Y. Chemical synthesis of stimuli-responsive guide RNA for conditional control of CRISPR-Cas9 gene editing. Chem Sci 2021; 12:9934-9945. [PMID: 34377390 PMCID: PMC8317661 DOI: 10.1039/d1sc01194d] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/18/2021] [Indexed: 12/23/2022] Open
Abstract
CRISPR-Cas9 promotes changes in identity or abundance of nucleic acids in live cells and is a programmable modality of broad biotechnological and therapeutic interest. To reduce off-target effects, tools for conditional control of CRISPR-Cas9 functions are under active research, such as stimuli-responsive guide RNA (gRNA). However, the types of physiologically relevant stimuli that can trigger gRNA are largely limited due to the lack of a versatile synthetic approach in chemistry to introduce diverse labile modifications into gRNA. In this work, we developed such a general method to prepare stimuli-responsive gRNA based on site-specific derivatization of 2′-O-methylribonucleotide phosphorothioate (PS-2′-OMe). We demonstrated CRISPR-Cas9-mediated gene editing in human cells triggered by oxidative stress and visible light, respectively. Our study tackles the synthetic challenge and paves the way for chemically modified RNA to play more active roles in gene therapy. Conditional control of CRISPR-Cas9 activity by reactive oxygen species and visible light is achieved using stimuli-responsive guide RNA synthesized by a general method based on RNA 2′-O-methylribonucleotide phosphorothioate.![]()
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Affiliation(s)
- Chunmei Gu
- 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
| | - Lu Xiao
- 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
| | - Jiachen Shang
- 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
| | - Xiao Xu
- 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
| | - Luo He
- 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
| | - 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
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29
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Charge-altering releasable transporters enable phenotypic manipulation of natural killer cells for cancer immunotherapy. Blood Adv 2021; 4:4244-4255. [PMID: 32898247 DOI: 10.1182/bloodadvances.2020002355] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/29/2020] [Indexed: 12/11/2022] Open
Abstract
Chimeric antigen receptor (CAR) natural killer (NK) cells are an emerging cell therapy with promising results in oncology trials. However, primary human NK cells are difficult to transfect, hampering both mechanistic studies and clinical applications of NK cells. Currently, NK cell CAR modification relies on viral vectors or cell activation. The former raises cost and tolerability issues, while the latter alters NK cell biology. Here, we report that readily synthesized and inexpensive nonviral charge-altering releasable transporters (CARTs) efficiently transfect primary human NK cells with messenger RNA without relying on NK cell activation. Compared with electroporation, CARTs transfect NK cells more efficiently, better preserve cell viability, and cause minimal reconfiguration of NK cell phenotype and function. We use CARTs to generate cytotoxic primary anti-CD19 CAR NK cells, demonstrating this technology can drive clinical applications of NK cells. To our knowledge, CARTs represent the first efficacious transfection technique for resting primary human NK cells that preserves NK cell phenotype and can enable new biological discoveries and therapeutic applications of this understudied lymphocyte subset.
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30
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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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31
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Lee YH, Yu E, Park CM. Programmable site-selective labeling of oligonucleotides based on carbene catalysis. Nat Commun 2021; 12:1681. [PMID: 33727561 PMCID: PMC7966772 DOI: 10.1038/s41467-021-21839-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 02/03/2021] [Indexed: 11/08/2022] Open
Abstract
Site-selective modification of oligonucleotides serves as an indispensable tool in many fields of research including research of fundamental biological processes, biotechnology, and nanotechnology. Here we report chemo- and regioselective modification of oligonucleotides based on rhodium(I)-carbene catalysis in a programmable fashion. Extensive screening identifies a rhodium(I)-catalyst that displays robust chemoselectivity toward base-unpaired guanosines in single and double-strand oligonucleotides with structurally complex secondary structures. Moreover, high regioselectivity among multiple guanosines in a substrate is achieved by introducing guanosine-bulge loops in a duplex. This approach allows the introduction of multiple unique functional handles in an iterative fashion, the utility of which is exemplified in DNA-protein cross-linking in cell lysates.
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Affiliation(s)
- Yang-Ha Lee
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea
| | - Eunsoo Yu
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea
| | - Cheol-Min Park
- Department of Chemistry, UNIST (Ulsan National Institute of Science & Technology), Ulsan, Korea.
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32
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Mino T, Sakamoto S, Hamachi I. Recent applications of N-acyl imidazole chemistry in chemical biology. Biosci Biotechnol Biochem 2021; 85:53-60. [PMID: 33577657 DOI: 10.1093/bbb/zbaa026] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/24/2020] [Indexed: 12/26/2022]
Abstract
N-Acyl imidazoles are unique electrophiles that exhibit moderate reactivity, relatively long-half life, and high solubility in water. Thanks to their tunable reactivity and chemical selectivity, the application of N-acyl imidazole derivatives has launched to a number of chemical biology researches, which include chemical synthesis of peptide/protein, chemical labeling of native proteins of interest (POIs), and structural analysis and functional manipulation of RNAs. Since proteins and RNAs play pivotal roles in numerous biological events in all living organisms, the methods that enable the chemical modification of endogenously existing POIs and RNAs in live cells may offer a variety of opportunities not only for fundamental scientific study but also for biotechnology and drug development. In this review, we discuss the recent progress of N-acyl imidazole chemistry that contributes to the chemical labeling and functional control of endogenous proteins and RNAs under multimolecularly crowded biological conditions of live cells.
