1
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Knutson SD, Pan CR, Bisballe N, Bloomer BJ, Raftopolous P, Saridakis I, MacMillan DWC. Parallel Proteomic and Transcriptomic Microenvironment Mapping (μMap) of Nuclear Condensates in Living Cells. J Am Chem Soc 2025; 147:488-497. [PMID: 39707993 PMCID: PMC11792175 DOI: 10.1021/jacs.4c11612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2024]
Abstract
Cellular activity is spatially organized across different organelles. While several structures are well-characterized, many organelles have unknown roles. Profiling biomolecular composition is key to understanding function but is difficult to achieve in the context of small, dynamic structures. Photoproximity labeling has emerged as a powerful tool for mapping these interaction networks, yet maximizing catalyst localization and reducing toxicity remains challenging in live cell applications. Here, we disclose a new intracellular photocatalyst with minimal cytotoxicity and off-target binding, and we utilize this catalyst for HaloTag-based microenvironment-mapping (μMap) to spatially catalog subnuclear condensates in living cells. We also specifically develop a novel RNA-focused workflow (μMap-seq) to enable parallel transcriptomic and proteomic profiling of these structures. After validating the accuracy of our approach, we generate a spatial map across the nucleolus, nuclear lamina, Cajal bodies, paraspeckles, and PML bodies. These results provide potential new insights into RNA metabolism and gene regulation while significantly expanding the μMap platform for improved live-cell proximity labeling in biological systems.
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Affiliation(s)
- Steve D Knutson
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Chenmengxiao Roderick Pan
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Niels Bisballe
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Brandon J Bloomer
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Philip Raftopolous
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - Iakovos Saridakis
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
| | - David W C MacMillan
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Merck Center for Catalysis at Princeton University, Princeton, New Jersey 08544, United States
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2
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Takasaki H, Kitazaki K, Hadano Y, Murase H, Lee J, Taniguchi Y, Sasaki S. New Nucleoside Derivatives for Hybridization-Assisted Catalysis of Site-Selective Acetylation of 2'-OH of RNA. Chem Pharm Bull (Tokyo) 2025; 73:457-466. [PMID: 40383643 DOI: 10.1248/cpb.c25-00068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2025]
Abstract
New nucleoside derivatives containing the imidazole (Imd), pyridine or pyrimidine catalytic group were designed for site-specific acetylation of 2'-OH of the RNA ribose moiety. When the RNA substrate was acetylated in the presence of acetic anhydride under alkaline conditions, Probe (Imd) containing the imidazole catalytic group acetylated with a high selectivity to the 2'-OH of the uridine opposite the catalytic nucleotide. Probe (Py-4N) containing the pyridine group showed a higher catalytic activity under neutral conditions with a high selectivity for the 2'-OH group of the 5' side of the uridine opposite the catalytic nucleotide in about 80% modification yield within 10 min. This study has shown that the oligodeoxynucleotide incorporating the new nucleotide derivative with the catalytic group can be a useful tool for site-selective acetylation of RNA 2'-OH.
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Affiliation(s)
- Hayate Takasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kentaro Kitazaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yurie Hadano
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hirotaka Murase
- Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Jeongsu Lee
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo, Nagasaki 859-3298, Japan
| | - Yosuke Taniguchi
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushimanaka, Kita-ku, Okayama 700-8530, Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
- Graduate School of Pharmaceutical Sciences, Nagasaki International University, 2825-7 Huis Ten Bosch Machi, Sasebo, Nagasaki 859-3298, Japan
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3
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Ma AD, Chen WJ, Sun WW, Wu B. Late-Stage Functionalization of Guanine-Based Nucleosides, Nucleotides, and Oligonucleotide: Synthesis and Derivatization of Tricyclic Nucleoside Analogues. Org Lett 2024; 26:10891-10896. [PMID: 39655873 DOI: 10.1021/acs.orglett.4c04024] [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: 12/21/2024]
Abstract
We report here the synthesis of tricyclic nucleoside analogues via acid-catalyzed cyclization of guanine with 1,1,3,3-tetramethoxypropane. The method enables the use of hydroxyl-unprotected antiviral drugs (acyclovir, ganciclovir, and penciclovir), guanosines, oligonucleotide, and triazole-linked nucleoside dimers as substrates. Nucleoside trimer and tetramer were synthesized by derivatization reactions.
