1
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Chen Y, Onizuka K, Nagatsugi F. Michael addition-activated alkylation of G-quadruplex DNA with methylamine-protected vinyl-quinazolinone derivatives. Bioorg Med Chem Lett 2024; 109:129855. [PMID: 38908766 DOI: 10.1016/j.bmcl.2024.129855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
The role of G-quadruplex (G4) in cellular processes can be investigated by the covalent modification of G4-DNA using alkylating reagents. Controllable alkylating reagents activated by external stimuli can react elegantly and selectively. Herein, we report a chemical activation system that can significantly boost the reaction rate of methylamine-protected vinyl-quinazolinone (VQ) derivative for the alkylation of G4-DNA. The two screened activators can transform low-reactive VQ-NHR' to highly reactive intermediates following the Michael addition mechanism. This approach expands the toolbox of activable G4 alkylating reagents.
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Affiliation(s)
- Yutong Chen
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan
| | - Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan; Division for the Establishment of Frontier Sciences of Organization for Advanced Studies, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan; Department of Chemistry, Graduate School of Science, Tohoku University, Aoba-ku, Sendai 980-8578, Japan.
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2
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Tomecki R, Drazkowska K, Madaj R, Mamot A, Dunin-Horkawicz S, Sikorski PJ. Expanding the Available RNA Labeling Toolbox With CutA Nucleotidyltransferase for Efficient Transcript Labeling with Purine and Pyrimidine Nucleotide Analogs. Chembiochem 2024:e202400202. [PMID: 38818670 DOI: 10.1002/cbic.202400202] [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: 03/05/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/01/2024]
Abstract
RNA labeling is an invaluable tool for investigation of the function and localization of nucleic acids. Labels are commonly incorporated into 3' end of RNA and the primary enzyme used for this purpose is RNA poly(A) polymerase (PAP), which belongs to the class of terminal nucleotidyltransferases (NTases). However, PAP preferentially adds ATP analogs, thus limiting the number of available substrates. Here, we report the use of another NTase, CutA from the fungus Thielavia terrestris. Using this enzyme, we were able to incorporate into the 3' end of RNA not only purine analogs, but also pyrimidine analogs. We engaged strain-promoted azide-alkyl cycloaddition (SPAAC) to obtain fluorescently labeled or biotinylated transcripts from RNAs extended with azide analogs by CutA. Importantly, modified transcripts retained their biological properties. Furthermore, fluorescently labeled mRNAs were suitable for visualization in cultured mammalian cells. Finally, we demonstrate that either affinity studies or molecular dynamic (MD) simulations allow for rapid screening of NTase substrates, what opens up new avenues in the search for the optimal substrates for this class of enzymes.
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Affiliation(s)
- Rafal Tomecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a, 02-106, Warsaw, Poland
| | - Karolina Drazkowska
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Rafal Madaj
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Adam Mamot
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Stanislaw Dunin-Horkawicz
- Laboratory of Structural Bioinformatics, Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Pawel J Sikorski
- Laboratory of Epitranscriptomics, Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Zwirki i Wigury 101, 02-089, Warsaw, Poland
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3
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Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [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: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
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Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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4
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Knaack JIH, Meier C. Out of the Dark, into the Light: Metabolic Fluorescent Labeling of Nucleic Acids. ChemMedChem 2024:e202400160. [PMID: 38712684 DOI: 10.1002/cmdc.202400160] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/08/2024]
Abstract
This review outlines recent advances in live-cell imaging techniques for nucleic acids. We describe the evolution of these methods, particularly highlighting the development of metabolic labeling approaches compatible with living systems using fluorescence-based labeling.
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Affiliation(s)
- J Iven H Knaack
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Chris Meier
- Department of Chemistry, Faculty of Sciences, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
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5
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Zhang Z, Wei W, Chen S, Yang J, Song D, Chen Y, Zhao Z, Chen J, Wang F, Wang J, Li Z, Liang Y, Yu H. Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity. J Am Chem Soc 2024; 146:7052-7062. [PMID: 38427585 DOI: 10.1021/jacs.4c00484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.
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Affiliation(s)
- Ze Zhang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Wanqing Wei
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China
| | - Siqi Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jintao Yang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Dongfan Song
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yinghan Chen
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zerun Zhao
- School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jiawen Chen
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Fulong Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Jiahuan Wang
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
| | - Zhe Li
- State Key Laboratory of Analytical Chemistry for Life Science, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing 210023, China
| | - Yong Liang
- State Key Laboratory of Coordination Chemistry, Jiangsu Key Laboratory of Advanced Organic Materials, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Hanyang Yu
- State Key Laboratory of Coordination Chemistry, Department of Biomedical Engineering, College of Engineering and Applied Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210023, China
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6
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Li T, Shu X, Gao M, Huang C, Li T, Cao J, Ying X, Liu D, Liu J. N4-Allylcytidine: a new nucleoside analogue for RNA labelling and chemical sequencing. RSC Chem Biol 2024; 5:225-235. [PMID: 38456037 PMCID: PMC10915972 DOI: 10.1039/d3cb00189j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/15/2023] [Indexed: 03/09/2024] Open
Abstract
RNA labelling has become indispensable in studying RNA biology. Nucleoside analogues with a chemical sequencing power represent desirable RNA labelling molecules because precise labelling information at base resolution can be obtained. Here, we report a new nucleoside analogue, N4-allylcytidine (a4C), which is able to tag RNA through both in vitro and in vivo pathways and further specifically reacts with iodine to form 3, N4-cyclized cytidine (cyc-C) in a catalyst-free, fast and complete manner. Full spectroscopic characterization concluded that cyc-C consisted of paired diastereoisomers with opposite chiral carbon centers in the fused 3, N4-five-membered ring. During RNA reverse transcription into complementary DNA, cyc-C induces base misincorporation due to the disruption of canonical hydrogen bonding by the cyclized structure and thus can be accurately identified by sequencing at single base resolution. With the chemical sequencing rationale of a4C, successful applications have been performed including pinpointing N4-methylcytidine methyltransferases' substrate modification sites, metabolically labelling mammalian cellular RNAs, and mapping active cellular RNA polymerase locations with the chromatin run-on RNA sequencing technique. Collectively, our work demonstrates that a4C is a promising molecule for RNA labelling and chemical sequencing and expands the toolkit for studying sophisticated RNA biology.
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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
| | - Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Minsong Gao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Chenyang Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Ting 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
| | - Jie Cao
- 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
| | - Xiner Ying
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University Yuhangtang Road 866 Hangzhou 310058 Zhejiang Province China
| | - Donghong 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
| | - 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
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7
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Kennebeck MM, Kaminsky CK, Massa MA, Das PK, Boyd RD, Bishka M, Tricarico JT, Silverman SK. DNAzyme-Catalyzed Site-Specific N-Acylation of DNA Oligonucleotide Nucleobases. Angew Chem Int Ed Engl 2024; 63:e202317565. [PMID: 38157448 PMCID: PMC10873475 DOI: 10.1002/anie.202317565] [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: 11/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/03/2024]
Abstract
We used in vitro selection to identify DNAzymes that acylate the exocyclic nucleobase amines of cytidine, guanosine, and adenosine in DNA oligonucleotides. The acyl donor was the 2,3,5,6-tetrafluorophenyl ester (TFPE) of a 5'-carboxyl oligonucleotide. Yields are as high as >95 % in 6 h. Several of the N-acylation DNAzymes are catalytically active with RNA rather than DNA oligonucleotide substrates, and eight of nine DNAzymes for modifying C are site-specific (>95 %) for one particular substrate nucleotide. These findings expand the catalytic ability of DNA to include site-specific N-acylation of oligonucleotide nucleobases. Future efforts will investigate the DNA and RNA substrate sequence generality of DNAzymes for oligonucleotide nucleobase N-acylation, toward a universal approach for site-specific oligonucleotide modification.
