1
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Reyes Y, Adhikary A, Wnuk SF. Nitrogen-Centered Radicals Derived from Azidonucleosides. Molecules 2024; 29:2310. [PMID: 38792171 PMCID: PMC11124349 DOI: 10.3390/molecules29102310] [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: 04/01/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Azido-modified nucleosides have been extensively explored as substrates for click chemistry and the metabolic labeling of DNA and RNA. These compounds are also of interest as precursors for further synthetic elaboration and as therapeutic agents. This review discusses the chemistry of azidonucleosides related to the generation of nitrogen-centered radicals (NCRs) from the azido groups that are selectively inserted into the nucleoside frame along with the subsequent chemistry and biological implications of NCRs. For instance, the critical role of the sulfinylimine radical generated during inhibition of ribonucleotide reductases by 2'-azido-2'-deoxy pyrimidine nucleotides as well as the NCRs generated from azidonucleosides by radiation-produced (prehydrated and aqueous) electrons are discussed. Regio and stereoselectivity of incorporation of an azido group ("radical arm") into the frame of nucleoside and selective generation of NCRs under reductive conditions, which often produce the same radical species that are observed upon ionization events due to radiation and/or other oxidative conditions that are emphasized. NCRs generated from nucleoside-modified precursors other than azidonucleosides are also discussed but only with the direct relation to the same/similar NCRs derived from azidonucleosides.
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Affiliation(s)
- Yahaira Reyes
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA;
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA;
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA;
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2
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Bardhan A, Brown W, Albright S, Tsang M, Davidson LA, Deiters A. Direct Activation of Nucleobases with Small Molecules for the Conditional Control of Antisense Function. Angew Chem Int Ed Engl 2024; 63:e202318773. [PMID: 38411401 DOI: 10.1002/anie.202318773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 02/28/2024]
Abstract
Conditionally controlled antisense oligonucleotides provide precise interrogation of gene function at different developmental stages in animal models. Only one example of small molecule-induced activation of antisense function exist. This has been restricted to cyclic caged morpholinos that, based on sequence, can have significant background activity in the absence of the trigger. Here, we provide a new approach using azido-caged nucleobases that are site-specifically introduced into antisense morpholinos. The caging group design is a simple azidomethylene (Azm) group that, despite its very small size, efficiently blocks Watson-Crick base pairing in a programmable fashion. Furthermore, it undergoes facile decaging via Staudinger reduction when exposed to a small molecule phosphine, generating the native antisense oligonucleotide under conditions compatible with biological environments. We demonstrated small molecule-induced gene knockdown in mammalian cells, zebrafish embryos, and frog embryos. We validated the general applicability of this approach by targeting three different genes.
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Affiliation(s)
- Anirban Bardhan
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Wes Brown
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Savannah Albright
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Michael Tsang
- Department of Cell Biology, Center for Integrative Organ Systems., University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Lance A Davidson
- Department of Bioengineering, Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, United States
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3
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Reyes Y, Mebel A, Wnuk SF. 6-azido and 6-azidomethyl uracil nucleosides. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:453-471. [PMID: 37859415 DOI: 10.1080/15257770.2023.2271023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 10/10/2023] [Indexed: 10/21/2023]
Abstract
Azido nucleosides have been utilized for click reactions, metabolic incorporation into cellular DNA, and fluorescent imaging of live cells. Two classes of 6-azido modified uracil nucleosides; one with azido group directly attached to uracil ring and second with azido group attached via methylene linker are described. The 6-azido-2'-deoxyuridine (6-AdU) was prepared in 55% overall yield by lithiation-based regioselective C6-iodination of silyl protected 2'-deoxyuridine followed by treatment with sodium azide and deprotection with TBAF. Lithiation-based C6-alkylation of the protected uridine with methyl iodide followed by the oxidation of the 6-methyl product with selenium dioxide and the subsequent mesylation and azidation of the resulting 6-hydroxymethyl group gave after deprotection 6-azidomethyluridine (6-AmU) in 61% overall yield. Direct lithiation-based C6-hydroxymethylation followed by mesylation/azidation sequence and deprotection provided 6-AmU or 6-azidomethyl-2'-deoxyuridine (6-AmdU). Yields for the lithiation-based regioselective C6-iodination and alkylation were higher for uridine than 2'-deoxyuridine derivatives and they appear to be less dependent on the sugar protection group used. Strain promoted click reactions of 6-AdU and 6-AmdU with symmetrically fused cyclopropyl cyclooctyne (OCT) provided fluorescent triazoles. DFT-calculated dihedral angles and energy differences for the favored anti and syn conformation of 6-AdU and 6-AmdU versus their C5 azido counterparts are discussed.
