1
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Gubu A, Zhang X, Lu A, Zhang B, Ma Y, Zhang G. Nucleic acid amphiphiles: Synthesis, properties, and applications. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 33:144-163. [PMID: 37456777 PMCID: PMC10345231 DOI: 10.1016/j.omtn.2023.05.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Nucleic acid amphiphiles, referring to nucleic acids modified with large hydrophobic groups, have been widely used in programmable bioengineering. Since nucleic acids are intrinsically hydrophilic, the hydrophobic groups endow nucleic acid amphiphiles with unique properties, such as self-assembling, interactions with artificial or biological membranes, and transmembrane transport. Importantly, the hybridization or target binding capability of oligonucleotide itself supplies nucleic acid amphiphiles with excellent programmability. As a result, this type of molecule has attracted considerable attention in academic studies and has enormous potential for further applications. For a comprehensive understanding of nucleic acid amphiphiles, we review the reported research on nucleic acid amphiphiles from their molecular design to final applications, in which we summarize the synthetic strategies for nucleic acid amphiphiles and draw much attention to their unique properties in different contexts. Finally, a summary of the applications of nucleic acid amphiphiles in drug development, bioengineering, and bioanalysis are critically discussed.
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Affiliation(s)
- Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Xueli Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences and Chemical Biology Center, Peking University, No. 38 Xueyuan Road, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
- Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen 518000, China
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2
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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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3
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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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4
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Jahns H, Degaonkar R, Podbevsek P, Gupta S, Bisbe A, Aluri K, Szeto J, Kumar P, LeBlanc S, Racie T, Brown CR, Castoreno A, Guenther DC, Jadhav V, Maier MA, Plavec J, Egli M, Manoharan M, Zlatev I. Small circular interfering RNAs (sciRNAs) as a potent therapeutic platform for gene-silencing. Nucleic Acids Res 2021; 49:10250-10264. [PMID: 34508350 PMCID: PMC8501968 DOI: 10.1093/nar/gkab724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/05/2021] [Accepted: 09/08/2021] [Indexed: 12/19/2022] Open
Abstract
In order to achieve efficient therapeutic post-transcriptional gene-silencing mediated by the RNA interference (RNAi) pathway, small interfering RNAs (siRNAs) must be chemically modified. Several supra-RNA structures, with the potential to stabilize siRNAs metabolically have been evaluated for their ability to induce gene silencing, but all have limitations or have not been explored in therapeutically relevant contexts. Covalently closed circular RNA transcripts are prevalent in eukaryotes and have potential as biomarkers and disease targets, and circular RNA mimics are being explored for use as therapies. Here we report the synthesis and evaluation of small circular interfering RNAs (sciRNAs). To synthesize sciRNAs, a sense strand functionalized with the trivalent N-acetylgalactosamine (GalNAc) ligand and cyclized using ‘click’ chemistry was annealed to an antisense strand. This strategy was used for synthesis of small circles, but could also be used for synthesis of larger circular RNA mimics. We evaluated various sciRNA designs in vitro and in vivo. We observed improved metabolic stability of the sense strand upon circularization and off-target effects were eliminated. The 5′-(E)-vinylphosphonate modification of the antisense strand resulted in GalNAc-sciRNAs that are potent in vivo at therapeutically relevant doses. Physicochemical studies and NMR-based structural analysis, together with molecular modeling studies, shed light on the interactions of this novel class of siRNAs, which have a partial duplex character, with the RNAi machinery.
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Affiliation(s)
- Hartmut Jahns
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Peter Podbevsek
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Swati Gupta
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Anna Bisbe
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Krishna Aluri
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - John Szeto
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Pawan Kumar
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Sarah LeBlanc
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | - Tim Racie
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | | | | | - Vasant Jadhav
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
| | | | - Janez Plavec
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia, EU
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | | | - Ivan Zlatev
- Alnylam Pharmaceuticals, Inc., Cambridge, MA 02142, USA
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5
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Fokina AA, Poletaeva YE, Burakova EA, Bakulina AY, Zatsepin TS, Ryabchikova EI, Stetsenko DA. Template-Assisted Assembly of DNA Nanostructures from Branched Oligonucleotides. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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6
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Fantoni NZ, El-Sagheer AH, Brown T. A Hitchhiker's Guide to Click-Chemistry with Nucleic Acids. Chem Rev 2021; 121:7122-7154. [PMID: 33443411 DOI: 10.1021/acs.chemrev.0c00928] [Citation(s) in RCA: 143] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Click chemistry is an immensely powerful technique for the fast and efficient covalent conjugation of molecular entities. Its broad scope has positively impacted on multiple scientific disciplines, and its implementation within the nucleic acid field has enabled researchers to generate a wide variety of tools with application in biology, biochemistry, and biotechnology. Azide-alkyne cycloadditions (AAC) are still the leading technology among click reactions due to the facile modification and incorporation of azide and alkyne groups within biological scaffolds. Application of AAC chemistry to nucleic acids allows labeling, ligation, and cyclization of oligonucleotides efficiently and cost-effectively relative to previously used chemical and enzymatic techniques. In this review, we provide a guide to inexperienced and knowledgeable researchers approaching the field of click chemistry with nucleic acids. We discuss in detail the chemistry, the available modified-nucleosides, and applications of AAC reactions in nucleic acid chemistry and provide a critical view of the advantages, limitations, and open-questions within the field.