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Affiliation(s)
- Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Caroline K Kaminsky
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Maria A Massa
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Prakriti K Das
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Michelle Bishka
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - J Tomas Tricarico
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
| | - Scott K Silverman
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL-61801, USA
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8
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Beghennou A, Rondot O, Corcé V, Botuha C. 1 H-1,2,3-triazolyl-1,6-naphthyridin-7(6 H)-ones as Potential Fluorescent Nucleoside Analogues: Synthesis and Optical Properties. Molecules 2024; 29:687. [PMID: 38338431 PMCID: PMC10856630 DOI: 10.3390/molecules29030687] [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: 12/08/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
In this article, we present the synthesis and the optical properties of three original molecules as potential fluorescent ribonucleoside analogues incorporating a 1,6-naphthyridin-7(6H)-one scaffold as a fluorescent nucleobase and a 1,2,3-triazole as a linkage. The nucleosides were prepared via a Cu alkyne-azide cycloaddition (CuAAC) reaction between a ribofuranosyl azide and a 4-ethynylpyridine partner. Construction of substituted 1,6-naphthyridin-7(6H)-ones was achieved through two additional steps. Optical property studies were investigated on nucleoside analogues. Powerful fluorescence properties have been evidenced with a remarkable change of emissivity depending on the polarity of the solvent, making these molecules suitable as a new class of artificial fluorescent nucleosides for investigating enzyme binding sites as well as probing nucleic acids. In addition, we are convinced that such analogues could be of great interest in the search for new antiviral or antitumoral drugs based on nucleosides.
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Affiliation(s)
| | | | - Vincent Corcé
- Institut Parisien de Chimie Moléculaire, CNRS UMR 9232, Sorbonne Université, F-75252 Paris, France; (A.B.); (O.R.)
| | - Candice Botuha
- Institut Parisien de Chimie Moléculaire, CNRS UMR 9232, Sorbonne Université, F-75252 Paris, France; (A.B.); (O.R.)
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9
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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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10
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Cappannini A, Ray A, Purta E, Mukherjee S, Boccaletto P, Moafinejad SN, Lechner A, Barchet C, Klaholz B, Stefaniak F, Bujnicki JM. MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic Acids Res 2024; 52:D239-D244. [PMID: 38015436 PMCID: PMC10767930 DOI: 10.1093/nar/gkad1083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/19/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB PDB database more effectively. To manage the increased number of modifications, adjustments to the nomenclature system were made. Updates in the RNA sequences section include the addition of new sequences and the reintroduction of sequence alignments for tRNAs and rRNAs. The protein section was updated and connected to structures from the RCSB PDB database and predictions by AlphaFold. MODOMICS now includes a data annotation system, with 'Evidence' and 'Estimated Reliability' features, offering clarity on data support and accuracy. This system is open to all MODOMICS entries, enhancing the accuracy of RNA modification data representation. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.
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Affiliation(s)
- Andrea Cappannini
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Angana Ray
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Elżbieta Purta
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Sunandan Mukherjee
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Pietro Boccaletto
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - S Naeim Moafinejad
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Antony Lechner
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Charles Barchet
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC, 1 rue Laurent Fries, Illkirch, France; Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale (Inserm) U964, Illkirch, France; Université de Strasbourg, Strasbourg, France
| | - Filip Stefaniak
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, ul. Ks. Trojdena 4, PL-02-109 Warsaw, Poland
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11
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Okuda T, Lenz AK, Seitz F, Vogel J, Höbartner C. A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells. Nat Chem 2023; 15:1523-1531. [PMID: 37667013 PMCID: PMC10624628 DOI: 10.1038/s41557-023-01320-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/08/2023] [Indexed: 09/06/2023]
Abstract
Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.
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Affiliation(s)
- Takumi Okuda
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ann-Kathrin Lenz
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Florian Seitz
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Center for Nanosystems Chemistry (CNC), Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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12
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Chandankar SS, Kondhare D, Leonard P, Seela F. Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine-7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts. J Org Chem 2023; 88:13149-13168. [PMID: 37669119 DOI: 10.1021/acs.joc.3c01370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Purine DNA represents an alternative pairing system formed by two purines in the base pair with the recognition elements of Watson-Crick DNA. Base functionalization of 7-deaza-2'-deoxyxanthosine with ethynyl and octadiynyl residues led to clickable side chain derivatives with short and long linker arms. As complementary bases, purine-2,6-diamine or 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides were used. 7-Deaza-7-iodo-2'-deoxyxanthosine served as a starting material for Sonogashira cross-coupling and the p-nitrophenylethyl group for base protection. Phosphoramidite building blocks for DNA synthesis were prepared. Oligonucleotides containing single modifications or runs of three purine base pairs embedded in 12-mer Watson-Crick DNA were synthesized and hybridized with complementary strands with purine- or 7-deazapurine-2,6-diamine located opposite to the xanthine derivatives. The stability of base pairs was evaluated in a comparative study on the basis of DNA melting experiments and Tm values. As 7-deazaxanthine and xanthine nucleosides form anionic forms at neutral pH, duplex stability became pK-dependent, and the system with 7-deazapurine displayed a significant higher stability as that containing xanthine. Alkynyl side chains are well accommodated in the purine-purine helix. Click adducts with pyrene showed that short linker arms destabilize duplexes, whereas long linkers increase duplex stability. CD and fluorescence measurements provide further insights into purine-purine base pairing.
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Affiliation(s)
- Somnath Shivaji Chandankar
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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13
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Shu X, Huang C, Li T, Cao J, Liu J. a 6A-seq: N 6-allyladenosine-based cellular messenger RNA metabolic labelling and sequencing. FUNDAMENTAL RESEARCH 2023; 3:657-664. [PMID: 38933292 PMCID: PMC11197751 DOI: 10.1016/j.fmre.2023.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/04/2023] [Accepted: 04/19/2023] [Indexed: 06/28/2024] Open
Abstract
The integration of RNA metabolic labelling by nucleoside analogues with high-throughput RNA sequencing has been harnessed to study RNA dynamics. The immunoprecipitation purification or chemical pulldown technique is generally required to enrich the analogue-labelled RNAs. Here we developed an a6A-seq method, which takes advantage of N6-allyladenosine (a6A) metabolic labelling on cellular mRNAs and profiles them in an immunoprecipitation-free and mutation-based manner. a6A plays a role as a chemical sequencing tag in that the iodination of a6A in mRNAs results in 1,N 6-cyclized adenosine (cyc-A), which induces base misincorporation during RNA reverse transcription, thus making a6A-labelled mRNAs detectable by sequencing. A nucleic acid melting assay was utilized to investigate why cyc-A prefers to be paired with guanine. a6A-seq was utilized to study cellular gene expression changes under a methionine-free stress condition. Compared with regular RNA-seq, a6A-seq could more sensitively detect the change of mRNA production over a time scale. The experiment of a6A-containing mRNA immunoprecipitation followed by qPCR successfully validated the high-throughput a6A-seq data. Together, our results show a6A-seq is an effective tool to study RNA dynamics.