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Affiliation(s)
- Yahaira Reyes
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Alexander Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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4
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Kurup HM, Kvach MV, Harjes S, Barzak FM, Jameson GB, Harjes E, Filichev VV. Design, Synthesis, and Evaluation of a Cross-Linked Oligonucleotide as the First Nanomolar Inhibitor of APOBEC3A. Biochemistry 2022; 61:2568-2578. [DOI: 10.1021/acs.biochem.2c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Harikrishnan M. Kurup
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Maksim V. Kvach
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Stefan Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Fareeda M. Barzak
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
| | - Geoffrey B. Jameson
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Elena Harjes
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
| | - Vyacheslav V. Filichev
- School of Natural Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Auckland 1142, New Zealand
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5
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Moreno S, Ramos Pittol JM, Hartl M, Micura R. Robust synthesis of 2'-azido modified RNA from 2'-amino precursors by diazotransfer reaction. Org Biomol Chem 2022; 20:7845-7850. [PMID: 36172831 DOI: 10.1039/d2ob01560a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Azides are versatile bioorthogonal reporter moieties that are commonly used for site-specific labeling and functionalization of RNA to probe its biology. The preparation of azido modified nucleic acids by solid-phase synthesis is problematic due to the inherent reactivity of P(III) species with azides according to the Staudinger reaction. Various strategies have been developed to bypass this limitation and are often time-consuming, low-yielding and labor-intensive. In particular, the synthesis of RNA with internal 2'-azido modifications is restricted to a single approach that employs P(V) chemistry instead of the widely used P(III) phosphoramidite chemistry. To fill this methodological gap, we present a novel convenient path toward 2'-azido RNA from readily accessible 2'-amino RNA through treatment with the diazotizing reagent fluorosulfuryl azide (FSO2N3). A diazotransfer reaction was established for oligoribonucleotides of different lengths and secondary structures. The robustness of the approach was further demonstrated for RNAs containing multiple 2'-azido moieties and for RNAs containing other sensitive modifications such as thiouridine or methylated nucleobases with a positive charge. The synthetic ease of generating 2'-azido RNA will pave the way for biotechnological applications, in particular for siRNA technologies and for referencing the growing number of RNA metabolic labeling approaches that rely on 2'-azido nucleosides.
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Affiliation(s)
- Sarah Moreno
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
| | - José M Ramos Pittol
- Institute of Biochemistry, Center for Chemistry and Biomedicine (CCB) Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Markus Hartl
- Institute of Biochemistry, Center for Chemistry and Biomedicine (CCB) Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry, Center for Molecular Biosciences Innsbruck, University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria.
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6
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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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7
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Müggenburg F, Biallas A, Debiais M, Smietana M, Müller S. Azido Functionalized Nucleosides Linked to Controlled Pore Glass as Suitable Starting Materials for Oligonucleotide Synthesis by the Phosphoramidite Approach. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Frederik Müggenburg
- Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
| | - Alexander Biallas
- Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
| | - Mégane Debiais
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron Université de Montpellier, CNRS, ENSCM Place Eugène Bataillon 34095 Montpellier France
| | - Sabine Müller
- Institut für Biochemie Universität Greifswald Felix-Hausdorff-Straße 4 17487 Greifswald Germany
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8
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Sengupta S, Das P. Application of diazonium chemistry in purine modifications: A focused review. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Saumitra Sengupta
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
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9
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Matsuda H, Yoshida E, Shinoda T, Sato K, Hara RI, Wada T. Solution-phase synthesis of oligodeoxyribonucleotides using the H-phosphonate method with N-unprotected 5′-phosphite monomers. RSC Adv 2021; 11:38094-38107. [PMID: 35498072 PMCID: PMC9044012 DOI: 10.1039/d1ra06619f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 11/17/2021] [Indexed: 11/21/2022] Open
Abstract
A new strategy for a solution-phase synthesis of oligodeoxyribonucleotides with 5′-phosphite monomers synthesized in a single step from unprotected 2′-deoxyribonucleosides.
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Affiliation(s)
- Hiromasa Matsuda
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- CMC Production Technology Laboratories, MTPC Production Technology & Supply Chain Management Division, Mitsubishi Tanabe Pharma Corporation, 3-16-89 Kashima, Yodogawa-ku, Osaka 532-8505, Japan
| | - Erina Yoshida
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Takaaki Shinoda
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Kazuki Sato
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
| | - Rintaro Iwata Hara
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Takeshi Wada
- Department of Medicinal and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba 278-8510, Japan
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10
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Abstract
Labeling of nucleic acids is required for many studies aiming to elucidate their functions and dynamics in vitro and in cells. Out of the numerous labeling concepts that have been devised, covalent labeling provides the most stable linkage, an unrivaled choice of small and highly fluorescent labels and - thanks to recent advances in click chemistry - an incredible versatility. Depending on the approach, site-, sequence- and cell-specificity can be achieved. DNA and RNA labeling are rapidly developing fields that bring together multiple areas of research: on the one hand, synthetic and biophysical chemists develop new fluorescent labels and isomorphic nucleobases as well as faster and more selective bioorthogonal reactions. On the other hand, the number of enzymes that can be harnessed for post-synthetic and site-specific labeling of nucleic acids has increased significantly. Together with protein engineering and genetic manipulation of cells, intracellular and cell-specific labeling has become possible. In this review, we provide a structured overview of covalent labeling approaches for nucleic acids and highlight notable developments, in particular recent examples. The majority of this review will focus on fluorescent labeling; however, the principles can often be readily applied to other labels. We will start with entirely chemical approaches, followed by chemo-enzymatic strategies and ribozymes, and finish with metabolic labeling of nucleic acids. Each section is subdivided into direct (or one-step) and two-step labeling approaches and will start with DNA before treating RNA.
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Affiliation(s)
- Nils Klöcker
- Institute of Biochemistry, University of Muenster, Corrensstraße 36, D-48149 Münster, Germany.