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Affiliation(s)
- Ao-Di Ma
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Wei-Jia Chen
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Wen-Wu Sun
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Bin Wu
- School of Pharmaceutical Sciences, South-Central Minzu University, Wuhan 430074, China
- Key Laboratory of Analytical Chemistry of the State Ethnic Affairs Commission, South-Central Minzu University, Wuhan 430074, China
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4
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Yamazaki H, Sugawara R, Takayama Y. Development of label-free light-controlled gene expression technologies using mid-IR and terahertz light. Front Bioeng Biotechnol 2024; 12:1324757. [PMID: 39465004 PMCID: PMC11502365 DOI: 10.3389/fbioe.2024.1324757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 09/25/2024] [Indexed: 10/29/2024] Open
Abstract
Gene expression is a fundamental process that regulates diverse biological activities across all life stages. Given its vital role, there is an urgent need to develop innovative methodologies to effectively control gene expression. Light-controlled gene expression is considered a favorable approach because of its ability to provide precise spatiotemporal control. However, current light-controlled technologies rely on photosensitive molecular tags, making their practical use challenging. In this study, we review current technologies for light-controlled gene expression and propose the development of label-free light-controlled technologies using mid-infrared (mid-IR) and terahertz light.
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Affiliation(s)
- Hirohito Yamazaki
- Top Runner Incubation Center for Academia-Industry Fusion, Nagaoka University of Technology, Nagaoka, Japan
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Ryusei Sugawara
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Yurito Takayama
- Department of Mechanical Engineering, Nagaoka University of Technology, Nagaoka, Japan
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5
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Boyd R, Kennebeck M, Miranda A, Liu Z, Silverman S. Site-specific N-alkylation of DNA oligonucleotide nucleobases by DNAzyme-catalyzed reductive amination. Nucleic Acids Res 2024; 52:8702-8716. [PMID: 39051544 PMCID: PMC11347174 DOI: 10.1093/nar/gkae639] [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: 06/06/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
DNA and RNA nucleobase modifications are biologically relevant and valuable in fundamental biochemical and biophysical investigations of nucleic acids. However, directly introducing site-specific nucleobase modifications into long unprotected oligonucleotides is a substantial challenge. In this study, we used in vitro selection to identify DNAzymes that site-specifically N-alkylate the exocyclic nucleobase amines of particular cytidine, guanosine, and adenosine (C, G and A) nucleotides in DNA substrates, by reductive amination using a 5'-benzaldehyde oligonucleotide as the reaction partner. The new DNAzymes each require one or more of Mg2+, Mn2+, and Zn2+ as metal ion cofactors and have kobs from 0.04 to 0.3 h-1, with rate enhancement as high as ∼104 above the splinted background reaction. Several of the new DNAzymes are catalytically active when an RNA substrate is provided in place of DNA. Similarly, several new DNAzymes function when a small-molecule benzaldehyde compound replaces the 5'-benzaldehyde oligonucleotide. These findings expand the scope of DNAzyme catalysis to include nucleobase N-alkylation by reductive amination. Further development of this new class of DNAzymes is anticipated to facilitate practical covalent modification and labeling of DNA and RNA substrates.
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Affiliation(s)
- Robert D Boyd
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Morgan M Kennebeck
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Aurora A Miranda
- Department of Chemistry, University of Illinois Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Zehui Liu
- 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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6
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Lorenzetto T, Bordignon F, Munarin L, Mancin F, Fabris F, Scarso A. Substrate Selectivity Imparted by Self-Assembled Molecular Containers and Catalysts. Chemistry 2024; 30:e202301811. [PMID: 37466005 DOI: 10.1002/chem.202301811] [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: 06/06/2023] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Recent trends in catalysis are devoted to mimicking some peculiar features of enzymes like site selectivity, through functional group recognition, and substrate selectivity, through recognition of the entire surface of the substrate. The latter is a specific feature of enzymes that is seldomly present in homogeneous catalysis. Supramolecular catalysis, thanks to the self-assembly of simple subunits, enables the creation of cavities and surfaces whose confinement effects drive the preferential binding of a substrate among others with consequent substrate selectivity. The topic is an emerging field that exploits recognition phenomena to discriminate the reagents based on their size and shape. This review deals this cutting-edge field of research covering examples of supramolecular self-assembled molecular containers and catalysts operating in organic as well as aqueous media, with special emphasis for catalytic systems dealing with direct competitive experiments involving two or more substrates.