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Affiliation(s)
- Takeharu Mino
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Seiji Sakamoto
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan.,ERATO, Japan Science and Technology Agency (JST), Chiyoda-ku, Tokyo, Japan
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33
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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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34
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Modell AE, Siriwardena SU, Shoba VM, Li X, Choudhary A. Chemical and optical control of CRISPR-associated nucleases. Curr Opin Chem Biol 2020; 60:113-121. [PMID: 33253976 DOI: 10.1016/j.cbpa.2020.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/10/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system of bacteria has furnished programmable nucleases (e.g., Cas9) that are transforming the field of genome editing with applications in basic and biomedical research, biotechnology, and agriculture. However, broader real-world applications of Cas9 require precision control of its activity over dose, time, and space as off-target effects, embryonic mosaicism, chromosomal translocations, and genotoxicity have been observed with elevated and/or prolonged nuclease activity. Here, we review chemical and optical methods for precision control of Cas9's activity.
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Affiliation(s)
- Ashley E Modell
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Sachini U Siriwardena
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Veronika M Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Xing Li
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA; Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA; Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, 02115, USA.
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35
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Knutson SD, Sanford AA, Swenson CS, Korn MM, Manuel BA, Heemstra JM. Thermoreversible Control of Nucleic Acid Structure and Function with Glyoxal Caging. J Am Chem Soc 2020; 142:17766-17781. [PMID: 33017148 DOI: 10.1021/jacs.0c08996] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Controlling the structure and activity of nucleic acids dramatically expands their potential for application in therapeutics, biosensing, nanotechnology, and biocomputing. Several methods have been developed to impart responsiveness of DNA and RNA to small-molecule and light-based stimuli. However, heat-triggered control of nucleic acids has remained largely unexplored, leaving a significant gap in responsive nucleic acid technology. Moreover, current technologies have been limited to natural nucleic acids and are often incompatible with polymerase-generated sequences. Here we show that glyoxal, a well-characterized compound that covalently attaches to the Watson-Crick-Franklin face of several nucleobases, addresses these limitations by thermoreversibly modulating the structure and activity of virtually any nucleic acid scaffold. Using a variety of DNA and RNA constructs, we demonstrate that glyoxal modification is easily installed and potently disrupts nucleic acid structure and function. We also characterize the kinetics of decaging and show that activity can be restored via tunable thermal removal of glyoxal adducts under a variety of conditions. We further illustrate the versatility of this approach by reversibly caging a 2'-O-methylated RNA aptamer as well as synthetic threose nucleic acid (TNA) and peptide nucleic acid (PNA) scaffolds. Glyoxal caging can also be used to reversibly disrupt enzyme-nucleic acid interactions, and we show that caging of guide RNA allows for tunable and reversible control over CRISPR-Cas9 activity. We also demonstrate glyoxal caging as an effective method for enhancing PCR specificity, and we cage a biostable antisense oligonucleotide for time-release activation and titration of gene expression in living cells. Together, glyoxalation is a straightforward and scarless method for imparting reversible thermal responsiveness to theoretically any nucleic acid architecture, addressing a significant need in synthetic biology and offering a versatile new tool for constructing programmable nucleic acid components in medicine, nanotechnology, and biocomputing.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Aimee A Sanford
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Colin S Swenson
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Megan M Korn
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Brea A Manuel
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M Heemstra
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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36
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Wang Y, Liu Y, Xie F, Lin J, Xu L. Photocontrol of CRISPR/Cas9 function by site-specific chemical modification of guide RNA. Chem Sci 2020; 11:11478-11484. [PMID: 34094391 PMCID: PMC8162494 DOI: 10.1039/d0sc04343e] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/25/2020] [Indexed: 12/27/2022] Open
Abstract
The function of CRISPR/Cas9 can be conditionally controlled by the rational engineering of guide RNA (gRNA) to target the gene of choice for precise manipulation of the genome. Particularly, chemically modified gRNA that can be activated by using specific stimuli provides a unique tool to expand the versatility of conditional control. Herein, unlike previous engineering of gRNA that generally focused on the RNA part only but neglected RNA-protein interactions, we aimed at the interactive sites between 2'-OH of ribose in the seed region of gRNA and the Cas9 protein and identified that chemical modifications at specific sites could be utilized to regulate the Cas9 activity. By introducing a photolabile group at these specific sites, we achieved optical control of Cas9 activity without disrupting the Watson-Crick base pairing. We further examined our design through CRISPR-mediated gene activation and nuclease cleavage in living cells and successfully manipulated the gene expression by using light irradiation. Our site-specific modification strategy exhibited a highly efficient and dynamic optical response and presented a new perspective for manipulating gRNA based on the RNA-protein interaction rather than the structure of RNA itself. In addition, these specific sites could also be potentially utilized for modification of other stimuli-responsive groups, which would further enrich the toolbox for conditional control of CRISPR/Cas9 function.