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11
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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12
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George JT, Azhar M, Aich M, Sinha D, Ambi UB, Maiti S, Chakraborty D, Srivatsan SG. Terminal Uridylyl Transferase Mediated Site-Directed Access to Clickable Chromatin Employing CRISPR-dCas9. J Am Chem Soc 2020; 142:13954-13965. [PMID: 32658470 PMCID: PMC7611130 DOI: 10.1021/jacs.0c06541] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Locus-specific interrogation of target genes employing functional probes such as proteins and small molecules is paramount in decoding the molecular basis of gene function and designing tools to modulate its downstream effects. In this context, CRISPR-based gene editing and targeting technologies have proved tremendously useful, as they can be programmed to target any gene of interest by simply changing the sequence of the single guide RNA (sgRNA). Although these technologies are widely utilized in recruiting genetically encoded functional proteins, display of small molecules using CRISPR system is not well developed due to the lack of adequate techniques. Here, we have devised an innovative technology called sgRNA-Click (sgR-CLK) that harnesses the power of bioorthogonal click chemistry for remodeling guide RNA to display synthetic molecules on target genes. sgR-CLK employs a novel posttranscriptional chemoenzymatic labeling platform wherein a terminal uridylyl transferase (TUTase) was repurposed to generate clickable sgRNA of choice by site-specific tailoring of multiple azide-modified nucleotide analogues at the 3' end. The presence of a minimally invasive azide handle assured that the sgRNAs are indeed functional. Notably, an azide-tailed sgRNA targeting the telomeric repeat served as a Trojan horse on the CRISPR-dCas9 system to guide synthetic tags (biotin) site-specifically on chromatin employing copper-catalyzed or strain-promoted click reactions. Taken together, sgR-CLK presents a significant advancement on the utility of bioorthogonal chemistry, TUTase, and the CRISPR toolbox, which could offer a simplified solution for site-directed display of small molecule probes and diagnostic tools on target genes.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | | | | | | | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Souvik Maiti
- Institute of Genomics and Integrative Biology (IGIB)-National Chemical Laboratory (NCL) Joint Center, Council of Scientific and Industrial Research-NCL, Pune 411008, India
| | | | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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13
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Mansot J, Aubert S, Duchemin N, Vasseur JJ, Arseniyadis S, Smietana M. A rational quest for selectivity through precise ligand-positioning in tandem DNA-catalysed Friedel-Crafts alkylation/asymmetric protonation. Chem Sci 2019; 10:2875-2881. [PMID: 30996865 PMCID: PMC6429601 DOI: 10.1039/c8sc05543b] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 01/22/2019] [Indexed: 12/28/2022] Open
Abstract
Covalent anchorage of a metallic co-factor to a DNA-based architecture is merely the only way to ensure an accurate positioning of a catalytic site within the chiral micro-environment offered by the DNA double helix. Ultimately, it also allows a fine-tuning of the catalytic pocket through simple synthetic modifications of the DNA sequence. Here, we report highly selective copper(ii)-catalysed asymmetric Friedel-Crafts conjugate addition/enantioselective protonation, which is due to a careful positioning of a bipyridine ligand within a DNA framework. Most importantly, this study unveils specific structural features that account for an optimal chirality transfer from the duplex to the Friedel-Crafts adducts.
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Affiliation(s)
- Justine Mansot
- Institut des Biomolécules Max Mousseron , CNRS , Université de Montpellier , ENSCM , Place Eugène Bataillon , 34095 Montpellier , France .
| | - Sidonie Aubert
- School of Biological and Chemical Sciences , Queen Mary University of London , Joseph Priestley Building, Mile End Road , London E1 4NS , UK .
| | - Nicolas Duchemin
- School of Biological and Chemical Sciences , Queen Mary University of London , Joseph Priestley Building, Mile End Road , London E1 4NS , UK .
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron , CNRS , Université de Montpellier , ENSCM , Place Eugène Bataillon , 34095 Montpellier , France .
| | - Stellios Arseniyadis
- School of Biological and Chemical Sciences , Queen Mary University of London , Joseph Priestley Building, Mile End Road , London E1 4NS , UK .
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron , CNRS , Université de Montpellier , ENSCM , Place Eugène Bataillon , 34095 Montpellier , France .
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14
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Abstract
The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.
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Affiliation(s)
- Mikael Madsen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
| | - Kurt V Gothelf
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry , Aarhus University , Gustav Wieds Vej 14 , DK - 8000 Aarhus C, Denmark
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15
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Abstract
The use of CuAAC chemistry to crosslink and stabilize oligonucleotides has been limited by the incompatibility of azides with the phosphoramidites used in automated oligonucleotide synthesis. Herein we report optimized reaction conditions to synthesize azide derivatives of thymidine and cytidine phosphoramidites. Investigation of the stability of the novel phosphoramidites using 31P NMR at room temperature showed less than 10% degradation after 6 hours. The azide modified thymidine was successfully utilized as an internal modifier in the standard phosphoramidite synthesis of a DNA sequence. The synthesized azide and alkyne derivatives of pyrimidines will allow efficient incorporation of azide and alkyne click pairs into nucleic acids, thus widening the applicability of click chemistry in investigating the chemistry of nucleic acids.