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Affiliation(s)
- Tommaso Lorenzetto
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, Venezia Mestre, 30172, Italy
| | - Francesca Bordignon
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, Venezia Mestre, 30172, Italy
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, via Marzolo 1, Padova, 35100, Italy
| | - Luca Munarin
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, Venezia Mestre, 30172, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università degli studi di Padova, via Marzolo 1, Padova, 35100, Italy
| | - Fabrizio Fabris
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, Venezia Mestre, 30172, Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Via Torino 155, Venezia Mestre, 30172, Italy
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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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Shioi R, Xiao L, Chatterjee S, Kool ET. Stereoselective RNA reaction with chiral 2'-OH acylating agents. Chem Sci 2023; 14:13235-13243. [PMID: 38023505 PMCID: PMC10664579 DOI: 10.1039/d3sc03067a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/29/2023] [Indexed: 11/24/2023] Open
Abstract
The reactivity of RNA 2'-OH groups with acylating agents has recently been investigated for high-yield conjugation of RNA strands. To date, only achiral molecules have been studied for this reaction, despite the complex chiral structure of RNA. Here we prepare a set of chiral acylimidazoles and study their stereoselectivity in RNA reactions. Reactions performed with unfolded and folded RNAs reveal that positional selectivity and reactivity vary widely with local RNA macro-chirality. We further document remarkable effects of chirality on reagent reactivity, identifying an asymmetric reagent with 1000-fold greater reactivity than prior achiral reagents. In addition, we identify a chiral compound with higher RNA structural selectivity than any previously reported RNA-mapping species. Further, azide-containing homologs of a chiral dimethylalanine reagent were synthesized and applied to local RNA labeling, displaying 92% yield and 16 : 1 diastereoselectivity. The results establish that reagent stereochemistry and chiral RNA structure are critical elements of small molecule-RNA reactions, and demonstrate new chemical strategies for selective RNA modification and probing.
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Affiliation(s)
- Ryuta Shioi
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | - Lu Xiao
- Department of Chemistry, Stanford University Stanford CA 94305 USA
| | | | - Eric T Kool
- Department of Chemistry, Stanford University Stanford CA 94305 USA
- Sarafan ChEM-H, Stanford University Stanford CA 94305 USA
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9
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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10
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Gutiérrez S, Tomás-Gamasa M, Mascareñas JL. Organometallic catalysis in aqueous and biological environments: harnessing the power of metal carbenes. Chem Sci 2022; 13:6478-6495. [PMID: 35756533 PMCID: PMC9172117 DOI: 10.1039/d2sc00721e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/15/2022] [Indexed: 11/24/2022] Open
Abstract
Translating the power of transition metal catalysis to the native habitats of enzymes can significantly expand the possibilities of interrogating or manipulating natural biological systems, including living cells and organisms. This is especially relevant for organometallic reactions that have shown great potential in the field of organic synthesis, like the metal-catalyzed transfer of carbenes. While, at first sight, performing metal carbene chemistry in aqueous solvents, and especially in biologically relevant mixtures, does not seem obvious, in recent years there has been a growing number of reports demonstrating the feasibility of the task. Either using small molecule metal catalysts or artificial metalloenzymes, a number of carbene transfer reactions that tolerate aqueous and biorelevant media are being developed. This review intends to summarize the most relevant contributions, and establish the state of the art in this emerging research field.
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Affiliation(s)
- Sara Gutiérrez
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - María Tomás-Gamasa
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
| | - José Luis Mascareñas
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela 15705 Santiago de Compostela Spain
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11
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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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12
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Ito Y, Hari Y. Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution. CHEM REC 2022; 22:e202100325. [PMID: 35119181 DOI: 10.1002/tcr.202100325] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
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