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Affiliation(s)
- Nicolò Zuin Fantoni
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, U.K
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7
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Saneyoshi H, Ono A. Design and Synthesis of Protecting Groups for Pro-oligo Type Nucleic Acid-based Drugs. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hisao Saneyoshi
- Department of Chemistry, Shiga University of Medical Science
| | - Akira Ono
- Department of Material and Life Chemistry, Kanagawa University
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8
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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9
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Saneyoshi H, Ono A. Development of Protecting Groups for Prodrug-Type Oligonucleotide Medicines. Chem Pharm Bull (Tokyo) 2018; 66:147-154. [PMID: 29386465 DOI: 10.1248/cpb.c17-00696] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In recent years, nucleic acid-based drug therapeutics have gained considerable attention for their potential in the treatment of various diseases. However, their therapeutic value is greatly hindered by the challenge of delivering them into cells. One possible strategy to improve cellular uptake is the use of "prodrug-type oligonucleotide medicine" in which negatively charged phosphodiester moieties are masked by bio-labile protecting groups. In this review, we describe our recent studies related to bio-labile protecting groups for phosphodiester moieties in the development of prodrug-type oligonucleotide medicines.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University
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10
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Farzan VM, Ulashchik EA, Martynenko-Makaev YV, Kvach MV, Aparin IO, Brylev VA, Prikazchikova TA, Maklakova SY, Majouga AG, Ustinov AV, Shipulin GA, Shmanai VV, Korshun VA, Zatsepin TS. Automated Solid-Phase Click Synthesis of Oligonucleotide Conjugates: From Small Molecules to Diverse N-Acetylgalactosamine Clusters. Bioconjug Chem 2017; 28:2599-2607. [PMID: 28921968 DOI: 10.1021/acs.bioconjchem.7b00462] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We developed a novel technique for the efficient conjugation of oligonucleotides with various alkyl azides such as fluorescent dyes, biotin, cholesterol, N-acetylgalactosamine (GalNAc), etc. using copper-catalysed alkyne-azide cycloaddition on the solid phase and CuI·P(OEt)3 as a catalyst. Conjugation is carried out in an oligonucleotide synthesizer in fully automated mode and is coupled to oligonucleotide synthesis and on-column deprotection. We also suggest a set of reagents for the construction of diverse conjugates. The sequential double-click procedure using a pentaerythritol-derived tetraazide followed by the addition of a GalNAc or Tris-GalNAc alkyne gives oligonucleotide-GalNAc dendrimer conjugates in good yields with minimal excess of sophisticated alkyne reagents. The approach is suitable for high-throughput synthesis of oligonucleotide conjugates ranging from fluorescent DNA probes to various multi-GalNAc derivatives of 2'-modified siRNA.
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Affiliation(s)
- Valentina M Farzan
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Egor A Ulashchik
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Yury V Martynenko-Makaev
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Maksim V Kvach
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - Tatiana A Prikazchikova
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia
| | - Svetlana Yu Maklakova
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia
| | - Alexander G Majouga
- Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,National University of Science and Technology "MISiS" , Leninskiy Prospect 4, Moscow 119991, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
| | - Vadim V Shmanai
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, Minsk 220072, Belarus
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry , Miklukho-Maklaya 16/10, Moscow 117997, Russia.,Gause Institute of New Antibiotics , Bolshaya Pirogovskaya 11, Moscow 119021, Russia
| | - Timofei S Zatsepin
- Center of Translational Biomedicine, Skolkovo Institute of Science and Technology , Skolkovo, Moscow 143026, Russia.,Department of Chemistry, Lomonosov Moscow State University , Leninskie gory 3, Moscow 119992, Russia.,Central Research Institute of Epidemiology , Novogireevskaya 3a, Moscow 111123, Russia
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11
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George JT, Srivatsan SG. Vinyluridine as a Versatile Chemoselective Handle for the Post-transcriptional Chemical Functionalization of RNA. Bioconjug Chem 2017; 28:1529-1536. [PMID: 28406614 DOI: 10.1021/acs.bioconjchem.7b00169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of modular and efficient methods to functionalize RNA with biophysical probes is very important in advancing the understanding of the structural and functional relevance of RNA in various cellular events. Herein, we demonstrate a two-step bioorthogonal chemical functionalization approach for the conjugation of multiple probes onto RNA transcripts using a 5-vinyl-modified uridine nucleotide analog (VUTP). VUTP, containing a structurally noninvasive and versatile chemoselective handle, was efficiently incorporated into RNA transcripts by in vitro transcription reactions. Furthermore, we show for the first time the use of a palladium-mediated oxidative Heck reaction in functionalizing RNA with fluorogenic probes by reacting vinyl-labeled RNA transcripts with appropriate boronic acid substrates. The vinyl label also permitted the post-transcriptional functionalization of RNA by a reagent-free inverse electron demand Diels-Alder (IEDDA) reaction in the presence of tetrazine substrates. Collectively, our results demonstrate that the incorporation of VUTP provides newer possibilities for the modular functionalization of RNA with variety of reporters.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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12
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Saneyoshi H, Kondo K, Iketani K, Ono A. Alkyne-linked reduction-activated protecting groups for diverse functionalization on the backbone of oligonucleotides. Bioorg Med Chem 2017; 25:3350-3356. [PMID: 28460887 DOI: 10.1016/j.bmc.2017.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/12/2017] [Accepted: 04/13/2017] [Indexed: 02/06/2023]
Abstract
A versatile conjugatable/bioreduction-responsive protecting group for phosphodiester moieties was designed, synthesized and incorporated into oligonucleotide strands. Subsequently, controlled pore glass-supported oligonucleotides were conjugated to a variety of functional molecules using a copper-catalyzed azide-alkyne cycloaddition reaction. The functionalized protecting groups were deprotected by a nitroreductase/NADH reduction system to give "naked" oligonucleotides. This method allowed the synthesis of oligonucleotide prodrugs bearing the functionalized protecting group at the desired sites and desired residues on oligodeoxyribonucleotide (ODN) backbones.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
| | - Kazuhiko Kondo
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Koichi Iketani
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University, 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan.
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13
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Saneyoshi H, Yamamoto Y, Kondo K, Hiyoshi Y, Ono A. Conjugatable and Bioreduction Cleavable Linker for the 5'-Functionalization of Oligonucleotides. J Org Chem 2017; 82:1796-1802. [PMID: 28112510 DOI: 10.1021/acs.joc.6b02527] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient conjugatable and bioreduction cleavable linker was designed and synthesized for the 5'-terminal ends of oligonucleotides. A phosphoramidite reagent bearing this linker was successfully applied to solid phase synthesis and incorporated at the 5'-terminal ends of oligonucleotides. The controlled pore glass (CPG)-supported oligonucleotides were subsequently conjugated to a diverse range of functional molecules using a CuAAC reaction. The synthesized oligonucleotide conjugates were then cleaved using a nitroreductase/NADH bioreduction system to release the naked oligonucleotides.