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16
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Igata Y, Saito-Tarashima N, Matsumoto D, Sagara K, Minakawa N. A 'catch and release' strategy towards HPLC-free purification of synthetic oligonucleotides by a combination of the strain-promoted alkyne-azide cycloaddition and the photocleavage. Bioorg Med Chem 2017; 25:5962-5967. [PMID: 28986115 DOI: 10.1016/j.bmc.2017.09.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 10/18/2022]
Abstract
A convenient strategy to purify oligonucleotides (ONs) synthesized by solid phase synthesis on an automatic DNA/RNA synthesizer was described. By attaching a photocleavable azide linker as the last phosphoramidite unit in the ON synthesis, only the desired full-length sequence was 'caught' on a controlled pore glass (CPG) resin possessing an aza-dimethoxycyclooctyne (DIBAC) derivative. Washing the resulting CPG resin to remove all unbounded species, the subsequent photoirradiation allowed the pure ONs to be 'released' without leaving any chemical modifications on native ON structure or chemical reagents from the solid phase ON synthesis.
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Affiliation(s)
- Yosuke Igata
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Noriko Saito-Tarashima
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Daiki Matsumoto
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Kazuyuki Sagara
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan
| | - Noriaki Minakawa
- Graduate School of Pharmaceutical Science, Tokushima University, Shomachi 1-78-1, Tokushima 770-8505, Japan.
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17
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Posttranscriptional chemical labeling of RNA by using bioorthogonal chemistry. Methods 2017; 120:28-38. [DOI: 10.1016/j.ymeth.2017.02.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 02/13/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
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18
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Thomann A, Zapp J, Hutter M, Empting M, Hartmann RW. Steering the azido-tetrazole equilibrium of 4-azidopyrimidines via substituent variation - implications for drug design and azide-alkyne cycloadditions. Org Biomol Chem 2016; 13:10620-30. [PMID: 26340222 DOI: 10.1039/c5ob01006c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This paper focuses on an interesting constitutional isomerism called azido-tetrazole equilibrium which is observed in azido-substituted N-heterocycles. We present a systematic investigation of substituent effects on the isomer ratio within a 2-substituted 4-azidopyrimidine model scaffold. NMR- and IR-spectroscopy as well as X-ray crystallography were employed for thorough analysis and characterization of synthesized derivatives. On the basis of this data, we demonstrate the possibility to steer this valence tautomerism towards the isomer of choice by means of substituent variation. We show that the tetrazole form can act as an efficient disguise for the corresponding azido group masking its well known reactivity in azide-alkyne cycloadditions (ACCs). In copper(I)-catalyzed AAC reactions, substituent-stabilized tetrazoles displayed a highly decreased or even abolished reactivity whereas azides and compounds in the equilibrium were directly converted. By use of an acid sensitive derivative, we provide, to our knowledge, the first experimental basis for a possible exploitation of this dynamic isomerism as a pH-dependent azide-protecting motif for selective SPAAC conjugations in aqueous media. Finally, we demonstrate the applicability and efficiency of stabilized tetrazolo[1,5-c]pyrimidines for Fragment-Based Drug Design (FBDD) in the field of quorum sensing inhibitors.
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Affiliation(s)
- A Thomann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization (DDOP), Campus C2.3, 66123 Saarbrücken, Germany.
| | - J Zapp
- Saarland University, Department of Pharmaceutical Biology, Campus C2.2, 66123 Saarbrücken, Germany
| | - M Hutter
- Saarland University, Center for Bioinformatics, Campus E2.1, 66123 Saarbrücken, Germany
| | - M Empting
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization (DDOP), Campus C2.3, 66123 Saarbrücken, Germany.
| | - R W Hartmann
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Department for Drug Design and Optimization (DDOP), Campus C2.3, 66123 Saarbrücken, Germany. and Saarland University, Department for Pharmaceutical and Medicinal Chemistry, Campus C2.3, 66123 Saarbrücken, Germany
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19
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Sawant AA, Mukherjee PP, Jangid RK, Galande S, Srivatsan SG. A clickable UTP analog for the posttranscriptional chemical labeling and imaging of RNA. Org Biomol Chem 2016; 14:5832-42. [PMID: 27173127 DOI: 10.1039/c6ob00576d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The development of robust tools and practical RNA labeling strategies that would facilitate the biophysical analysis of RNA in both cell-free and cellular systems will have profound implications in the discovery of new RNA diagnostic tools and therapeutic strategies. In this context, we describe the development of a new alkyne-modified UTP analog, 5-(1,7-octadinyl)uridine triphosphate (ODUTP), which serves as an efficient substrate for the introduction of a clickable alkyne label into RNA transcripts by bacteriophage T7 RNA polymerase and mammalian cellular RNA polymerases. The ODU-labeled RNA is effectively used by reverse transcriptase to produce cDNA, a property which could be utilized in expanding the chemical space of a RNA library in the aptamer selection scheme. Further, the alkyne label on RNA provides a convenient tool for the posttranscriptional chemical functionalization with a variety of biophysical tags (fluorescent, affinity, amino acid and sugar) by using alkyne-azide cycloaddition reaction. Importantly, the ability of endogenous RNA polymerases to specifically incorporate ODUTP into cellular RNA transcripts enabled the visualization of newly transcribing RNA in cells by microscopy using click reactions. In addition to a clickable alkyne group, ODU contains a Raman scattering label (internal disubstituted alkyne), which exhibits characteristic Raman shifts that fall in the Raman-silent region of cells. Our results indicate that an ODU label could potentially facilitate two-channel visualization of RNA in cells by using click chemistry and Raman spectroscopy. Taken together, ODU represents a multipurpose ribonucleoside tool, which is expected to provide new avenues to study RNA in cell-free and cellular systems.