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Affiliation(s)
- Yang Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Yan Liu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Fan Xie
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Jiao Lin
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
| | - Liang Xu
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry, Sun Yat-Sen University Guangzhou 510275 China
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37
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Xiao L, Habibian M, Kool ET. Site-Selective RNA Functionalization via DNA-Induced Structure. J Am Chem Soc 2020; 142:16357-16363. [PMID: 32865995 PMCID: PMC7962339 DOI: 10.1021/jacs.0c06824] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Methods for RNA functionalization at specific sites are in high demand but remain a challenge, particularly for RNAs produced by transcription rather than by total synthesis. Recent studies have described acylimidazole reagents that react in high yields at 2'-OH groups stochastically at nonbase-paired regions, covering much of the RNA in scattered acyl esters. Localized reactions, if possible, could prove useful in many applications, providing functional handles at specific sites and sequences of the biopolymer. Here, we describe a DNA-directed strategy for in vitro functionalization of RNA at site-localized 2'-OH groups. The method, RNA Acylation at Induced Loops (RAIL), utilizes complementary helper DNA oligonucleotides that expose gaps or loops at selected positions while protecting the remainder in DNA-RNA duplexes. Reaction with an acylimidazole reagent is then carried out, providing high yields of 2'-OH conjugation at predetermined sites. Experiments reveal optimal helper oligodeoxynucleotide designs and conditions for the reaction, and tests of the approach are carried out to control localized ribozyme activities and to label RNAs with dual-color fluorescent dyes. The RAIL approach offers a simple and novel strategy for site-selective labeling and control of RNAs, potentially of any length and origin.
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Affiliation(s)
- Lu Xiao
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Maryam Habibian
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
| | - Eric T. Kool
- Department of Chemistry, ChEM-H Institute and Stanford Cancer Institute, Stanford University, Stanford, California 94305, United States
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38
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George JT, Azhar M, Aich M, Sinha D, Ambi UB, Maiti S, Chakraborty D, Srivatsan SG. Terminal Uridylyl Transferase Mediated Site-Directed Access to Clickable Chromatin Employing CRISPR-dCas9. J Am Chem Soc 2020; 142:13954-13965. [PMID: 32658470 PMCID: PMC7611130 DOI: 10.1021/jacs.0c06541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Locus-specific interrogation of target genes employing functional probes such as proteins and small molecules is paramount in decoding the molecular basis of gene function and designing tools to modulate its downstream effects. In this context, CRISPR-based gene editing and targeting technologies have proved tremendously useful, as they can be programmed to target any gene of interest by simply changing the sequence of the single guide RNA (sgRNA). Although these technologies are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using CRISPR system is not well developed due to the lack of adequate techniques. Here, we have devised an innovative technology called sgRNA-Click (sgR-CLK) that harnesses the power of bioorthogonal click chemistry for remodeling guide RNA to display synthetic molecules on target genes. sgR-CLK employs a novel posttranscriptional chemoenzymatic labeling platform wherein a terminal uridylyl transferase (TUTase) was repurposed to generate clickable sgRNA of choice by site-specific tailoring of multiple azide-modified nucleotide analogues at the 3' end. The presence of a minimally invasive azide handle assured that the sgRNAs are indeed functional. Notably, an azide-tailed sgRNA targeting the telomeric repeat served as a Trojan horse on the CRISPR-dCas9 system to guide synthetic tags (biotin) site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Taken together, sgR-CLK presents a significant advancement on the utility of bioorthogonal chemistry, TUTase, and the CRISPR toolbox, which could offer a simplified solution for site-directed display of small molecule probes and diagnostic tools on target genes.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | | | | | | | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Souvik Maiti
- Institute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research-NCL, Pune 411008, India
| | | | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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39
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Wang S, Wei L, Wang JQ, Ji H, Xiong W, Liu J, Yin P, Tian T, Zhou X. Light-Driven Activation of RNA-Guided Nucleic Acid Cleavage. ACS Chem Biol 2020; 15:1455-1463. [PMID: 32378871 DOI: 10.1021/acschembio.0c00105] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As one of the most favorable stimuli, photoactivation provides an advantageous way to manipulate biological objects. In the current study, we have successfully demonstrated the use of light activation guide RNA (gRNA) strategy for controlling CRISPR systems. By conjugating photolabile protecting groups, the CRISPR functions became minimal, but exposure of acylated gRNAs to 365 nm light triggers the removal of masking groups, leading to the rescue of CRISPR functions. Furthermore, our strategy has been successfully used to control gene editing in human cells. This proof-of-concept study therefore demonstrates the promising potential of our strategy to versatile applications in chemical biology.
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Affiliation(s)
- Shaoru Wang
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Lai Wei
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jia-Qi Wang
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Huimin Ji
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Wei Xiong
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Jian Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Tian Tian
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Sauvage Center for Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Institute of Advanced Studies, Wuhan University, Wuhan 430072, China
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