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Affiliation(s)
- Hisao Saneyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuta Yamamoto
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Kazuhiko Kondo
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Yuki Hiyoshi
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
| | - Akira Ono
- Department of Material and Life Chemistry, Faculty of Engineering, Kanagawa University , 3-27-1 Rokkakubashi, Kanagawa-ku, Yokohama 221-8686, Japan
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14
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Kanasty RL, Vegas AJ, Ceo LM, Maier M, Charisse K, Nair JK, Langer R, Anderson DG. Sequence-Defined Oligomers from Hydroxyproline Building Blocks for Parallel Synthesis Applications. Angew Chem Int Ed Engl 2016; 55:9529-33. [PMID: 27365192 PMCID: PMC5245870 DOI: 10.1002/anie.201602748] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 05/04/2016] [Indexed: 01/01/2023]
Abstract
The functionality of natural biopolymers has inspired significant effort to develop sequence-defined synthetic polymers for applications including molecular recognition, self-assembly, and catalysis. Conjugation of synthetic materials to biomacromolecules has played an increasingly important role in drug delivery and biomaterials. We developed a controlled synthesis of novel oligomers from hydroxyproline-based building blocks and conjugated these materials to siRNA. Hydroxyproline-based monomers enable the incorporation of broad structural diversity into defined polymer chains. Using a perfluorocarbon purification handle, we were able to purify diverse oligomers through a single solid-phase extraction method. The efficiency of synthesis was demonstrated by building 14 unique trimers and 4 hexamers from 6 diverse building blocks. We then adapted this method to the parallel synthesis of hundreds of materials in 96-well plates. This strategy provides a platform for the screening of libraries of modified biomolecules.
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Affiliation(s)
- Rosemary L Kanasty
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
| | - Arturo J Vegas
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Luke M Ceo
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, MA, 02215, USA
| | - Martin Maier
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA, 02142, USA
| | | | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Division of Health Science Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Daniel G Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main St., Cambridge, MA, 02142, USA.
- Department of Anesthesiology, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA.
- Division of Health Science Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Harvard-MIT Division of Health Science and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
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15
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Kanasty RL, Vegas AJ, Ceo LM, Maier M, Charisse K, Nair JK, Langer R, Anderson DG. Sequence-Defined Oligomers from Hydroxyproline Building Blocks for Parallel Synthesis Applications. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602748] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rosemary L. Kanasty
- Department of Chemical Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
| | - Arturo J. Vegas
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Department of Chemistry; Boston University; 590 Commonwealth Avenue Boston MA 02215 USA
| | - Luke M. Ceo
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Department of Chemistry; Boston University; 590 Commonwealth Avenue Boston MA 02215 USA
| | - Martin Maier
- Alnylam Pharmaceuticals; 300 Third Street Cambridge MA 02142 USA
| | - Klaus Charisse
- Alnylam Pharmaceuticals; 300 Third Street Cambridge MA 02142 USA
| | | | - Robert Langer
- Department of Chemical Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Division of Health Science Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- Institute for Medical Engineering and Science; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA. Harvard-MIT Division of Health Science and Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
| | - Daniel G. Anderson
- Department of Chemical Engineering; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- David H. Koch Institute for Integrative Cancer Research; Massachusetts Institute of Technology; 500 Main St. Cambridge MA 02142 USA
- Department of Anesthesiology; Boston Children's Hospital; 300 Longwood Ave Boston MA 02115 USA
- Division of Health Science Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
- Institute for Medical Engineering and Science; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA. Harvard-MIT Division of Health Science and Technology; Massachusetts Institute of Technology; 77 Massachusetts Avenue Cambridge MA 02139 USA
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16
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Castro V, Rodríguez H, Albericio F. CuAAC: An Efficient Click Chemistry Reaction on Solid Phase. ACS COMBINATORIAL SCIENCE 2016; 18:1-14. [PMID: 26652044 DOI: 10.1021/acscombsci.5b00087] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Click chemistry is an approach that uses efficient and reliable reactions, such as Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC), to bind two molecular building blocks. CuAAC has broad applications in medicinal chemistry and other fields of chemistry. This review describes the general features and applications of CuAAC in solid-phase synthesis (CuAAC-SP), highlighting the suitability of this kind of reaction for peptides, nucleotides, small molecules, supramolecular structures, and polymers, among others. This versatile reaction is expected to become pivotal for meeting future challenges in solid-phase chemistry.
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Affiliation(s)
- Vida Castro
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
| | - Hortensia Rodríguez
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
- School
of Chemistry, Yachay Tech, Yachay City of Knowledge, Urcuqui, Ecuador
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology 08028-Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, 08028-Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona, 08028-Barcelona, Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001-Durban, South Africa
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17
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Cao T, Nie J, Cai LY, Zhang XH, Zhang DW, Zhou YL, Zhang XX. A cupric ion triggered DNA diode based on a tandem linkage–cleavage reaction. Chem Commun (Camb) 2016; 52:12490-12493. [DOI: 10.1039/c6cc07293c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A novel DNA functional element, a DNA diode, was developed based on a tandem linkage–cleavage process consisting of click chemistry and DNAzyme.
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Affiliation(s)
- Ting Cao
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Ji Nie
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Liang-Yuan Cai
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Xiao-Hui Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - De-Wen Zhang
- School of Engineering and Materials Science
- Queen Mary University of London
- London E1 4NS
- UK
- China Academy of Engineering Physics
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)
- MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering
- College of Chemistry
- Peking University
- Beijing 100871
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18
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Kath-Schorr S. Cycloadditions for Studying Nucleic Acids. Top Curr Chem (Cham) 2015; 374:4. [PMID: 27572987 DOI: 10.1007/s41061-015-0004-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 11/30/2015] [Indexed: 12/13/2022]
Abstract
Cycloaddition reactions for site-specific or global modification of nucleic acids have enabled the preparation of a plethora of previously inaccessible DNA and RNA constructs for structural and functional studies on naturally occurring nucleic acids, the assembly of nucleic acid nanostructures, therapeutic applications, and recently, the development of novel aptamers. In this chapter, recent progress in nucleic acid functionalization via a range of different cycloaddition (click) chemistries is presented. At first, cycloaddition/click chemistries already used for modifying nucleic acids are summarized, ranging from the well-established copper(I)-catalyzed alkyne-azide cycloaddition reaction to copper free methods, such as the strain-promoted azide-alkyne cycloaddition, tetrazole-based photoclick chemistry and the inverse electron demand Diels-Alder cycloaddition reaction between strained alkenes and tetrazine derivatives. The subsequent sections contain selected applications of nucleic acid functionalization via click chemistry; in particular, site-specific enzymatic labeling in vitro, either via DNA and RNA recognizing enzymes or by introducing unnatural base pairs modified for click reactions. Further sections report recent progress in metabolic labeling and fluorescent detection of DNA and RNA synthesis in vivo, click nucleic acid ligation, click chemistry in nanostructure assembly and click-SELEX as a novel method for the selection of aptamers.