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Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India.
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20
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Ozols K, Cīrule D, Novosjolova I, Stepanovs D, Liepinsh E, Bizdēna Ē, Turks M. Development of N6-methyl-2-(1,2,3-triazol-1-yl)-2′-deoxyadenosine as a novel fluorophore and its application in nucleotide synthesis. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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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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22
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Yamada K, Wahba AS, Bernatchez JA, Ilina T, Martínez-Montero S, Habibian M, Deleavey GF, Götte M, Parniak MA, Damha MJ. Nucleotide Sugar Pucker Preference Mitigates Excision by HIV-1 RT. ACS Chem Biol 2015; 10:2024-33. [PMID: 26131619 DOI: 10.1021/acschembio.5b00263] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of DNA primers containing nucleotides with various sugar pucker conformations at the 3'-terminus were chemically synthesized by solid-phase synthesis. The ability of wild-type (WT) HIV-1 reverse transcriptase (RT) and AZT-resistant (AZTr) RT to excise the 3'-terminal nucleotide was assessed. Nucleosides with a preference for the North conformation were more refractory to excision by both WT-RT and AZTr-RT. We found that DNA primers that contain North puckered-nucleotides at the 3'-terminus can also affect the translocation status of the RT/template/primer complex, which provides an underlying mechanism to avoid being excised. Together, these results point to a correlation between the sugar conformation of the 3'-terminal nucleotide, the precise position of HIV-1 RT on its nucleic acid substrate, and, in turn, its catalytic function. Nucleotide sugar conformation is therefore an important parameter in defining the susceptibility to RT-catalyzed phosphorolytic excision.
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Affiliation(s)
- Ken Yamada
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Alexander S. Wahba
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Jean A. Bernatchez
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
| | - Tatiana Ilina
- Department
of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Saúl Martínez-Montero
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Maryam Habibian
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Glen F. Deleavey
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Matthias Götte
- Department
of Biochemistry, McGill University, 3655 Sir William Osler Promenade, Montreal, Quebec H3G1Y6, Canada
- Department
of Microbiology and Immunology, McGill University, 3775 University, Montreal, Quebec H3A 2B4, Canada
| | - Michael A. Parniak
- Department
of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, 450 Technology Drive, Pittsburgh, Pennsylvania 15219-3143, United States
| | - Masad J. Damha
- Department
of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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23
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Sawant AA, Tanpure AA, Mukherjee PP, Athavale S, Kelkar A, Galande S, Srivatsan SG. A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA. Nucleic Acids Res 2015; 44:e16. [PMID: 26384420 PMCID: PMC4737177 DOI: 10.1093/nar/gkv903] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 08/31/2015] [Indexed: 12/21/2022] Open
Abstract
Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple and modular posttranscriptional chemical labeling and imaging technique for RNA by using a novel toolbox comprised of azide-modified UTP analogs. These analogs facilitate the enzymatic incorporation of azide groups into RNA, which can be posttranscriptionally labeled with a variety of probes by click and Staudinger reactions. Importantly, we show for the first time the specific incorporation of azide groups into cellular RNA by endogenous RNA polymerases, which enabled the imaging of newly transcribing RNA in fixed and in live cells by click reactions. This labeling method is practical and provides a new platform to study RNA in vitro and in cells.
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Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Progya P Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Soumitra Athavale
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ashwin Kelkar
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjeev Galande
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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24
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Wojciechowski F, Groß A, Holder IT, Knörr L, Drescher M, Hartig JS. Pulsed EPR spectroscopy distance measurements of DNA internally labelled with Gd(3+)-DOTA. Chem Commun (Camb) 2015; 51:13850-3. [PMID: 26236790 DOI: 10.1039/c5cc04234h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gd(3+) is increasingly used in EPR spectroscopy due to its increased intracellular stability and signal-to-noise ratios. Here we present the incorporation of Gd(3+)-DOTA into internal positions in DNA. Distance measurements via pulsed Electron Paramagnetic Resonance (EPR) spectroscopy in vitro and in cellula proved enhanced stability and efficiency compared to nitroxide labels.
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Affiliation(s)
- Filip Wojciechowski
- Department of Chemistry, University of Konstanz, Universitätsstr. 10, Konstanz, Germany.