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Affiliation(s)
- Xiao Shu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Chenyang Huang
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Tengwei Li
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
| | - Jie Cao
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
- Life Sciences Institute, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
| | - Jianzhao Liu
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Zheda Road 38, Hangzhou 310027, China
- Life Sciences Institute, Zhejiang University, 866 Yuhangtang Rd, Hangzhou 310058, China
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14
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Bassi T, Hirlinger A, Grayson L, Vantourout J, Toor N. Fluorescent labeling of RNA and DNA on the Hoogsteen edge using sulfinate chemistry. RNA (NEW YORK, N.Y.) 2023; 29:1437-1451. [PMID: 37277186 PMCID: PMC10573292 DOI: 10.1261/rna.079679.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/12/2023] [Indexed: 06/07/2023]
Abstract
We have devised a single pot, low-cost method to add azide groups to unmodified nucleic acids without the need for enzymes or chemically modified nucleoside triphosphates. This involves reacting an azide-containing sulfinate salt with the nucleic acid, leading to replacement of C-H bonds on the nucleobase aromatic rings with C-R, where R is the azide-containing linker derived from the original sulfinate salt. With the addition of azide functional groups, the modified nucleic acid can easily be reacted with any alkyne-labeled compound of interest, including fluorescent dyes as shown in this work. This methodology enables the fluorescent labeling of a wide variety of nucleic acids, including natively folded RNAs, under mild conditions with minimal effects upon biochemical function and ribozyme catalysis. To demonstrate this, we show that a pair of labeled complementary ssDNA oligonucleotides (oligos) can hybridize to form dsDNA, even when labeled with multiple fluorophores per oligo. In addition, we also demonstrate that two different group II introns can splice when prelabeled internally with fluorophores, using our method. Broadly, this demonstrates that sulfinate modification of RNA is compatible with ribozyme function and Watson-Crick pairing, while preserving the labile backbone.
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Affiliation(s)
- Tiziano Bassi
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Anastassia Hirlinger
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Leah Grayson
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
| | - Julien Vantourout
- Department of Chemistry, Scripps Research, La Jolla, California 92037, USA
| | - Navtej Toor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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15
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Basran K, Bujalska A, Karimi A, Luedtke NW. Formal [4 + 2] Cycloadditions of Maleimides on Duplex DNA. Bioconjug Chem 2023; 34:977-982. [PMID: 37290129 DOI: 10.1021/acs.bioconjchem.3c00090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Near-quantitative DNA bioconjugation and detailed mechanistic investigations of reactions involving 5-(vinyl)-2'-deoxyuridine (VdU) and maleimides are reported. According to accelerated reaction rates in solvents with increasing polarity and trends in product stereochemistry, VdU-maleimide reactions proceed via a formal [4 + 2] stepwise cycloaddition. In contrast, 5-(1,3-butadienyl)-2'-deoxyuridine (BDdU) reacts with maleimides in a concerted [4 + 2] Diels-Alder cycloaddition. VdU-maleimide reactions enable high-yielding bioconjugation of duplex DNA in vitro (>90%) as well as metabolic labeling experiments in cells.
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Affiliation(s)
- Kaleena Basran
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ashkan Karimi
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montreal, Quebec H3A 0B8, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec H3G 1Y6, Canada
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16
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Satusky MJ, Johnson CV, Erie DA. Rapid, inexpensive, sequence-independent fluorescent labeling of phosphorothioate DNA. Biophys J 2023; 122:1211-1218. [PMID: 36793216 PMCID: PMC10111259 DOI: 10.1016/j.bpj.2023.02.011] [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: 08/26/2022] [Revised: 01/23/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Fluorescently labeled oligonucleotides are powerful tools for characterizing DNA processes; however, their use is limited by the cost and sequence requirements of current labeling technologies. Here, we develop an easy, inexpensive, and sequence-independent method for site-specifically labeling DNA oligonucleotides. We utilize commercially synthesized oligonucleotides containing phosphorothioate diester(s) in which a nonbridging oxygen is replaced with a sulfur (PS-DNA). The increased nucleophilicity of the thiophosphoryl sulfur relative to the phosphoryl oxygen permits selective reactivity with iodoacetamide compounds. As such, we leverage a long-existing bifunctional linker, N,N'-bis(α-iodoacetyl)-2-2'-dithiobis(ethylamine) (BIDBE), that reacts with PS-DNAs to leave a free thiol, allowing conjugation of the wide variety of commercial maleimide-functionalized compounds. We optimized BIDBE synthesis and its attachment to PS-DNA and then fluorescently labeled the BIDBE-PS-DNA using standard protocols for labeling cysteines. We purified the individual epimers, and using single-molecule Förster resonance energy transfer (FRET), we show that the FRET efficiency is independent of the epimeric attachment. Subsequently, we demonstrate that an epimeric mixture of double-labeled Holliday junctions (HJs) can be used to characterize their conformational properties in the absence and presence of the structure-specific endonuclease Drosophila melanogaster Gen. Finally, we use a biochemical activity assay to show that this double-labeled HJ is functional for cleavage by Gen and that the double-labeled HJ allows multiple DNA species to be identified in a single experiment. In conclusion, our results indicate that dye-labeled BIDBE-PS-DNAs are comparable to commercially labeled DNAs at a significantly reduced cost. Notably, this technology could be applied to other maleimide-functionalized compounds, such as spin labels, biotin, and proteins. The sequence independence of labeling, coupled with its ease and low cost, enables unrestricted exploration of dye placement and choice, providing the potential for creation of differentially labeled DNA libraries and opening previously inaccessible experimental avenues.
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Affiliation(s)
- Matthew J Satusky
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Caitlin V Johnson
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina
| | - Dorothy A Erie
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina; Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina.
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17
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Chatterjee S, Shioi R, Kool ET. Sulfonylation of RNA 2'-OH groups. ACS CENTRAL SCIENCE 2023; 9:531-539. [PMID: 36968531 PMCID: PMC10037496 DOI: 10.1021/acscentsci.2c01237] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Indexed: 06/18/2023]
Abstract
The nucleophilic reactivity of RNA 2'-OH groups in water has proven broadly useful in probing, labeling, and conjugating RNA. To date, reactions selective to ribose 2'-OH have been limited to bond formation with short-lived carbonyl electrophiles. Here we report that many activated small-molecule sulfonyl species can exhibit extended lifetimes in water and retain 2'-OH reactivity. The data establish favorable aqueous solubility for selected reagents and successful RNA-selective reactions at stoichiometric and superstoichiometric yields, particularly for aryl sulfonyltriazole species. We report that the latter are considerably more stable than most prior carbon electrophiles in aqueous environments and tolerate silica chromatography. Furthermore, an azide-substituted sulfonyltriazole reagent is developed to introduce labels into RNA via click chemistry. In addition to high-yield reactions, we find that RNA sulfonylation can also be performed under conditions that give trace yields necessary for structure mapping. Like acylation, the reaction occurs with selectivity for unpaired nucleotides over those in the duplex structure, and a sulfonate adduct causes reverse transcriptase stops, suggesting potential use in RNA structure analysis. Probing of rRNA is demonstrated in human cells, indicating possible cell permeability. The sulfonyl reagent class enables a new level of control, selectivity, versatility, and ease of preparation for RNA applications.
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Affiliation(s)
- Sayantan Chatterjee
- Department of Chemistry, Stanford
University, Stanford, California 94305, United States
| | - Ryuta Shioi
- 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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18
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Michenfelder RT, Delafresnaye L, Truong VX, Barner-Kowollik C, Wagenknecht HA. DNA labelling in live cells via visible light-induced [2+2] photocycloaddition. Chem Commun (Camb) 2023; 59:4012-4015. [PMID: 36920883 DOI: 10.1039/d3cc00817g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
We introduce a visible light-driven (λmax = 451 nm) photo-chemical strategy for labelling of DNA in living HeLa cells via the [2+2] cycloaddition of a styrylquinoxaline moiety, which we incorporate into both the DNA and the fluorescent label. Our methodology offers advanced opportunities for the mild remote labelling of DNA in water while avoiding UV light activation.