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Affiliation(s)
- Stephanie Kath-Schorr
- LIMES Institute, Chemical Biology and Medicinal Chemistry Unit, University of Bonn, Bonn, Germany.
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19
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Photocontrolled micellar aggregation of amphiphilic DNA-azobenzene conjugates. Colloids Surf B Biointerfaces 2015; 135:126-132. [DOI: 10.1016/j.colsurfb.2015.07.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 07/05/2015] [Indexed: 11/16/2022]
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20
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Merkel M, Peewasan K, Arndt S, Ploschik D, Wagenknecht HA. Copper-Free Postsynthetic Labeling of Nucleic Acids by Means of Bioorthogonal Reactions. Chembiochem 2015; 16:1541-53. [DOI: 10.1002/cbic.201500199] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Indexed: 12/25/2022]
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21
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Zayas J, Annoual M, Das JK, Felty Q, Gonzalez WG, Miksovska J, Sharifai N, Chiba A, Wnuk SF. Strain Promoted Click Chemistry of 2- or 8-Azidopurine and 5-Azidopyrimidine Nucleosides and 8-Azidoadenosine Triphosphate with Cyclooctynes. Application to Living Cell Fluorescent Imaging. Bioconjug Chem 2015; 26:1519-32. [PMID: 26086070 DOI: 10.1021/acs.bioconjchem.5b00300] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Strain-promoted click chemistry of nucleosides and nucleotides with an azido group directly attached to the purine and pyrimidine rings with various cyclooctynes in aqueous solution at ambient temperature resulted in efficient formation (3 min to 3 h) of fluorescent, light-up, triazole products. The 2- and 8-azidoadenine nucleosides reacted with fused cyclopropyl cyclooctyne, dibenzylcyclooctyne, or monofluorocyclooctyne to produce click products functionalized with hydroxyl, amino, N-hydroxysuccinimide, or biotin moieties. The 5-azidouridine and 5-azido-2'-deoxyuridine were similarly converted to the analogous triazole products in quantitative yields in less than 5 min. The 8-azido-ATP quantitatively afforded the triazole product with fused cyclopropyl cyclooctyne in aqueous acetonitrile (3 h). The novel triazole adducts at the 2- or 8-position of adenine or 5-position of uracil rings induce fluorescence properties which were used for direct imaging in MCF-7 cancer cells without the need for traditional fluorogenic reporters. FLIM of the triazole click adducts demonstrated their potential utility for dynamic measuring and tracking of signaling events inside single living cancer cells.
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Affiliation(s)
| | | | | | | | | | | | - Nima Sharifai
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
| | - Akira Chiba
- §Department of Biology, University of Miami, Coral Gables, Florida 33146, United States
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22
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Someya T, Ando A, Kimoto M, Hirao I. Site-specific labeling of RNA by combining genetic alphabet expansion transcription and copper-free click chemistry. Nucleic Acids Res 2015; 43:6665-76. [PMID: 26130718 PMCID: PMC4538826 DOI: 10.1093/nar/gkv638] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/10/2015] [Indexed: 12/16/2022] Open
Abstract
Site-specific labeling of long-chain RNAs with desired molecular probes is an imperative technique to facilitate studies of functional RNA molecules. By genetic alphabet expansion using an artificial third base pair, called an unnatural base pair, we present a post-transcriptional modification method for RNA transcripts containing an incorporated azide-linked unnatural base at specific positions, using a copper-free click reaction. The unnatural base pair between 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) functions in transcription. Thus, we chemically synthesized a triphosphate substrate of 4-(4-azidopentyl)-pyrrole-2-carbaldehyde (N3-PaTP), which can be site-specifically introduced into RNA, opposite Ds in templates by T7 transcription. The N3-Pa incorporated in the transcripts was modified with dibenzocyclooctyne (DIBO) derivatives. We demonstrated the transcription of 17-, 76- and 260-mer RNA molecules and their site-specific labeling with Alexa 488, Alexa 594 and biotin. This method will be useful for preparing RNA molecules labeled with any functional groups of interest, toward in vivo experiments.
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Affiliation(s)
- Tatsuhiko Someya
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ami Ando
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Michiko Kimoto
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan PRESTO, JST, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Ichiro Hirao
- RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan TagCyx Biotechnologies, 1-6-126 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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23
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Brun O, Elduque X, Pedroso E, Grandas A. On-Resin Conjugation of Diene-Polyamides and Maleimides via Diels-Alder Cycloaddition. J Org Chem 2015; 80:6093-101. [PMID: 25985351 DOI: 10.1021/acs.joc.5b00592] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The reaction between maleimides and resin-linked diene-polyamides allows the latter to be used in the preparation of conjugates. Conjugation takes place by reacting the insoluble, hydrophobic diene component either with water-soluble dienophiles or with dienophiles requiring mixtures of water and organic solvents. Experimental conditions can be adjusted to furnish the target conjugate in good yield with no need of adding large excesses of soluble reagent. In case protected maleimides are used, maleimide deprotection and Diels-Alder cycloaddition can be simultaneously carried out to render conjugates with different linking positions. On-resin conjugation is followed by an acidic treatment that removes the polyamide protecting groups with no harm to the cycloadduct, in contrast with the unreacted diene that is indeed degraded under these conditions. Cycloadducts incorporating suitable functional groups can undergo subsequent additional conjugation reactions in solution to furnish double conjugates.
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Affiliation(s)
- Omar Brun
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Xavier Elduque
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Enrique Pedroso
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
| | - Anna Grandas
- Departament de Química Orgànica, Facultat de Química and IBUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain
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24
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Shoji T, Kim S, Yamamoto K, Kawai T, Okada Y, Chiba K. Anodic Substitution Reaction of Proline Derivatives Using the 2,4,6-Trimethoxyphenyl Leaving Group. Org Lett 2014; 16:6404-7. [DOI: 10.1021/ol503198p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Takao Shoji
- Laboratory of Bio-organic
Chemistry, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Shokaku Kim
- Laboratory of Bio-organic
Chemistry, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Keisuke Yamamoto
- Laboratory of Bio-organic
Chemistry, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Tomomitsu Kawai
- Laboratory of Bio-organic
Chemistry, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Yohei Okada
- Laboratory of Bio-organic
Chemistry, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
| | - Kazuhiro Chiba
- Laboratory of Bio-organic
Chemistry, Tokyo University of Agriculture and Technology, 3-5-8
Saiwai-cho, Fuchu, Tokyo 183-8509, Japan
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25
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Zewge D, Gosselin F, Kenski DM, Li J, Jadhav V, Yuan Y, Nerurkar SS, Tellers DM, Flanagan WM, Davies IW. High-throughput chemical modification of oligonucleotides for systematic structure-activity relationship evaluation. Bioconjug Chem 2014; 25:2222-32. [PMID: 25398098 DOI: 10.1021/bc500453q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Chemical modification of siRNA is achieved in a high-throughput manner (96-well plate format) by copper catalyzed azide-alkyne cycloadditions. This transformation can be performed in one synthetic operation at up to four positions with complete specificity, good yield, and acceptable purity. As demonstrated here, this approach extends the current synthetic options for oligonucleotide modifications and simultaneously facilitates the systematic, rapid biological evaluation of modified siRNA.