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25
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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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26
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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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27
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28
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Novosjolova I, Bizdēna Ē, Turks M. Synthesis and Applications of Azolylpurine and Azolylpurine Nucleoside Derivatives. European J Org Chem 2015. [DOI: 10.1002/ejoc.201403527] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Estalayo-Adriàn S, Lartia R, Meyer A, Vasseur JJ, Morvan F, Defrancq E. Assessment of the Full Compatibility of Copper(I)-Catalyzed Alkyne-Azide Cycloaddition and Oxime Click Reactions for bis-Labelling of Oligonucleotides. ChemistryOpen 2014; 4:169-73. [PMID: 25969815 PMCID: PMC4420589 DOI: 10.1002/open.201402099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 12/23/2022] Open
Abstract
The conjugation of oligonucleotides with reporters is of great interest for improving their intrinsic properties or endowing new ones. In this context, we report herein a new procedure for the bis-labelling of oligonucleotides through oxime ligation (Click-O) and copper(I)-catalyzed alkyne–azide cycloaddition (Click-H). 5′-Azido and 3′-aldehyde precursors were incorporated into oligonucleotides, and subsequent coupling reactions through Click-O and Click-H (or vice versa) were successfully achieved. In particular, we exhaustively investigated the full compatibility of each required step for both tethering strategies. The results demonstrate that click Huisgen and click oxime reactions are fully compatible. However, whilst both approaches can deliver the targeted doubly conjugated oligonucleotide, the route involving click oxime ligation prior to click Huisgen is significantly more successful. Thus the reactions investigated here can be considered to be key elements of the chemical toolbox for the synthesis of highly sophisticated bioconjugates.
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Affiliation(s)
- Sandra Estalayo-Adriàn
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
| | - Rémy Lartia
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247 CNRS, Université de Montpellier 34095, Montpellier Cedex 5, France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250, Université Grenoble Alpes 38041, Grenoble Cedex 9, France
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30
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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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31
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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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32
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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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33
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Higuchi Y, Furukawa K, Miyazawa T, Minakawa N. Development of a new dumbbell-shaped decoy DNA using a combination of the unnatural base pair ImO(N):NaN(O) and a CuAAC reaction. Bioconjug Chem 2014; 25:1360-9. [PMID: 24965879 DOI: 10.1021/bc500225r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We describe the synthesis and potential application of a new dumbbell-shaped decoy DNA prepared using a combination of the base pair ImO(N):NaN(O) and a copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. The CuAAC reaction between the azido group on the 5'-end of oligodeoxynucleotide (ODN) and the ethynyl group on the NaN(O) base of the opposite strand did not proceed, whereas that between the azido group and the flexible hexynyl group on the NaN(O) base of the opposite strand proceeded smoothly to give a new dumbbell-shaped double-stranded ODN (dsODN). The resulting dsODN had extremely high thermal stability and exhibited exonuclease resistance. In addition, the terminal modification did not affect its helical structure, and thus, the dumbbell-shaped dsODN displayed promising in vitro activity in a competition assay with the NF-kB p50 transcription factor homodimer.
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Affiliation(s)
- Yosuke Higuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokushima , Shomachi 1-78-1, Tokushima 770-8505, Japan
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34
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Elduque X, Pedroso E, Grandas A. Orthogonal protection of peptides and peptoids for cyclization by the thiol-ene reaction and conjugation. J Org Chem 2014; 79:2843-53. [PMID: 24617567 DOI: 10.1021/jo500427c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cyclic peptides and peptoids were prepared using the thiol-ene Michael-type reaction. The linear precursors were provided with additional functional groups allowing for subsequent conjugation: an orthogonally protected thiol, a protected maleimide, or an alkyne. The functional group for conjugation was placed either within the cycle or in an external position. The click reactions employed for conjugation with suitably derivatized nucleoside or oligonucleotides were either cycloadditions (Diels-Alder, Cu(I)-catalyzed azide-alkyne) or the same Michael-type reaction as for cyclization.
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Affiliation(s)
- Xavier Elduque
- Departament de Química Orgànica i IBUB, Facultat de Química, Universitat de Barcelona , Martí i Franquès 1-11, 08028 Barcelona, Spain
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35
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Aralov AV, Chakhmakhchieva OG. [Protection of 2'-hydroxyls in the chemical synthesis of oligoribonucleotides]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2013; 39:3-25. [PMID: 23844504 DOI: 10.1134/s1068162013010020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The review is devoted to the chemical synthesis of oligoribonucleotides and the protecting groups used. In particular the existent methods of blocking 2'-OH function in nucleotide monomers for the RNA synthesis are discussed in detail.
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36
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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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37
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Ichikawa S, Ueno H, Sunadome T, Sato K, Matsuda A. Tris(azidoethyl)amine hydrochloride; a versatile reagent for synthesis of functionalized dumbbell oligodeoxynucleotides. Org Lett 2013; 15:694-7. [PMID: 23339424 DOI: 10.1021/ol400001w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Triazole-cross-linked oligodeoxynucleotides were synthesized using the Cu(I) catalyzed alkyne-azide cycloaddition with tris(azidoethyl)amine hydrochloride and oligodeoxynucleotides possessing N-3-(propargyl)thymidine at both the 3'- and 5'-termini. Further installation of a functional molecule to the dumbbell oligodeoxynucleotides was achieved by utilizing the remaining azide group.
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Affiliation(s)
- Satoshi Ichikawa
- Kita-12, Nishi-6, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.