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Affiliation(s)
- Rita T Michenfelder
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 6, Karlsruhe 76131, Germany.
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT), 2 George St, Brisbane QLD 4000, Australia.
| | - Laura Delafresnaye
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT), 2 George St, Brisbane QLD 4000, Australia.
| | - Vinh X Truong
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT), 2 George St, Brisbane QLD 4000, Australia.
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), 2 Fusionopolis Way, 138634, Singapore.
| | - Christopher Barner-Kowollik
- School of Chemistry and Physics, Centre for Materials Science, Queensland University of Technology (QUT), 2 George St, Brisbane QLD 4000, Australia.
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, Eggenstein-Leopoldshafen 76344, Germany.
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber Weg 6, Karlsruhe 76131, Germany.
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19
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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20
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Kanlidere Z. Template-Directed Incorporation of Functional Molecules into DNA. Chembiochem 2023; 24:e202200554. [PMID: 36520932 DOI: 10.1002/cbic.202200554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
We report a versatile method for the incorporation of functional molecules into oligonucleotides carrying reactive groups by using a template-directed postsynthetic approach in the solution phase. For this purpose, we prepared oligonucleotides carrying an amino group on the backbone by using an acylic threoninol scaffold. The resulting oligonucleotides could be used to introduce almost any molecule carrying aldehyde, which can be, among other things, a metal-binding ligand or a fluorophore. In our study, we incorporated aldehyde-bearing phenanthroline, a metal-binding ligand, into oligonucleotides by template-directed reversible conjugation. We observed that the use of an abasic sugar site instead of a natural nucleobase in the template strand increased the yield of conjugation and induced selective incorporation of the phenanthroline. This method could lead progress in the development of probes for the recognition of abasic regions in duplex DNA. Moreover, template-directed formation of metal ligand-oligonucleotide conjugates might have potential applications in hybrid biocatalysis for enantioselective transformations.
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Affiliation(s)
- Zeynep Kanlidere
- Department of Basic Pharmaceutical Sciences, Faculty of Pharmacy, Acibadem Mehmet Ali Aydinlar University, Kayisdagi Cad. No: 32 Atasehir, 34752, Istanbul, Turkey
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21
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He M, Sato Y, Nishizawa S. Classical thiazole orange and its regioisomer as fluorogenic probes for nucleolar RNA imaging in living cells. Analyst 2023; 148:636-642. [PMID: 36602142 DOI: 10.1039/d2an01804g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In contrast to well-established DNA-selective dyes for live cell imaging, RNA-selective dyes have been less developed owing to the challenges of making small molecules have RNA selectivity over DNA. Two kinds of dyes are now commercially available for nucleolar RNA imaging in cells, but these two dyes do not apply to living cells and have limited use in fixed and permeabilized cells. Herein, we report on thiazole orange (TO), a well-known nucleic acid stain, as a promising fluorogenic dye for nucleolar RNA imaging in living cells. TO shows clear response selectivity for RNA over DNA with a significant light-up property upon binding to RNA (λem = 532 nm, I/I0 = 580-fold, and Φbound/Φfree = 380) and is even applicable to wash-free imaging of living cells. More interestingly, 2TO, a regioisomer of TO in which the benzothiazole unit is connected to position 2 in the quinoline ring, performs much better (λem = 532 nm, I/I0 = 430-fold, Φbound/Φfree = 1200), having superior selectivity for RNA in both solution and living cells. The comparison with TO derivatives carrying different substituents at N1 of the quinoline ring reveals that the slight change in the TO framework significantly affects RNA selectivity, photostability and membrane permeability.
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Affiliation(s)
- Mengmeng He
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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22
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Wang W, Deng J, Zhang Y, Li J. A Small-Molecule Probe with a Dual Function of miRNA Inhibition and Target identification. Chemistry 2023; 29:e202202013. [PMID: 36253322 DOI: 10.1002/chem.202202013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Indexed: 11/07/2022]
Abstract
By virtue of their key roles in pathologies, miRNAs represent a promising class of therapeutic targets. While high-fidelity small-molecule modulators of miRNAs can be identified via high-throughput screening using cellular reporter systems, their modes of action are elusive due to the lack of proper tools. Here, we report a small-molecule probe, 1 a, that is capable of elucidating its biological target along miRNA inhibition. Derived from norathyriol, a nature product, 1 a possessed a bioorthogonal alkyne moiety for subsequent labeling via copper-catalyzed azide-alkyne cycloaddition chemistry. We demonstrated that 1 a inhibited a panel of different miRNAs by blocking their loading onto argonaute 2 (AGO2), which is the key protein responsible for miRNA function. With the alkyne handle, we successfully identified AGO2 as an intracellular target of 1 a. Therefore, this work presents a novel small-molecule tool for suppressing and probing miRNA regulatory pathways.
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Affiliation(s)
- Weishan Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, P. R. China
| | - Jiafang Deng
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, P. R. China
| | - Yan Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, P. R. China
| | - Jinbo Li
- State Key Laboratory of Analytical Chemistry for Life Sciences, Jiangsu Key Laboratory of Advanced Organic Materials, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, 210023, P. R. China
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23
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Lakshman MK. Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents, and Beyond. CHEM REC 2023; 23:e202200182. [PMID: 36166699 DOI: 10.1002/tcr.202200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/26/2022] [Indexed: 01/24/2023]
Abstract
Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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24
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Dhami I, Thadke SA, Ly DH. Development of the Right- and Left-Handed Gamma Peptide Nucleic Acid Building Blocks for On-Resin Chemical Functionalization. J Org Chem 2022; 87:13873-13881. [PMID: 36190146 DOI: 10.1021/acs.joc.2c01560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gamma peptide nucleic acids (PNAs) are a promising class of nucleic acid mimics that adopt either a right- or left-handed helical motif as individual strands and hybridize to DNA or RNA with high affinity and sequence specificity, or not at all, depending on the helical sense. They are attractive as antisense and antigene reagents, as well as building blocks for molecular self-assembly; however, they have not been widely adopted due to their relatively poor biophysical attributes and the challenge in chemical modifications. Here, we report the development of a set of universal monomers, four each for both the right- and left-handed conformers, that permit rapid and selective on-resin chemical functionalization and diversification. The system is modular, permitting incorporation of different chemical groups in the backbone without causing adverse effects on hybridization. The approach overcomes the need to prepare a new set of monomers each time a different chemical group is introduced in the backbone. The newly added synthetic flexibility, along with superior hybridization property, recognition orthogonality, and helical sense translational capability, significantly expands the scope of gamma PNA in biology, biotechnology, and molecular engineering.
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Affiliation(s)
- Isha Dhami
- Department of Chemistry and Institute for Bimolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Shivaji A Thadke
- Department of Chemistry and Institute for Bimolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
| | - Danith H Ly
- Department of Chemistry and Institute for Bimolecular Design and Discovery (IBD), Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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25
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Kaiser F, Endeward B, Collauto A, Scheffer U, Prisner TF, Göbel MW. Spin-Labeled Riboswitch Synthesized from a Protected TPA Phosphoramidite Building Block. Chemistry 2022; 28:e202201822. [PMID: 35903916 PMCID: PMC9804336 DOI: 10.1002/chem.202201822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Indexed: 01/05/2023]
Abstract
The nitroxide TPA (2,2,5,5-tetramethyl-pyrrolin-1-oxyl-3-acetylene) is an excellent spin label for EPR studies of RNA. Previous synthetic methods, however, are complicated and require special equipment. Herein, we describe a uridine derived phosphoramidite with a photocaged TPA unit attached. The light sensitive 2-nitrobenzyloxymethyl group can be removed in high yield by short irradiation at 365 nm. Based on this approach, a doubly spin-labeled 27mer neomycin sensing riboswitch was synthesized and studied by PELDOR. The overall thermal stability of the fold is not much reduced by TPA. In-line probing nevertheless detected changes in local mobility.