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Affiliation(s)
- Daniel Zewge
- Department of Process Chemistry, Merck Research Laboratories , Rahway, New Jersey 07065, United States
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26
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Mäkilä J, Jadhav S, Kiviniemi A, Käkelä M, Liljenbäck H, Poijärvi-Virta P, Laitala-Leinonen T, Lönnberg H, Roivainen A, Virta P. Synthesis of multi-galactose-conjugated 2'-O-methyl oligoribonucleotides and their in vivo imaging with positron emission tomography. Bioorg Med Chem 2014; 22:6806-13. [PMID: 25464879 DOI: 10.1016/j.bmc.2014.10.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 10/22/2014] [Accepted: 10/24/2014] [Indexed: 12/22/2022]
Abstract
(68)Ga labelled 2'-O-methyl oligoribonucleotides (anti-miR-15b) bearing one, three or seven d-galactopyranoside residues have been prepared and their distribution in healthy rats has been studied by positron emission tomography (PET). To obtain the heptavalent conjugate, an appropriately protected 1,4,7-triazacyclononane-1,4,7-triacetic acid (NOTA) precursor bearing a 4-[4-(4,4'-dimethoxytrityloxy)butoxy]phenyl side arm was first immobilized via a base labile linker to the support and the oligonucleotide was assembled on the detritylated hydroxyl function of this handle. A phosphoramidite building block bearing two phthaloyl protected aminooxy groups and one protected hydroxyl function was introduced into the 5'-terminus. One acetylated galactopyranoside was coupled as a phosphoramidite to the hydroxyl function, the phthaloyl protections were removed on-support and two trivalent galactopyranoside clusters were attached as aldehydes by on-support oximation. A two-step cleavage with aqueous alkali and ammonia released the conjugate in a fully deprotected form, allowing radiolabelling with (68)Ga in solution. The mono- and tri-galactose conjugates were obtained in a closely related manner. In vivo imaging in rats with PET showed remarkable galactose-dependent liver targeting of the conjugates.
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Affiliation(s)
- Jussi Mäkilä
- Skeletal Biology Consortium, Department of Cell Biology and Anatomy, University of Turku, FI-20520 Turku, Finland
| | - Satish Jadhav
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Anu Kiviniemi
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Meeri Käkelä
- Turku PET Centre, University of Turku and Turku University Hospital, FI-20520 Turku, Finland
| | - Heidi Liljenbäck
- Turku PET Centre, University of Turku and Turku University Hospital, FI-20520 Turku, Finland; Turku Center for Disease Modelling, University of Turku, FI-20520 Turku, Finland
| | | | - Tiina Laitala-Leinonen
- Skeletal Biology Consortium, Department of Cell Biology and Anatomy, University of Turku, FI-20520 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland
| | - Anne Roivainen
- Turku PET Centre, University of Turku and Turku University Hospital, FI-20520 Turku, Finland; Turku Center for Disease Modelling, University of Turku, FI-20520 Turku, Finland
| | - Pasi Virta
- Department of Chemistry, University of Turku, FI-20014 Turku, Finland.
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27
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Fomich MA, Kvach MV, Navakouski MJ, Weise C, Baranovsky AV, Korshun VA, Shmanai VV. Azide phosphoramidite in direct synthesis of azide-modified oligonucleotides. Org Lett 2014; 16:4590-3. [PMID: 25156193 DOI: 10.1021/ol502155g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Azide and phosphoramidite functions were found to be compatible within one molecule and stable for months in solution kept frozen at -20 °C. An azide-carrying phosphoramidite was used for direct introduction of multiple azide modifications into synthetic oligonucleotides. A series of azide-containing oligonucleotides were modified further using click reactions with alkynes.
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Affiliation(s)
- Maksim A Fomich
- Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus , Surganova 13, 220072 Minsk, Belarus
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28
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Abendroth F, Seitz O. Double-Clicking Peptides onto Phosphorothioate Oligonucleotides: Combining Two Proapoptotic Agents in One Molecule. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406674] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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29
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Abendroth F, Seitz O. Double-clicking peptides onto phosphorothioate oligonucleotides: combining two proapoptotic agents in one molecule. Angew Chem Int Ed Engl 2014; 53:10504-9. [PMID: 25138283 DOI: 10.1002/anie.201406674] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Indexed: 11/05/2022]
Abstract
Described here is a method for the conjugation of phosphorothioate oligonucleotides (PSOs) with peptides. PSOs are key to antisense technology. Peptide-PSO conjugates may improve target specificity, tissue distribution, and cellular uptake of PSOs. However, the highly nucleophilic phosphorothioate structure poses a challenge to conjugation chemistry. Herein, we introduce a new method which involves a sequence of oxime ligation and strain-promoted [2+3] cycloaddition. The usefulness of the method was demonstrated in the synthesis of peptide-PSO conjugates that targeted two suppressors of both the intrinsic and the extrinsic pathway of apoptosis. It is shown that the activity of a PSO sequence targeted against mRNA from c-Flip can be enhanced by conjugation with a peptide mimetic designed to inhibit the X-linked inhibitor of apoptosis protein (XIAP).
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Affiliation(s)
- Frank Abendroth
- Department of Chemistry, Humboldt University Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
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30
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Kommagalla Y, Cornea S, Riehle R, Torchilin V, Degterev A, Ramana CV. Optimization of the anti-cancer activity of phosphatidylinositol-3 kinase pathway inhibitor PITENIN-1: switching a thiourea with 1,2,3-triazole. MEDCHEMCOMM 2014; 5:1359-1363. [PMID: 25505943 DOI: 10.1039/c4md00109e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We previously reported encouraging in vitro and in vivoanti-cancer activity of N-((3-chloro-2-hydroxy-5-nitrophenyl)carbamothioyl)benzamide (termed PITENIN-1). In the current work, we describe the structure-activity relationship study of PIT-1 series, based on the replacement of central thiourea unit with a 1,2,3-triazole, which leads to increased liver microsomal stability, drug likeness and toxicity towards cancer cells.
