1
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Bristiel A, Cadinot M, Pizzonero M, Taran F, Urban D, Guignard R, Guianvarc'h D. 2'-Modified Thymidines with Bioorthogonal Cyclopropene or Sydnone as Building Blocks for Copper-Free Postsynthetic Functionalization of Chemically Synthesized Oligonucleotides. Bioconjug Chem 2023; 34:1613-1621. [PMID: 37669427 DOI: 10.1021/acs.bioconjchem.3c00284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
The development of facile methods for conjugating relevant probes, ligands, or delivery agents onto oligonucleotides (ONs) is highly desirable both for fundamental studies in chemical biology and for improving the pharmacology of ONs in medicinal chemistry. Numerous efforts have been focused on the introduction of bioorthogonal groups onto phosphoramidite building blocks, allowing the controlled chemical synthesis of reactive ONs for postsynthetic modifications. Among these building blocks, alkyne, cyclooctynes, trans-cyclooctene, and norbornene have been proved to be compatible with automated solid-phase chemistry. Herein, we present the development of novel 2'-functionalized nucleoside phosphoramidite monomers comprising bioorthogonal methylcyclopropene or sydnone moieties and their introduction for the first time to ON solid-phase synthesis. Traceless ON postsynthetic modifications with reactive complementary probes were successfully achieved through either inverse electron-demand Diels-Alder (iEDDA) reactions or strain-promoted sydnone-alkyne cycloaddition (SPSAC). These results expand the set of bioorthogonal phosphoramidite building blocks to generate ONs for postsynthetic labeling.
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Affiliation(s)
- Alexandra Bristiel
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, 91405, Orsay, France
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Manon Cadinot
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Mathieu Pizzonero
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Frédéric Taran
- CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SCBM, Université Paris-Saclay, Gif-sur-Yvette 91191, France
| | - Dominique Urban
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, 91405, Orsay, France
| | - Raphaël Guignard
- Unité Drug Design Small Molecules, Institut de Recherche et Développement Servier Paris-Saclay, 22 route 128, Gif-sur-Yvette 91190, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), UMR 8182, 91405, Orsay, France
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2
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Govindarajan A, Gnanasambandam V. Toward Intracellular Bioconjugation Using Transition-Metal-Free Techniques. Bioconjug Chem 2021; 32:1431-1454. [PMID: 34197073 DOI: 10.1021/acs.bioconjchem.1c00173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Bioconjugation is the chemical strategy of covalent modification of biomolecules, using either an external reagent or other biomolecules. Since its inception in the twentieth century, the technique has grown by leaps and bounds, and has a variety of applications in chemical biology. However, it is yet to reach its full potential in the study of biochemical processes in live cells, mainly because the bioconjugation strategies conflict with cellular processes. This has mostly been overcome by using transition metal catalysts, but the presence of metal centers limit them to in vitro use, or to the cell surface. These hurdles can potentially be circumvented by using metal-free strategies. However, the very modifications that are necessary to make such metal-free reactions proceed effectively may impact their biocompatibility. This is because biological processes are easily perturbed and greatly depend on the prevailing inter- and intracellular environment. With this taken into consideration, this review analyzes the applicability of the transition-metal-free strategies reported in this decade to the study of biochemical processes in vivo.
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Affiliation(s)
- Aaditya Govindarajan
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
| | - Vasuki Gnanasambandam
- Department of Chemistry, Pondicherry University, Kalapet, Puducherry - 605014, India
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3
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Török G, Cserép GB, Telek A, Arany D, Váradi M, Homolya L, Kellermayer M, Kele P, Németh K. Large Stokes-shift bioorthogonal probes for STED, 2P-STED and multi-color STED nanoscopy. Methods Appl Fluoresc 2021; 9:015006. [PMID: 33427202 DOI: 10.1088/2050-6120/abb363] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Synthesis and multiple STED imaging applications of four, red-emitting (610-670 nm), tetrazine-functionalized fluorescent probes (CBRD = Chemical Biology Research group Dye 1-4) with large Stokes-shift is presented. Present studies revealed the super-resolution microscopy applicability of the probes as demonstrated through bioorthogonal labeling scheme of cytoskeletal proteins actin and keratin-19, and mitochondrial protein TOMM20. Furthermore, super-resolved images of insulin receptors in live-cell bioorthogonal labeling schemes through a genetically encoded cyclooctynylated non-canonical amino acid are also presented. The large Stokes-shifts and the wide spectral bands of the probes enabled the use of two common depletion lasers (660 nm and 775 nm). The probes were also found suitable for super-resolution microscopy in combination with two-photon excitation (2P-STED) resulting in improved spatial resolution. One of the dyes was also used together with two commercial dyes in the three-color STED imaging of intracellular structures.