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Affiliation(s)
- Frank Kaiser
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Burkhard Endeward
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Alberto Collauto
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Ute Scheffer
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Thomas F. Prisner
- Institute for Physical and Theoretical ChemistryGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
| | - Michael W. Göbel
- Institute for Organic Chemistry and Chemical BiologyGoethe University FrankfurtMax-von-Laue-Strasse 760438Frankfurt am MainGermany
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26
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Moreno S, Ramos Pittol JM, Hartl M, Micura R. Robust synthesis of 2'-azido modified RNA from 2'-amino precursors by diazotransfer reaction. Org Biomol Chem 2022; 20:7845-7850. [PMID: 36172831 DOI: 10.1039/d2ob01560a] [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
Azides are versatile bioorthogonal reporter moieties that are commonly used for site-specific labeling and functionalization of RNA to probe its biology. The preparation of azido modified nucleic acids by solid-phase synthesis is problematic due to the inherent reactivity of P(III) species with azides according to the Staudinger reaction. Various strategies have been developed to bypass this limitation and are often time-consuming, low-yielding and labor-intensive. In particular, the synthesis of RNA with internal 2'-azido modifications is restricted to a single approach that employs P(V) chemistry instead of the widely used P(III) phosphoramidite chemistry. To fill this methodological gap, we present a novel convenient path toward 2'-azido RNA from readily accessible 2'-amino RNA through treatment with the diazotizing reagent fluorosulfuryl azide (FSO2N3). A diazotransfer reaction was established for oligoribonucleotides of different lengths and secondary structures. The robustness of the approach was further demonstrated for RNAs containing multiple 2'-azido moieties and for RNAs containing other sensitive modifications such as thiouridine or methylated nucleobases with a positive charge. The synthetic ease of generating 2'-azido RNA will pave the way for biotechnological applications, in particular for siRNA technologies and for referencing the growing number of RNA metabolic labeling approaches that rely on 2'-azido nucleosides.
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Affiliation(s)
- Sarah Moreno
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
| | - José M Ramos Pittol
- Institute of Biochemistry, Center for Chemistry and Biomedicine (CCB) Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Markus Hartl
- Institute of Biochemistry, Center for Chemistry and Biomedicine (CCB) Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
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27
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Qin G, Yang J, Zhao C, Ren J, Qu X. Manipulating complex chromatin folding via CRISPR-guided bioorthogonal chemistry. Proc Natl Acad Sci U S A 2022; 119:e2204725119. [PMID: 36037371 PMCID: PMC9457169 DOI: 10.1073/pnas.2204725119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
Precise manipulation of chromatin folding is important for understanding the relationship between the three-dimensional genome and nuclear function. Existing tools can reversibly establish individual chromatin loops but fail to manipulate two or more chromatin loops. Here, we engineer a powerful CRISPR system which can manipulate multiple chromatin contacts using bioorthogonal reactions, termed the bioorthogonal reaction-mediated programmable chromatin loop (BPCL) system. The multiinput BPCL system employs engineered single-guide RNAs recognized by discrete bioorthogonal adaptors to independently and dynamically control different chromatin loops formation without cross-talk in the same cell or to establish hubs of multiway chromatin contacts. We use the BPCL system to successfully juxtapose the pluripotency gene promoters to enhancers and activate their endogenous expression. BPCL enables us to independently engineer multiway chromatin contacts without cross-talk, which provides a way to precisely dissect the high complexity and dynamic nature of chromatin folding.
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Affiliation(s)
- Geng Qin
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Jie Yang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Chuanqi Zhao
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Jinsong Ren
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
| | - Xiaogang Qu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People’s Republic of China
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Changchun 130022, People’s Republic of China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei 230026, People’s Republic of China
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28
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Efficient DNA fluorescence labeling via base excision trapping. Nat Commun 2022; 13:5043. [PMID: 36028479 PMCID: PMC9418136 DOI: 10.1038/s41467-022-32494-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 08/03/2022] [Indexed: 01/19/2023] Open
Abstract
Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.
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29
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Wang D, Shalamberidze A, Arguello AE, Purse BW, Kleiner RE. Live-Cell RNA Imaging with Metabolically Incorporated Fluorescent Nucleosides. J Am Chem Soc 2022; 144:14647-14656. [PMID: 35930766 PMCID: PMC9940818 DOI: 10.1021/jacs.2c04142] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence imaging is a powerful method for probing macromolecular dynamics in biological systems; however, approaches for cellular RNA imaging are limited to the investigation of individual RNA constructs or bulk RNA labeling methods compatible primarily with fixed samples. Here, we develop a platform for fluorescence imaging of bulk RNA dynamics in living cells. We show that fluorescent bicyclic and tricyclic cytidine analogues can be metabolically incorporated into cellular RNA by overexpression of uridine-cytidine kinase 2. In particular, metabolic feeding with the tricyclic cytidine-derived nucleoside tC combined with confocal imaging enables the investigation of RNA synthesis, degradation, and trafficking at single-cell resolution. We apply our imaging modality to study RNA metabolism and localization during the oxidative stress response and find that bulk RNA turnover is greatly accelerated upon NaAsO2 treatment. Furthermore, we identify cytoplasmic RNA granules containing RNA transcripts generated during oxidative stress that are distinct from canonical stress granules and P-bodies and co-localize with the RNA helicase DDX6. Taken together, our work provides a powerful approach for live-cell RNA imaging and reveals how cells reshape RNA transcriptome dynamics in response to oxidative stress.
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Affiliation(s)
- Danyang Wang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Ana Shalamberidze
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | | | - Byron W. Purse
- Department of Chemistry and Biochemistry and the Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Ralph E. Kleiner
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
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30
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Arney JW, Weeks KM. RNA-Ligand Interactions Quantified by Surface Plasmon Resonance with Reference Subtraction. Biochemistry 2022; 61:1625-1632. [PMID: 35802500 PMCID: PMC9357220 DOI: 10.1021/acs.biochem.2c00177] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structured RNAs bind ligands and are attractive targets for small-molecule drugs. A wide variety of analytical methods have been used to characterize RNA-ligand interactions, but our experience is that most have significant limitations in terms of material requirements and applicability to complex RNAs. Surface plasmon resonance (SPR) potentially overcomes these limitations, but we find that the standard experimental framework measures notable nonspecific electrostatic-mediated interactions, frustrating analysis of weak RNA binders. SPR measurements are typically quantified relative to a non-target reference channel. Here, we show that referencing to a channel containing a non-binding control RNA enables subtraction of nonspecific binding contributions, allowing measurements of accurate and specific binding affinities. We validated this approach for small-molecule binders of two riboswitch RNAs with affinities ranging from nanomolar to millimolar, including low-molecular-mass fragment ligands. SPR implemented with reference subtraction reliably discriminates specific from nonspecific binding, uses RNA and ligand material efficiently, and enables rapid exploration of the ligand-binding landscape for RNA targets.
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Affiliation(s)
- J. Winston Arney
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
| | - Kevin M. Weeks
- Department of Chemistry, University of North Carolina, Chapel Hill, NC
27599-3290
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31
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Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG. Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J Am Chem Soc 2022; 144:10556-10569. [PMID: 35666775 DOI: 10.1021/jacs.2c03454] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.