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Affiliation(s)
- Yadagiri Kommagalla
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
| | - Sinziana Cornea
- Department of Developmental, Molecular and Chemical Biology, Tufts University, 136 Harrison Avenue, Boston, MA 02111
| | - Robert Riehle
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, 140 The Fenway, Boston, MA 02115
| | - Vladimir Torchilin
- Department of Pharmaceutical Sciences, Bouve College of Health Sciences, Northeastern University, 140 The Fenway, Boston, MA 02115
| | - Alexei Degterev
- Department of Developmental, Molecular and Chemical Biology, Tufts University, 136 Harrison Avenue, Boston, MA 02111
| | - Chepuri V Ramana
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune, India 411008
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31
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Ren X, Gerowska M, El-Sagheer AH, Brown T. Enzymatic incorporation and fluorescent labelling of cyclooctyne-modified deoxyuridine triphosphates in DNA. Bioorg Med Chem 2014; 22:4384-90. [PMID: 24953951 DOI: 10.1016/j.bmc.2014.05.050] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 05/16/2014] [Accepted: 05/22/2014] [Indexed: 11/25/2022]
Abstract
The amino group of 5-aminopropargyl-2'-deoxyuridine-5'-triphosphate was labelled with dibenzocyclooctyne (DIBO) and two derivatives of bicyclo [6.1.0] non-4-yne (BCN) with short and long linkers to produce three different cycloalkyne-modified deoxyuridine triphosphates. BCN was successfully incorporated into DNA at multiple sites by enzyme-mediated primer extension and the polymerase chain reaction (PCR). Efficient fluorescent labelling of the BCN-DNA and DIBO-DNA with Cy3-azide was demonstrated.
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Affiliation(s)
- Xiaomei Ren
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Marta Gerowska
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK; Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK.
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32
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Kupryushkin MS, Nekrasov MD, Stetsenko DA, Pyshnyi DV. Efficient functionalization of oligonucleotides by new achiral nonnucleosidic monomers. Org Lett 2014; 16:2842-5. [PMID: 24820262 DOI: 10.1021/ol500668n] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A novel synthetic strategy has been designed for preparation of achiral nonnucleosidic phosphoramidite monomers for automated solid-phase oligonucleotide synthesis. It is based on O-DMTr-protected 4-(2-hydroxyethyl)-morpholine-2,3-dione as the key compound and a family of building blocks obtained by its ring-opening by primary aliphatic amines. A series of nonnucleosidic phosphoramidites containing various side-chain functionalities was synthesized, and corresponding oligodeoxyribonucleotides incorporating modified units in single or multiple positions along the chain were prepared.
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Affiliation(s)
- Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
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33
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Sletten EM, de Almeida G, Bertozzi CR. A homologation approach to the synthesis of difluorinated cycloalkynes. Org Lett 2014; 16:1634-7. [PMID: 24588780 PMCID: PMC3993865 DOI: 10.1021/ol500260d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Difluorinated cyclooctynes are important
reagents for labeling
azido-biomolecules through copper-free click chemistry. Here, a safe,
scalable synthesis of a difluorinated cyclooctyne is reported, which
involves a key homologation/ring-expansion reaction. Sequential ring
expansions were also employed to synthesize and study a novel difluorinated
cyclononyne.
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Affiliation(s)
- Ellen M Sletten
- Department of Chemistry, University of California , Berkeley, California 94720, United States
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34
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Santner T, Hartl M, Bister K, Micura R. Efficient access to 3'-terminal azide-modified RNA for inverse click-labeling patterns. Bioconjug Chem 2014; 25:188-95. [PMID: 24358989 PMCID: PMC3898571 DOI: 10.1021/bc400513z] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2013] [Revised: 12/14/2013] [Indexed: 01/22/2023]
Abstract
Labeled RNA becomes increasingly important for molecular diagnostics and biophysical studies on RNA with its diverse interaction partners, which range from small metabolites to large macromolecular assemblies, such as the ribosome. Here, we introduce a fast synthesis path to 3'-terminal 2'-O-(2-azidoethyl) modified oligoribonucleotides for subsequent bioconjugation, as exemplified by fluorescent labeling via Click chemistry for an siRNA targeting the brain acid-soluble protein 1 gene (BASP1). Importantly, the functional group pattern is inverse to commonly encountered alkyne-functionalized "click"-able RNA and offers increased flexibility with respect to multiple and stepwise labeling of the same RNA molecule. Additionally, our route opens up a minimal step synthesis of 2'-O-(2-aminoethyl) modified pyrimidine nucleoside phosphoramidites which are of widespread use to generate amino-modified RNA for N-hydroxysuccinimide (NHS) ester-based conjugations.
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Affiliation(s)
- Tobias Santner
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
| | - Markus Hartl
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
| | - Klaus Bister
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute
of Organic Chemistry and Institute of Biochemistry, Center for Molecular
Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
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35
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Holstein JM, Schulz D, Rentmeister A. Bioorthogonal site-specific labeling of the 5′-cap structure in eukaryotic mRNAs. Chem Commun (Camb) 2014; 50:4478-81. [DOI: 10.1039/c4cc01549e] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A chemo-enzymatic approach for site-specific labeling of 5′-capped RNAs based on strain-promoted azide–alkyne cycloaddition (SPAAC) was developed.