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Affiliation(s)
- György Török
- Chemical Biology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary. Department of Biophysics and Radiation Biology, Semmelweis University, Tűzoltó u. 37-47., H-1094 Budapest, Hungary. Laboratory of Molecular Cell Biology, Institute of Enzymology, Research Centre for Natural Sciences, Magyar tudósok krt. 2., H-1117 Budapest, Hungary
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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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Ganz D, Harijan D, Wagenknecht HA. Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry. RSC Chem Biol 2020; 1:86-97. [PMID: 34458750 PMCID: PMC8341813 DOI: 10.1039/d0cb00047g] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes. Efficient bioorthogonal chemistry and in particular cycloadditions fullfill the requirements for cellular applications. The broadly applied Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC), however, is limited to labellings in vitro and in fixed cells due to the cytotoxicity of copper salts. Currently, there are three types of copper-free cycloadditions used for nucleic acid labelling in the cellular environment: (i) the ring-strain promoted azide-alkyne cycloaddition (SPAAC), (ii) the "photoclick" 1,3-dipolar cycloadditions, and (iii) the Diels-Alder reactions with inverse electron demand (iEDDA). We review only those building blocks for chemical synthesis on solid phase of DNA and RNA and for enzymatic DNA and RNA preparation, which were applied for labelling of DNA and RNA in situ or in vivo, i.e. in the cellular environment, in fixed or in living cells, by the use of bioorthogonal cycloaddition chemistry. Additionally, we review the current status of orthogonal dual and triple labelling of DNA and RNA in vitro to demonstrate their potential for future applications in situ or in vivo.
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Affiliation(s)
- Dorothée Ganz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Dennis Harijan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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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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Tera M, Luedtke NW. Three-Component Bioorthogonal Reactions on Cellular DNA and RNA. Bioconjug Chem 2019; 30:2991-2997. [DOI: 10.1021/acs.bioconjchem.9b00630] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Masayuki Tera
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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8
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He Z, Chen Y, Wang Y, Wang J, Mo J, Fu B, Wang Z, Du Y, Zhou X. A rapidly photo-activatable light-up fluorescent nucleoside and its application in DNA base variation sensing. Chem Commun (Camb) 2018; 52:8545-8. [PMID: 27315545 DOI: 10.1039/c6cc03098j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A new DNA building block (d(Tet)U) bearing a tetrazole and allyloxy group at N-phenyl ring linked through an aminopropynyl linker to the 5-position of 2'-deoxyuridine was synthesized. The modified DNA can be lit up via a photoinduced intramolecular tetrazole-alkene cycloaddition reaction, but quenched when the fully-matched double strand is formed. This conspicuous difference in fluorescence could open a door for DNA single nucleotide polymorphism (SNP) typing.
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Affiliation(s)
- Zhiyong He
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Yuqi Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Jiaqi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Jing Mo
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Boshi Fu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Zijing Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Yuhao Du
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
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9
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Naik A, Alzeer J, Triemer T, Bujalska A, Luedtke NW. Chemoselective Modification of Vinyl DNA by Triazolinediones. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702554] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Anu Naik
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Jawad Alzeer
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Therese Triemer
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Anna Bujalska
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Nathan W. Luedtke
- Department of Chemistry; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
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10
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Naik A, Alzeer J, Triemer T, Bujalska A, Luedtke NW. Chemoselective Modification of Vinyl DNA by Triazolinediones. Angew Chem Int Ed Engl 2017; 56:10850-10853. [PMID: 28561928 DOI: 10.1002/anie.201702554] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/09/2017] [Indexed: 11/10/2022]
Abstract
A new method for the post-synthetic modification of nucleic acids was developed that involves mixing a phenyl triazolinedione (PTAD) derivative with DNA containing a vinyl nucleobase. The resulting reactions proceeded through step-wise mechanisms, giving either a formal [4+2] cycloaddition product, or, depending on the context of nucleobase, PTAD addition along with solvent trapping to give a secondary alcohol in water. Catalyst-free addition between PTAD and the terminal alkene of 5-vinyl-2'-deoxyuridine (VdU) was exceptionally fast, with a second-order rate constant of 2×103 m-1 s-1 . PTAD derivatives selectively reacted with VdU-containing oligonucleotides in a conformation-selective manner, with higher yields observed for G-quadruplex versus duplex DNA. These results demonstrate a new strategy for copper-free bioconjugation of DNA that can potentially be used to probe nucleic acid conformations in cells.