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Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Heike M Kropp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Samra Ludmann
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - 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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32
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Loehr MO, Luedtke NW. A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2022; 61:e202112931. [PMID: 35139255 DOI: 10.1002/anie.202112931] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 12/21/2022]
Abstract
Chemical modification of nucleic acids in living cells can be sterically hindered by tight packing of bioorthogonal functional groups in chromatin. To address this limitation, we report here a dual enhancement strategy for nucleic acid-templated reactions utilizing a fluorogenic intercalating agent capable of undergoing inverse electron-demand Diels-Alder (IEDDA) reactions with DNA containing 5-vinyl-2'-deoxyuridine (VdU) or RNA containing 5-vinyl-uridine (VU). Reversible high-affinity intercalation of a novel acridine-tetrazine conjugate "PINK" (KD =5±1 μM) increases the reaction rate of tetrazine-alkene IEDDA on duplex DNA by 60 000-fold (590 M-1 s-1 ) as compared to the non-templated reaction. At the same time, loss of tetrazine-acridine fluorescence quenching renders the reaction highly fluorogenic and detectable under no-wash conditions. This strategy enables live-cell dynamic imaging of acridine-modified nucleic acids in dividing cells.
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Affiliation(s)
- Morten O Loehr
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec, H3A 0B8, Canada
| | - Nathan W Luedtke
- Department of Chemistry, McGill University, 801 Sherbrooke St. West, Montréal, Québec, H3A 0B8, Canada.,Department of Pharmacology and Therapeutics, McGill University, 3655 Prom. Sir William Osler, Montréal, Québec H3G 1Y6, Canada
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33
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Alom KM, Kumara GSR, Seo YJ. Unnatural nucleotide-based rkDNA probe combined with graphene oxide for detection of alkaline phosphatase activity. Bioorg Med Chem Lett 2022; 64:128694. [PMID: 35314327 DOI: 10.1016/j.bmcl.2022.128694] [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: 02/15/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 11/18/2022]
Abstract
In this study we developed a fluorescent double-stranded DNA, incorporating an unnatural dUrk nucleotide, that we used as a probe for the detection of alkaline phosphatase (ALP) based on enzymatic cleavage of the non-fluorescent complementary strand. Primer extension performed using the unnatural nucleotide triphosphate dUrkTP and the natural deoxynucleotide triphosphates dATP, dCTP, and dGTP provided a simple fluorescent DNA strand that hybridized with the 5́-monophosphate non-fluorescent complementary strand. When applying the 5́-phosphate recognition and cleavage properties of lambda exonuclease (λ-exo), this probe could bind to graphene oxide (GO) and quench the fluorescence (in the absence of ALP) or not bind to GO and retain its fluorescence (in the presence of ALP). We obtained strongly fluorescent DNA strands through simple incorporation of multiple A sites in the complementary sequence, thereby increasing the number of dUrk residues during primer extension. This unnatural nucleotide-based rkDNA probing system exhibited high fluorescence differentiation for discriminating the status of ALP. This rkDNA-GO probing system appears to be a promising tool for monitoring the activity of disease-associated enzymes.
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Affiliation(s)
- Kazi Morshed Alom
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, Republic of Korea
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 561-756, Republic of Korea.
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34
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Bollu A, Peters A, Rentmeister A. Chemo-Enzymatic Modification of the 5' Cap To Study mRNAs. Acc Chem Res 2022; 55:1249-1261. [PMID: 35420432 DOI: 10.1021/acs.accounts.2c00059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The central dogma of molecular biology hinges on messenger RNA (mRNA), which presents a blueprint of the genetic information encoded in the DNA and serves as a template for translation into proteins. In addition to its fundamental importance in basic research, this class of biomolecules has recently become the first approved Covid vaccine, underscoring its utility in medical applications.Eukaryotic mRNA is heavily processed, including the 5' cap as the primary hallmark. This 5' cap protects mRNA from degradation by exoribonucleases but also interacts specifically with several proteins and enzymes to ensure mRNA turnover and processing, like splicing, export from the nucleus to the cytoplasm, and initiation of translation. The absence of a 5' cap leads to a strong immune response, and the methylation status contributes to distinguishing self from non-self RNA.Non-natural modifications of the 5' cap provide an avenue to label mRNAs and make them accessible to analyses, which is important to study their cellular localization, trafficking, and binding partners. They bear potential to engineer mRNAs, e.g., more stable or immunogenic mRNAs that are still translated, by impacting select interactions in a distinct manner. The modification of the 5' cap itself is powerful as it can be applied to make long mRNAs (∼1000 nt, not directly accessible by solid-phase synthesis) by in vitro transcription.This Account describes our contribution to the field of chemo-enzymatic modification of mRNA at the 5' cap. Our approach relies on RNA methyltransferases (MTases) with promiscuous activity on analogues of their natural cosubstrate S-adenosyl-L-methionine (AdoMet). We will describe how RNA MTases in combination with non-natural cosubstrates provide access to site-specific modification of different positions of the 5' cap, namely, the N2 and N7 position of guanosine and the N6 position of adenosine as the transcription start nucleotide (TSN) and exemplify strategies to make long mRNAs with modified 5' caps.We will compare the chemical and enzymatic synthesis of the AdoMet analogues used for this purpose. We could overcome previous limitations in methionine adenosyltransferase (MAT) substrate scope by engineering variants (termed PC-MATs) with the ability to convert methionine analogues with benzylic and photocaging groups at the sulfonium ion.The final part of this Account will highlight applications of the modified mRNAs. Like in many chemo-enzymatic approaches, a versatile strategy is to install small functional groups enzymatically and use them as handles in subsequent bioorthogonal reactions. We showed fluorescent labeling of mRNAs via different types of click chemistry in vitro and in cells. In a second line of applications, we used the handles to make mRNAs amenable for analyses, most notably next-generation sequencing. In the case of extremely promiscuous enzymes, the direct installation of photo-cross-linking groups was successful also and provided a way to covalently bind protein-interaction partners. Finally, the non-natural modifications of mRNAs can also modulate the properties of mRNAs. Propargylation of Am as the transcription start nucleotide at its N6 position maintained the translation of mRNAs but increased their immunogenicity. The installation of photocaging groups provides a way to revert these effects and control interactions by light.
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Affiliation(s)
- Amarnath Bollu
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Aileen Peters
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry Westfälische Wilhelms-Universität Münster, University of Münster, Corrensstrasse 36, 48149 Münster, Germany
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35
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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36
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Liu D, Shu X, Xiang S, Li T, Huang C, Cheng M, Cao J, Hua Y, Liu J. N4 -allyldeoxycytidine: A New DNA Tag with Chemical Sequencing Power for Pinpointing Labelling Sites, Mapping Epigenetic Mark, and in situ Imaging. Chembiochem 2022; 23:e202200143. [PMID: 35438823 DOI: 10.1002/cbic.202200143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/18/2022] [Indexed: 11/08/2022]
Abstract
DNA tagging with base analogs has found numerous applications. To precisely record the DNA labelling information, it will be highly beneficial to develop chemical sequencing tags that can be encoded into DNA as regular bases and decoded as mutant bases upon a mild, efficient and bioorthognal chemical treatment. Here we reported such a DNA tag, N4-allyldeoxycytidine (a4dC), to label and identify DNA by in vitro assays. The iodination of a4dC led to fast and complete formation of 3, N4-cyclized deoxycytidine, which induced base misincorporation during DNA replication and thus could be located at single base resolution. We explored the applications of a4dC in pinpointing DNA labelling sites at single base resolution, mapping epigenetic mark N4-methyldeoxycytidine, and imaging nucleic acids in situ. In addition, mammalian cellular DNA could be metabolically labelled with a4dC. Together,our study sheds light on the design of next generation DNA tags with chemical sequencing power.