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38
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Uzagare MC, Claußnitzer I, Gerrits M, Bannwarth W. A Novel Method for the Labelling of Peptides and Proteins through a Bioorthogonal Staudinger Reaction by Using 2-Cyanoethyl Phosphoramidites. Chembiochem 2012; 13:2204-8. [DOI: 10.1002/cbic.201200528] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Indexed: 11/11/2022]
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39
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Gerland B, Goudot A, Pourceau G, Meyer A, Vidal S, Souteyrand E, Vasseur JJ, Chevolot Y, Morvan F. Synthesis of Homo- and Heterofunctionalized Glycoclusters and Binding to Pseudomonas aeruginosa Lectins PA-IL and PA-IIL. J Org Chem 2012; 77:7620-6. [DOI: 10.1021/jo300826u] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Béatrice Gerland
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Alice Goudot
- Institut des Nanotechnologies
de Lyon (INL), Université de Lyon, UMR 5270 CNRS Ecole Centrale de Lyon, 36 Avenue Guy de Collongue,
69134 Ecully Cedex, France
| | - Gwladys Pourceau
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Albert Meyer
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Sébastien Vidal
- Institut de Chimie et Biochimie
Moléculaires et Supramoléculaires (ICBMS), Laboratoire
de Chimie Organique 2 - Glycochimie, UMR 5246 CNRS, Université Claude Bernard Lyon 1, 43 Boulevard du 11 Novembre 1918,
69622 Villeurbanne, France
| | - Eliane Souteyrand
- Institut des Nanotechnologies
de Lyon (INL), Université de Lyon, UMR 5270 CNRS Ecole Centrale de Lyon, 36 Avenue Guy de Collongue,
69134 Ecully Cedex, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
| | - Yann Chevolot
- Institut des Nanotechnologies
de Lyon (INL), Université de Lyon, UMR 5270 CNRS Ecole Centrale de Lyon, 36 Avenue Guy de Collongue,
69134 Ecully Cedex, France
| | - François Morvan
- Institut des Biomolécules
Max Mousseron (IBMM), UMR 5247 CNRS - Université Montpellier 1, Université Montpellier 2, Place
Eugène Bataillon, CC1704, 34095 Montpellier Cedex 5, France
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40
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Lakshman MK, Kumar A, Balachandran R, Day BW, Andrei G, Snoeck R, Balzarini J. Synthesis and biological properties of C-2 triazolylinosine derivatives. J Org Chem 2012; 77:5870-83. [PMID: 22758929 DOI: 10.1021/jo300628y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
O(6)-(Benzotriazol-1H-yl)guanosine and its 2'-deoxy analogue are readily converted to the O(6)-allyl derivatives that upon diazotization with t-BuONO and TMS-N(3) yield the C-2 azido derivatives. We have previously analyzed the solvent-dependent azide·tetrazole equilibrium of C-6 azidopurine nucleosides, and in contrast to these, the O(6)-allyl C-2 azido nucleosides appear to exist predominantly in the azido form, relatively independent of solvent polarity. In the presently described cases, the tetrazole appears to be very minor. Consistent with the presence of the azido functionality, each neat C-2 azide displayed a prominent IR band at 2126-2130 cm(-1). A screen of conditions for the ligation of the azido nucleosides with alkynes showed that CuCl in t-BuOH/H(2)O is optimal, yielding C-2 1,2,3-triazolyl nucleosides in 70-82% yields. Removal of the silyl groups with Et(3)N·3HF followed by deallylation with PhSO(2)Na/Pd(PPh(3))(4) gave the C-2 triazolylinosine nucleosides. In a continued demonstration of the versatility of O(6)-(benzotriazol-1H-yl)purine nucleosides, one C-2 triazolylinosine derivative was converted to two adenosine analogues via these intermediates, under mild conditions. Products were desilylated for biological assays. The two C-2 triazolyl adenosine analogues demonstrated pronounced antiproliferative activity in human ovarian and colorectal carcinoma cell cultures. When evaluated for antiviral activity against a broad spectrum of DNA and RNA viruses, some of the C-2 triazolylinosine derivatives showed modest inhibitory activity against cytomegalovirus.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry, The City College and The City University of New York, 160 Convent Avenue, New York, New York 10031, USA.
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41
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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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42
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Aralov AV, Klykov VN, Chakhmakhcheva OG, Efimov VA. [Monomers containing 2'-o-alkoxymethyl groups as synthons for the synthesis of oligoribonucleotides by the phosphotriester method]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2012; 37:654-61. [PMID: 22332361 DOI: 10.1134/s1068162011050025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A general scheme for the synthesis of ribonucleotide monomers containing alkoxymethyl group in 2'-O-position for the solid-phase phosphotriester oligonucleotide synthesis using O-nucleophilic intramolecular catalysis has been developed. In particular, the monomers containing 2'-O-modifying 2-azidoethoxymethyl, propargyloxymethyl, or 3,4-cyclocarbonatebutoxymethyl groups has been prepared.
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43
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Morvan F, Vidal S, Souteyrand E, Chevolot Y, Vasseur JJ. DNA glycoclusters and DNA-based carbohydrate microarrays: From design to applications. RSC Adv 2012. [DOI: 10.1039/c2ra21550k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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44
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Rao H, Sawant AA, Tanpure AA, Srivatsan SG. Posttranscriptional chemical functionalization of azide-modified oligoribonucleotides by bioorthogonal click and Staudinger reactions. Chem Commun (Camb) 2011; 48:498-500. [PMID: 22006199 DOI: 10.1039/c1cc15659d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Direct incorporation of azide groups into RNA oligonucleotides by in vitro transcription reactions in the presence of a new azide-modified UTP analogue, and subsequent posttranscriptional chemical labeling of azide-modified oligoribonucleotide transcripts by click and Staudinger reactions are described. This postsynthetic labeling protocol is robust and modular, and offers an alternative access to RNA labeled with biophysical probes.