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Affiliation(s)
| | - Daniela Schulz
- Institute of Biochemistry
- University of Muenster
- D-48149 Münster, Germany
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36
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Graifer D, Karpova G. General approach for introduction of various chemical labels in specific RNA locations based on insertion of amino linkers. Molecules 2013; 18:14455-69. [PMID: 24287984 PMCID: PMC6269657 DOI: 10.3390/molecules181214455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 11/12/2013] [Accepted: 11/18/2013] [Indexed: 01/06/2023] Open
Abstract
Introduction of reporter groups at designed RNA sites is a widely accepted approach to gain information about the molecular environment of RNAs in their complexes with other biopolymers formed during various cellular processes. A general approach to obtain RNAs bearing diverse reporter groups at designed locations is based on site-specific insertion of groups containing primary aliphatic amine functions (amino linkers) with their subsequent selective derivatization by appropriate chemicals. This article is a brief review on methods for site-specific introduction of amino linkers in different RNAs. These methods comprise: (i) incorporation of a nucleoside carrying an amino-linker or a function that can be substituted with it into oligoribonucleotides in the course of their chemical synthesis; (ii) assembly of amino linker-containing RNAs from short synthetic fragments via their ligation; (iii) synthesis of amino linker-modified RNAs using T7 RNA polymerase; (iv) insertion of amino linkers into unmodified RNAs at functional groups of a certain type such as the 5'-phosphates and N7 of guanosine residues and (v) introduction of an amino linker into long highly structured RNAs exploiting an approach based on sequence-specific modification of nucleic acids. Particular reporter groups used for derivatization of amino linker-containing RNAs together with types of RNA derivatives obtained and fields of their application are presented.
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Affiliation(s)
- Dmitri Graifer
- Laboratory of Ribosome Structure and Functions, Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Prospect Lavrentieva 8, Novosibirsk 630090, Russia.
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37
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Jawalekar AM, Malik S, Verkade JMM, Gibson B, Barta NS, Hodges JC, Rowan A, van Delft FL. Oligonucleotide tagging for copper-free click conjugation. Molecules 2013; 18:7346-63. [PMID: 23884112 PMCID: PMC6270431 DOI: 10.3390/molecules18077346] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Revised: 05/24/2013] [Accepted: 06/05/2013] [Indexed: 01/24/2023] Open
Abstract
Copper-free click chemistry between cyclooctynes and azide is a mild, fast and selective technology for conjugation of oligonucleotides. However, technology for site-specific introduction of the requisite probes by automated protocols is scarce, while the reported cyclooctynes are large and hydrophobic. In this work, it is demonstrated that the introduction of bicyclo[6.1.0]nonyne (BCN) into synthetic oligonucleotides is feasible by standard solid-phase phosphoramidite chemistry. A range of phosphoramidite building blocks is presented for incoporation of BCN or azide, either on-support or in solution. The usefulness of the approach is demonstrated by the straightforward and high-yielding conjugation of the resulting oligonucleotides, including biotinylation, fluorescent labeling, dimerization and attachment to polymer.
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Affiliation(s)
- Anup M. Jawalekar
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
| | - Sudip Malik
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
| | | | - Brian Gibson
- Berry and Associates, Inc., 2434 Bishop Circle East, Dexter, MI 48130, USA; E-Mails: (B.G.); (N.S.B.); (J.C.H.)
| | - Nancy S. Barta
- Berry and Associates, Inc., 2434 Bishop Circle East, Dexter, MI 48130, USA; E-Mails: (B.G.); (N.S.B.); (J.C.H.)
| | - John C. Hodges
- Berry and Associates, Inc., 2434 Bishop Circle East, Dexter, MI 48130, USA; E-Mails: (B.G.); (N.S.B.); (J.C.H.)
| | - Alan Rowan
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
| | - Floris L. van Delft
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mails: (A.M.J.); (S.M.); (A.R.)
- SynAffix BV, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands; E-Mail:
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38
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Guzaev AP. Solid-phase supports for oligonucleotide synthesis. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2013; Chapter 3:3.1.1-3.1.60. [PMID: 23775808 DOI: 10.1002/0471142700.nc0301s53] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This unit attempts to provide a reasonably complete inventory of over 280 solid supports available to oligonucleotide chemists for preparation of natural and 3'-modified oligonucleotides. Emphasis is placed on non-nucleosidic solid supports. The relationship between the structural features of linkers and their behavior in oligonucleotide synthesis and deprotection is discussed wherever the relevant observations are available.
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39
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Garcia-Hartjes J, Dommerholt J, Wennekes T, van Delft FL, Zuilhof H. Electronic Effects versus Distortion Energies During Strain-Promoted Alkyne-Azide Cycloadditions: A Theoretical Tool to Predict Reaction Kinetics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201201627] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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40
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Shelbourne M, Brown T, El-Sagheer AH, Brown T. Fast and efficient DNA crosslinking and multiple orthogonal labelling by copper-free click chemistry. Chem Commun (Camb) 2013; 48:11184-6. [PMID: 22892959 DOI: 10.1039/c2cc35084j] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new dibenzocyclooctyne-thymidine monomers were incorporated into oligonucleotides and crosslinked to azide-labelled complementary strands across the DNA grooves. Equivalent reactions were successful using a (bicyclo[6.1.0]nonyne) alkyne. Oligonucleotides containing internal cyclooctyne and amino groups were simultaneously reacted with azides and NHS esters of different fluorescent dyes to produce functional genetic probes.
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41
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Thirumurugan P, Matosiuk D, Jozwiak K. Click Chemistry for Drug Development and Diverse Chemical–Biology Applications. Chem Rev 2013; 113:4905-79. [DOI: 10.1021/cr200409f] [Citation(s) in RCA: 1309] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Prakasam Thirumurugan
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Dariusz Matosiuk
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
| | - Krzysztof Jozwiak
- Laboratory
of Medical Chemistry and Neuroengineering, Department of Chemistry, and ‡Department of
Synthesis and Chemical Technology of Pharmaceutical Substances, Medical University of Lublin, Lublin
20093, Poland
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42
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Ikeda Y, Kawasaki H, Ichinohe S, Nagasaki Y. Facile solid-phase synthesis of a highly stable poly(ethylene glycol)-oligonucleotide conjugate. J Mater Chem B 2013; 1:529-535. [PMID: 32260824 DOI: 10.1039/c2tb00031h] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel solid-phase synthesis method for poly(ethylene glycol) (PEG)-oligonucleotide conjugates was developed to increase the stability of therapeutic oligonucleotides such as antisense oligonucleotides and siRNA. A prepared solid phase was pre-installed with PEG to provide oligonucleotides modified with PEG at the 3' terminus. Compared with the conventional liquid-phase synthesis method, the developed solid-phase method is simple and reproducible. PEGylation at the 3' terminus was confirmed to stabilize not only DNA but also RNA more than PEGylation at the 5' terminus, which has been widely used so far.
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Affiliation(s)
- Yutaka Ikeda
- Graduate School of Pure and Applied Science, University of Tsukuba, Japan.