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Affiliation(s)
- Donghong Liu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Xiao Shu
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Siying Xiang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Tengwei Li
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Chenyang Huang
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Mohan Cheng
- Zhejiang University, Department of polymer science and engineering, CHINA
| | - Jie Cao
- Zhejiang University, Life Sciences Institute; Department of Polymer Science and Engineering, CHINA
| | - Yuejin Hua
- Zhejiang University, he MOE Key Laboratory of Biosystems Homeostasis & Protection; Department of Infectious Diseases, Sir Run Run Shaw Hospital, College of Medicine, CHINA
| | - Jianzhao Liu
- Zhejiang University, Department of Polymer Science and Engineering, Zheda road 38, 310007, hangzhou, CHINA
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37
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Bissessar D, Egly J, Achard T, Steffanut P, Mauro M, Bellemin-Laponnaz S. A stable and photoreactive copper iodide cubane suitable for direct post‐functionalization. Eur J Inorg Chem 2022. [DOI: 10.1002/ejic.202200101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Damien Bissessar
- IPCMS: Institut de physique et chimie des materiaux de Strasbourg DMO FRANCE
| | - Julien Egly
- IPCMS: Institut de physique et chimie des materiaux de Strasbourg DMO FRANCE
| | - Thierry Achard
- IPCMS: Institut de physique et chimie des materiaux de Strasbourg DMO FRANCE
| | | | - Matteo Mauro
- IPCMS: Institut de physique et chimie des materiaux de Strasbourg DMO FRANCE
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38
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Loehr MO, Luedtke NW. A Kinetic and Fluorogenic Enhancement Strategy for Labeling of Nucleic Acids. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202112931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Morten O. Loehr
- Department of Chemistry McGill University 801 Sherbrooke St. West Montréal Québec, H3A 0B8 Canada
| | - Nathan W. Luedtke
- Department of Chemistry McGill University 801 Sherbrooke St. West Montréal Québec, H3A 0B8 Canada
- Department of Pharmacology and Therapeutics McGill University 3655 Prom. Sir William Osler Montréal Québec H3G 1Y6 Canada
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39
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Wang S, Chen D, Gao L, Liu Y. Short Oligonucleotides Facilitate Co-transcriptional Labeling of RNA at Specific Positions. J Am Chem Soc 2022; 144:5494-5502. [PMID: 35293210 DOI: 10.1021/jacs.2c00020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Labeling RNA molecules at specific positions is critical for RNA research and applications. Such methods are in high demand but still a challenge, especially those that enable native co-synthesis rather than post-synthesis labeling of long RNAs. The method we developed in this work meets these requirements, in which a leader RNA is extended on the hybrid solid-liquid phase by an engineered transcriptional complex following the pause-restart mode. A custom-designed short oligonucleotide is used to functionalize the engineered complex. This remarkable co-transcriptional labeling method incorporates labels into RNAs in high yields with great flexibility. We demonstrate the method by successfully introducing natural modifications, a fluorescent nucleotide analogue and a donor-acceptor fluorophore pair to specific sites located at an internal loop, a pseudoknot, a junction, a helix, and the middle of consecutive identical nucleotides of various RNAs. This newly developed method overcomes efficiency and position-choosing constraints that have hampered routine strategies to label RNAs beyond 200 nucleotides (nt).
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Affiliation(s)
- Siyu Wang
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Dian Chen
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lingzhi Gao
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yu Liu
- State Key Laboratory of Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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40
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Leone D, Pohl R, Hubálek M, Kadeřábková M, Krömer M, Sýkorová V, Hocek M. Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins. Chemistry 2022; 28:e202104208. [DOI: 10.1002/chem.202104208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Marta Kadeřábková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
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41
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Ludford P, Yang S, Bucardo MS, Tor Y. A New Variant of Emissive RNA Alphabets. Chemistry 2022; 28:e202104472. [PMID: 35018663 PMCID: PMC8891053 DOI: 10.1002/chem.202104472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 12/15/2022]
Abstract
A new fluorescent ribonucleoside alphabet (mth N) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (th N) and isothiazole[4,3-d]pyrimidine (tz N) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding mth N/mth NTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the mth N alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.
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Affiliation(s)
- Paul Ludford
- University of California San Diego, Chemistry and Biochemistry, UNITED STATES
| | - Shenghua Yang
- University of California San Diego, Chemistry and Biochemistry, UNITED STATES
| | - Marcela S Bucardo
- University of California San Diego, Chemistry and Biochemistry, UNITED STATES
| | - Yitzhak Tor
- University of California, San Diego, Department of Chemistry and Biochemistry, 9500 Gilman Drive, MC 0358, 92093-0358, La Jolla, UNITED STATES
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42
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Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
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Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
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43
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Müggenburg F, Müller S. Azide-modified Nucleosides as Versatile Tools for Bioorthogonal Labeling and Functionalization. CHEM REC 2022; 22:e202100322. [PMID: 35189013 DOI: 10.1002/tcr.202100322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 02/06/2023]
Abstract
Azide-modified nucleosides are important building blocks for RNA and DNA functionalization by click chemistry based on azide-alkyne cycloaddition. This has put demand on synthetic chemistry to develop approaches for the preparation of azide-modified nucleoside derivatives. We review here the available methods for the synthesis of various nucleosides decorated with azido groups at the sugar residue or nucleobase, their incorporation into oligonucleotides and cellular RNAs, and their application in azide-alkyne cycloadditions for labelling and functionalization.
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Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
| | - Sabine Müller
- Institut für Biochemie, Universität Greifswald, Felix-Hausdorff-Straße 4, 17487, Greifswald, Germany
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44
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Abstract
Fast and efficient site-specific labeling of long RNAs is one of the main bottlenecks limiting distance measurements by means of Förster resonance energy transfer (FRET) or electron paramagnetic resonance (EPR) spectroscopy. Here, we present an optimized protocol for dual end-labeling with different fluorophores at the same time meeting the restrictions of highly labile and degradation-sensitive RNAs. We describe in detail the dual-labeling of a catalytically active wild-type group II intron as a typical representative of long functional RNAs. The modular procedure chemically activates the 5'-phosphate and the 3'-ribose for bioconjugation with a pair of fluorophores, as shown herein, or with spin labels. The mild reaction conditions preserve the structural and functional integrity of the biomacromolecule and results in covalent, dual-labeled RNA in its pre-catalytic state in yields suitable for both ensemble and single-molecule FRET experiments.