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Affiliation(s)
- Harita Rao
- Indian Institute of Science Education and Research, Sai Trinity Building, Pashan, Pune 411021, India
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45
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Lartia R, Murat P, Dumy P, Defrancq E. Versatile introduction of azido moiety into oligonucleotides through diazo transfer reaction. Org Lett 2011; 13:5672-5. [PMID: 21958022 DOI: 10.1021/ol202397e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of a diazo transfer (DZT) reagent enables clean and efficient conversion of aminated oligodeoxyribonucleotides (ODNs) into their azido counterparts under mild conditions. ODNs bearing an amino tether at the 3', 5', or any internal position could be modified in this manner thus demonstrating the versatility of this reaction. Easy access to such azido-modified ODNs is of great interest for conjugation in particular through copper catalyzed 1,3-dipolar cycloaddition (CuAAC reaction).
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Affiliation(s)
- Rémy Lartia
- Département de Chimie Moléculaire, UMR CNRS 5250, Université Joseph Fourier, BP 53, 38041 Grenoble Cedex 9, France
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46
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Coppola C, Simeone L, De Napoli L, Montesarchio D. On the Compatibility of Azides in Phosphoramidite-Based Couplings: Synthesis of a Novel, Convertible Azido-Functionalized CyPLOS Analogue. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001057] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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47
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Aigner M, Hartl M, Fauster K, Steger J, Bister K, Micura R. Chemical synthesis of site-specifically 2'-azido-modified RNA and potential applications for bioconjugation and RNA interference. Chembiochem 2011; 12:47-51. [PMID: 21171007 PMCID: PMC3193913 DOI: 10.1002/cbic.201000646] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 11/01/2010] [Indexed: 01/13/2023]
Affiliation(s)
- Michaela Aigner
- Institute of Organic Chemistry, Center for Molecular Biosciences CMBI, University of Innsbruck, 6020 Innsbruck, Austria
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48
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Ustinov AV, Stepanova IA, Dubnyakova VV, Zatsepin TS, Nozhevnikova EV, Korshun VA. Modification of nucleic acids using [3 + 2]-dipolar cycloaddition of azides and alkynes. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:437-81. [DOI: 10.1134/s1068162010040011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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49
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Efimov VA, Aralov AV, Klykov VN, Chakhmakhcheva OG. Synthesis of RNA by the rapid phosphotriester method using azido-based 2'-O-protecting groups. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2010; 28:846-65. [PMID: 20183623 DOI: 10.1080/15257770903170286] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The azidomethyl and 2-(azidomethyl)benzoyl as 2'-OH protecting groups are reported for preparation of oligoribonucleotides by the phosphotriester solid-phase method using O-nucleophilic intramolecular catalysis. The procedures for the synthesis of the corresponding monomer synthons were developed and the usefulness of the application of 2'-O-azidomethyl and 2'-O-2-(azidomethyl)benzoyl groups was examined in the synthesis of different RNA fragments with a chain length of 15-22 nucleotides. The azidomethyl group was found to be more preferable for effective synthesis of oligoribonucleotides. Hybridization properties of RNAs toward their complementary oligonucleotides were examined before and after the removal of 2'-O-azidomethyl groups.
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Affiliation(s)
- V A Efimov
- Russian Academy of Sciences, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.
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50
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Ostaci RV, Damiron D, Grohens Y, Léger L, Drockenmuller E. Click chemistry grafting of poly(ethylene glycol) brushes to alkyne-functionalized pseudobrushes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1304-1310. [PMID: 19785428 DOI: 10.1021/la902482q] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A versatile method for the grafting of azide-terminated polymer chains to alkyne-functionalized pseudobrushes by the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition has been developed. First, poly[(propargyl methacrylate)-r-(glycidyl methacrylate)-r-(methyl methacrylate)] random copolymers with monomer ratios of respectively 27/27/46, 41/31/28, and 45/55/0 were synthesized by RAFT polymerization. Then, dense alkyne-functionalized pseudobrushes were grafted in melt by thermal ring-opening of the glycidyl groups by the silanols from the silicon substrate. Finally, the grafting of tailor-made alpha-methoxy-omega-azido-poly(ethylene glycol)s (M(w) approximately 5000, 20,000, and 50,000 g/mol) by Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition was performed in sealed reactors at 60 degrees C for 72 h using a polymer weight fraction of 10% in tetrahydrofuran and Cu(PPh(3))(3)Br/DIPEA as the catalytic system. Alkyne-functionalized pseudobrushes and poly(ethylene glycol) brushes were characterized by ellipsometry, scanning probe microscopy, and water contact angle measurements. This "grafting-to" approach represents a fast and versatile method to provide thick and homogeneous polymer brushes with a high surface coverage. A major benefit of this strategy is the tunable and versatile tethering of alkyne functionalities to silicon substrates using a straightforward spin-coating procedure.
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Affiliation(s)
- Roxana-Viorela Ostaci
- Ingénierie des Matériaux Polymères (UMR CNRS 5223), Université Claude Bernard Lyon 1, 15 Boulevard Latarjet, 69622 Villeurbanne Cedex, France
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