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43
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Chan DPY, Owen SC, Shoichet MS. Double Click: Dual Functionalized Polymeric Micelles with Antibodies and Peptides. Bioconjug Chem 2013; 24:105-13. [DOI: 10.1021/bc300511a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Dianna P. Y. Chan
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomaterials & Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Room 514 − 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Shawn C. Owen
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomaterials & Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Room 514 − 160 College Street, Toronto, ON, M5S 3E1, Canada
| | - Molly S. Shoichet
- Department of Chemical Engineering & Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
- Institute of Biomaterials & Biomedical Engineering, Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Room 514 − 160 College Street, Toronto, ON, M5S 3E1, Canada
- Department of Chemistry, University of Toronto, 80 St. George
Street, Toronto, ON, M5S 3H6, Canada
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44
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Yang WJ, Neoh KG, Kang ET, Lay-Ming Teo S, Rittschof D. Stainless steel surfaces with thiol-terminated hyperbranched polymers for functionalization via thiol-based chemistry. Polym Chem 2013. [DOI: 10.1039/c3py00009e] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Eltepu L, Jayaraman M, Rajeev KG, Manoharan M. An immobilized and reusable Cu(I) catalyst for metal ion-free conjugation of ligands to fully deprotected oligonucleotides through click reaction. Chem Commun (Camb) 2012; 49:184-6. [PMID: 23172132 DOI: 10.1039/c2cc36811k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Chelation of Cu(I) ions to an immobilized hydrophilic tris(triazolylmethyl)amine chelator on a solid support allowed synthesis of RNA oligonucleotide conjugates from completely deprotected alkyne-oligonucleotides. No oligonucleotide strand degradation or metal ion contamination was observed. Furthermore, use of the immobilized copper(I) ion overcame regioselectivity issues associated with strain-promoted copper-free azide-alkyne cycloaddition.
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Affiliation(s)
- Laxman Eltepu
- Drug Discovery, Alnylam Pharmaceuticals, 300 Third Street, Cambridge, MA 02142, USA
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46
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Efthymiou T, Gong W, Desaulniers JP. Chemical architecture and applications of nucleic acid derivatives containing 1,2,3-triazole functionalities synthesized via click chemistry. Molecules 2012; 17:12665-703. [PMID: 23103533 PMCID: PMC6268694 DOI: 10.3390/molecules171112665] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Revised: 10/19/2012] [Accepted: 10/19/2012] [Indexed: 11/16/2022] Open
Abstract
There is considerable attention directed at chemically modifying nucleic acids with robust functional groups in order to alter their properties. Since the breakthrough of copper-assisted azide-alkyne cycloadditions (CuAAC), there have been several reports describing the synthesis and properties of novel triazole-modified nucleic acid derivatives for potential downstream DNA- and RNA-based applications. This review will focus on highlighting representative novel nucleic acid molecular structures that have been synthesized via the “click” azide-alkyne cycloaddition. Many of these derivatives show compatibility for various applications that involve enzymatic transformation, nucleic acid hybridization, molecular tagging and purification, and gene silencing. The details of these applications are discussed. In conclusion, the future of nucleic acid analogues functionalized with triazoles is promising.
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Affiliation(s)
| | | | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe St N, Oshawa, ON L1H 7K4, Canada
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47
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El-Sagheer AH, Brown T. Click Chemistry – a Versatile Method for Nucleic Acid Labelling, Cyclisation and Ligation. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The copper-catalysed [3+2] alkyne azide cycloaddition reaction (the CuAAC reaction) is the classic example of ‘click’ chemistry, a relatively new concept that has been influential in many areas of science. It is used in the nucleic acid field for DNA cross-linking, oligonucleotide ligation and cyclisation, DNA and RNA labelling, attaching DNA to surfaces, producing modified nucleobases and backbones, synthesising ribozymes and monitoring nucleic acid biosynthesis. More recently a related click reaction, the ring strain-promoted azide–alkyne [3+2] cycloaddition (SPAAC) reaction has been used successfully in DNA strand ligation and labelling. This does not require copper catalysis, and therefore has many potential uses in vivo. In this review we discuss recent developments in nucleic acid click chemistry and their applications in biology, biotechnology and nanotechnology.
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Affiliation(s)
- Afaf H. El-Sagheer
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Chemistry Branch Dept. of Science and Mathematics Faculty of Petroleum and Mining Engineering, Suez Canal University, Suez, 43721 Egypt
| | - Tom Brown
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
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48
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Chakrabarty R, Stang PJ. Post-assembly functionalization of organoplatinum(II) metallacycles via copper-free click chemistry. J Am Chem Soc 2012; 134:14738-41. [PMID: 22917086 DOI: 10.1021/ja3070073] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We describe the use of a strain-promoted copper-free click reaction in the post-self-assembly functionalization of organoplatinum(II) metallacycles. The coordination-driven self-assembly of a 120° cyclooctyne-tethered dipyridyl donor with 60° and 120° di-Pt(II) acceptors forms molecular rhomboids and hexagons bearing cyclooctynes. These species undergo post-self-assembly [3+2] Huisgen cycloaddition with a variety of azides to give functionalized ensembles under mild conditions.
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Affiliation(s)
- Rajesh Chakrabarty
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, USA
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49
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Optimization of acetonitrile co-solvent and copper stoichiometry for pseudo-ligandless click chemistry with nucleic acids. Bioorg Med Chem Lett 2012; 22:5313-6. [DOI: 10.1016/j.bmcl.2012.06.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Revised: 06/05/2012] [Accepted: 06/11/2012] [Indexed: 12/26/2022]
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50
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Rao H, Tanpure AA, Sawant AA, Srivatsan SG. Enzymatic incorporation of an azide-modified UTP analog into oligoribonucleotides for post-transcriptional chemical functionalization. Nat Protoc 2012; 7:1097-112. [PMID: 22576108 DOI: 10.1038/nprot.2012.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the detailed experimental procedure for the synthesis of an azide-modified uridine triphosphate analog and its effective incorporation into an oligoribonucleotide by in vitro transcription reactions. Furthermore, procedures for labeling azide-modified oligoribonucleotides post-transcriptionally with biophysical probes by copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) and Staudinger reactions are also provided. This post-transcriptional chemical modification protocol is simple and modular, and it affords labeled oligonucleotides in reasonable amounts for biophysical assays. The procedure for enzymatic incorporation of the monophosphate of azide-modified UTP into an oligoribonucleotide transcript takes ∼2 d, and subsequent post-transcriptional chemical functionalization of the transcript takes about 2 d.
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Affiliation(s)
- Harita Rao
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
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