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Affiliation(s)
- Esra Ahunbay
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Fabio D Steffen
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Roland K O Sigel
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
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45
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Moreno S, Brunner M, Delazer I, Rieder D, Lusser A, Micura R. Synthesis of 4-thiouridines with prodrug functionalization for RNA metabolic labeling. RSC Chem Biol 2022; 3:447-455. [PMID: 35441143 PMCID: PMC8985182 DOI: 10.1039/d2cb00001f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 02/18/2022] [Indexed: 12/22/2022] Open
Abstract
Metabolic labeling has emerged as a powerful tool to endow RNA with reactive handles allowing for subsequent chemical derivatization and processing. Recently, thiolated nucleosides, such as 4-thiouridine (4sU), have attracted great interest in metabolic labeling-based RNA sequencing approaches (TUC-seq, SLAM-seq, TimeLapse-seq) to study cellular RNA expression and decay dynamics. For these and other applications (e.g. PAR-CLIP), thus far only the naked nucleoside 4sU has been applied. Here we examined the concept of derivatizing 4sU into a 5′-monophosphate prodrug that would allow for cell permeation and potentially improve labeling efficiency by bypassing the rate-limiting first step of 5′ phosphorylation of the nucleoside into the ultimately bioactive 4sU triphosphate (4sUTP). To this end, we developed robust synthetic routes towards diverse 4sU monophosphate prodrugs. Using metabolic labeling assays, we found that most of the newly introduced 4sU prodrugs were well tolerated by the cells. One derivative, the bis(4-acetyloxybenzyl) 5′-monophosphate of 4sU, was also efficiently incorporated into nascent RNA. Synthetic access to 4-thiouridine (4sU) derivatives with monophosphate prodrug patterns creates additional possibilities for metabolic labeling of RNA for different applications.![]()
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Affiliation(s)
- Sarah Moreno
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Isabel Delazer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innrain 82, 6020 Innsbruck, Austria
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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46
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Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2021; 33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tracking and mapping the nascent RNA molecules in cells is essential for deciphering embryonic development and neuronal differentiation. Here, we utilized 4-thiouridine (s4U) as a metabolic tag to label nascent RNA and developed a fluorescence imaging method based on the DNA-templated oxidative amination (DTOA) reaction of s4U. The DTOA reaction occurred between amine-modified DNA and s4U-containing RNA with high sequence specificity and chemical selectivity. Target nascent mRNAs in HeLa cells, including those encoding green fluorescent proteins (GFPs) and endogenous BAG-1, were thus lit up selectively by DTOA-based fluorescence in situ hybridization (DTOA FISH). We believe the DTOA conjugation chemistry shown in this study could be generally applied to investigate the spatial distribution of nascent transcription dynamics in cellular processes.
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Affiliation(s)
- 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
| | - 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
| | - Jingyi Wang
- 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
| | - Aijun Tong
- 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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47
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Müggenburg F, Biallas A, Debiais M, Smietana M, Müller S. Azido Functionalized Nucleosides Linked to Controlled Pore Glass as Suitable Starting Materials for Oligonucleotide Synthesis by the Phosphoramidite Approach. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
| | - Alexander Biallas
- Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
| | - Mégane Debiais
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Sabine Müller
- Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
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48
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Krell K, Pfeuffer B, Rönicke F, Chinoy ZS, Favre C, Friscourt F, Wagenknecht HA. Fast and Efficient Postsynthetic DNA Labeling in Cells by Means of Strain-Promoted Sydnone-Alkyne Cycloadditions. Chemistry 2021; 27:16093-16097. [PMID: 34633713 PMCID: PMC9297951 DOI: 10.1002/chem.202103026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Indexed: 12/16/2022]
Abstract
Sydnones are highly stable mesoionic 1,3‐dipoles that react with cyclooctynes through strain‐promoted sydnone‐alkyne cycloaddition (SPSAC). Although sydnones have been shown to be valuable bioorthogonal chemical reporters for the labeling of proteins and complex glycans, nucleic acids have not yet been tagged by SPSAC. Evaluation of SPSAC kinetics with model substrates showed fast reactions with cyclooctyne probes (up to k=0.59 M−1 s−1), and two different sydnones were effectively incorporated into both 2’‐deoxyuridines at position 5, and 7‐deaza‐2’‐deoxyadenosines at position 7. These modified nucleosides were synthetically incorporated into single‐stranded DNAs, which were successfully postsynthetically labeled with cyclooctyne probes both in vitro and in cells. These results show that sydnones are versatile bioorthogonal tags and have the premise to become essential tools for tracking DNA and potentially RNA in living cells.
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Affiliation(s)
- Katja Krell
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Bastian Pfeuffer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
| | - Zoeisha S Chinoy
- Institut Européen de Chimie et Biologie and ISM CNRS UMR5255, Université de Bordeaux, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Camille Favre
- Institut Européen de Chimie et Biologie and ISM CNRS UMR5255, Université de Bordeaux, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Frédéric Friscourt
- Institut Européen de Chimie et Biologie and ISM CNRS UMR5255, Université de Bordeaux, 2 Rue Robert Escarpit, 33607, Pessac, France
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131, Karlsruhe, Germany
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49
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Choi MH, Nguyen VT, Ravi Kumara GS, Seo YJ. RNA Polymerase-Mediated Stepwise RNA-Primed RNA Polymerization for Site-Specific Multiple Labeling into RNA: A Fluorescence Resonance Energy Transfer Probe Detects the Structural Change of an RNA G-Quadruplex. ACS Synth Biol 2021; 10:3139-3147. [PMID: 34762391 DOI: 10.1021/acssynbio.1c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we report a stepwise RNA-primed RNA polymerization method for the site-specific incorporation of multiple fluorescent moieties into RNA, mediated by an RNA polymerase. A screen of several RNA polymerases revealed that T7 RNA polymerase was the only one that functioned in the RNA-primed RNA polymerization. In the first fluorescence labeling step, a fluorescent rUthioTP residue was incorporated directly into the RNA using T7 RNA polymerase; the second fluorescence labeling step was performed using a post-labeling strategy: directly introducing an rUamiTP residue into RNA, using T7 RNA polymerase, and then reacting with ylidenemalononitrile enamine (P3). The whole process for the site-specific introduction of the multiple labeled moieties was performed through stepwise RNA-primed RNA polymerization. Interestingly, the resulting multiple-labeled RNA exhibited fluorescence resonance energy transfer (FRET) between the two fluorescent labels in the RNA. We optimized the FRET-breaking point in the RNA by changing of distance between the two fluorescent labels and then used this property for the detection of the structural change of the RNA. The FRET signal increased in intensity upon the transformation of the RNA from a single-strand structure to the G-quadruplex. This approach for site-specific FRET labeling into RNA using RNA polymerase suggests the possibility of performing other diverse site-specific modifications at predefined positions in RNA.
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Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
| | - Van Thang Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
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50
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Tomecki R, Kobylecki K, Drazkowska K, Hyjek-Skladanowska M, Dziembowski A. Reproducible and efficient new method of RNA 3'-end labelling by CutA nucleotidyltransferase-mediated CC-tailing. RNA Biol 2021; 18:623-639. [PMID: 34766865 DOI: 10.1080/15476286.2021.1999104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Despite the development of non-radioactive DNA/RNA labelling methods, radiolabelled nucleic acids are commonly used in studies focused on the determination of RNA fate. Nucleic acid fragments with radioactive nucleotide analoguesincorporated into the body or at the 5' or 3' terminus of the molecule can serve as probes in hybridization-based analyses of in vivo degradation and processing of transcripts. Radiolabelled oligoribonucleotides are utilized as substrates in biochemical assays of various RNA metabolic enzymes, such as exo- and endoribonucleases, nucleotidyltransferases or helicases. In some applications, the placement of the label is not a concern, while in other cases it is required that the radioactive mark is located at the 5'- or 3'-end of the molecule. An unsurpassed method for 5'-end RNA labelling employs T4 polynucleotide kinase (PNK) and [γ-32P]ATP. In the case of 3'-end labelling, several different possibilities exist. However, they require the use of costly radionucleotide analogues. Previously, we characterized an untypical nucleotidyltransferase named CutA, which preferentially incorporates cytidines at the 3'-end of RNA substrates. Here, we demonstrate that this unusual feature can be used for the development of a novel, efficient, reproducible and economical method of RNA 3'-end labelling by CutA-mediated cytidine tailing. The labelling efficiency is comparable to that achieved with the most common method applied to date, i.e. [5'-32P]pCp ligation to the RNA 3'-terminus catalysed by T4 RNA ligase I. We show the utility of RNA substrates labelled using our new method in exemplary biochemical assays assessing directionality of two well-known eukaryotic exoribonucleases, namely Dis3 and Xrn1.
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Affiliation(s)
- Rafal Tomecki
- Laboratory of Rna Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Kamil Kobylecki
- Laboratory of Rna Biology, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | | | - Andrzej Dziembowski
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland.,Laboratory of Rna Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
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