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Affiliation(s)
- Anu Naik
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jawad Alzeer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Therese Triemer
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Anna Bujalska
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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11
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Tang Y, Wang T, Chen M, He X, Qu X, Feng X. Tension promoted circular probe for highly selective microRNA detection and imaging. Biosens Bioelectron 2016; 85:151-156. [DOI: 10.1016/j.bios.2016.05.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 05/01/2016] [Accepted: 05/02/2016] [Indexed: 11/16/2022]
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12
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Eördögh Á, Steinmeyer J, Peewasan K, Schepers U, Wagenknecht HA, Kele P. Polarity Sensitive Bioorthogonally Applicable Far-Red Emitting Labels for Postsynthetic Nucleic Acid Labeling by Copper-Catalyzed and Copper-Free Cycloaddition. Bioconjug Chem 2016; 27:457-64. [DOI: 10.1021/acs.bioconjchem.5b00557] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ádám Eördögh
- Chemical
Biology Research Group, Institute of Organic Chemistry, Research Centre
for Natural Sciences, Hungarian Academy of Sciences. Magyar tudósok
krt. 2, H-1117, Budapest, Hungary
| | - Jeannine Steinmeyer
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Krisana Peewasan
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Ute Schepers
- Institute
of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), H.-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Achim Wagenknecht
- Institute
of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Péter Kele
- Chemical
Biology Research Group, Institute of Organic Chemistry, Research Centre
for Natural Sciences, Hungarian Academy of Sciences. Magyar tudósok
krt. 2, H-1117, Budapest, Hungary
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13
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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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14
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Lázár L, Nagy M, Borbás A, Herczegh P, Zsuga M, Kéki S. Conjugation of Bioactive Molecules to a Fluorescent Dithiomaleimide by Photoinduced and BEt3-Initiated Thio-Click Reactions. European J Org Chem 2015. [DOI: 10.1002/ejoc.201501116] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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15
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Dadová J, Vrábel M, Adámik M, Brázdová M, Pohl R, Fojta M, Hocek M. Azidopropylvinylsulfonamide as a New Bifunctional Click Reagent for Bioorthogonal Conjugations: Application for DNA–Protein Cross‐Linking. Chemistry 2015; 21:16091-102. [DOI: 10.1002/chem.201502209] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Jitka Dadová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
| | - Milan Vrábel
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
| | - Matej Adámik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno (Czech Republic)
| | - Marie Brázdová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno (Czech Republic)
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
| | - Miroslav Fojta
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, 61265 Brno (Czech Republic)
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno (Czech Republic)
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nám. 2, 16610 Prague 6 (Czech Republic)
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843 Prague 2 (Czech Republic)
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16
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Cserép GB, Herner A, Kele P. Bioorthogonal fluorescent labels: a review on combined forces. Methods Appl Fluoresc 2015; 3:042001. [DOI: 10.1088/2050-6120/3/4/042001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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17
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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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18
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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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Wang K, Wang D, Ji K, Chen W, Zheng Y, Dai C, Wang B. Post-synthesis DNA modifications using a trans-cyclooctene click handle. Org Biomol Chem 2015; 13:909-15. [PMID: 25407744 PMCID: PMC4377304 DOI: 10.1039/c4ob02031f] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Post-synthesis DNA modification is a very useful method for DNA functionalization. This is achieved by using a modified NTP, which has a handle for further modifications, replacing the corresponding natural NTP in polymerase-catalyzed DNA synthesis. Subsequently, the handle can be used for further functionalization after PCR, preferably through a very fast reaction. Herein we describe polymerase-mediated incorporation of trans-cyclooctene modified thymidine triphosphate (TCO-TTP). Subsequently, the trans-cyclooctene group was reacted with a tetrazine tethered to other functional groups through a very fast click reaction. The utility of this DNA functionalization method was demonstrated with the incorporation of a boronic acid group and a fluorophore. The same approach was also successfully used in modifying a known aptamer for fluorescent labelling applications.
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Affiliation(s)
- Ke Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302-3965, USA.
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Arndt S, Wagenknecht HA. "Photoclick" postsynthetic modification of DNA. Angew Chem Int Ed Engl 2014; 53:14580-2. [PMID: 25359534 DOI: 10.1002/anie.201407874] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 09/12/2014] [Indexed: 12/31/2022]
Abstract
A new DNA building block bearing a push-pull-substituted diaryltetrazole linked to the 5-position of 2'-deoxyuridine through an aminopropynyl group was synthesized. The accordingly modified oligonucleotide allows postsynthetic labeling with a maleimide-modified sulfo-Cy3 dye, N-methylmaleimide, and methylmethacrylate as dipolarophiles by irradiation at 365 nm (LED). The determined rate constant of (23±7) M(-1) s(-1) is remarkably high with respect to other copper-free bioorthogonal reactions and comparable with the copper-catalyzed cycloaddition between azides and acetylenes.
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Affiliation(s)
- Stefanie Arndt
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
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