1
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Rudenko AY, Mariasina SS, Sergiev PV, Polshakov VI. Analogs of S-Adenosyl-L-Methionine in Studies of Methyltransferases. Mol Biol 2022; 56:229-250. [PMID: 35440827 PMCID: PMC9009987 DOI: 10.1134/s002689332202011x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 01/02/2023]
Abstract
Methyltransferases (MTases) play an important role in the functioning of living systems, catalyzing the methylation reactions of DNA, RNA, proteins, and small molecules, including endogenous compounds and drugs. Many human diseases are associated with disturbances in the functioning of these enzymes; therefore, the study of MTases is an urgent and important task. Most MTases use the cofactor S‑adenosyl‑L‑methionine (SAM) as a methyl group donor. SAM analogs are widely applicable in the study of MTases: they are used in studies of the catalytic activity of these enzymes, in identification of substrates of new MTases, and for modification of the substrates or substrate linking to MTases. In this review, new synthetic analogs of SAM and the problems that can be solved with their usage are discussed.
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Affiliation(s)
- A. Yu. Rudenko
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Zelinsky Institute of Organic Chemistry, 119991 Moscow, Russia
| | - S. S. Mariasina
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - P. V. Sergiev
- Institute of Functional Genomics, Moscow State University, 119991 Moscow, Russia
| | - V. I. Polshakov
- Faculty of Fundamental Medicine, Moscow State University, 119991 Moscow, Russia
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2
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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3
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DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:535-562. [DOI: 10.1007/978-3-031-11454-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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4
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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5
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Sirasunthorn N, Jailwala A, Gerber A, Comstock LR. Evaluation of
N
‐Mustard Analogues of
S
‐Adenosyl‐L‐methionine with Eukaryotic DNA Methyltransferase 1. ChemistrySelect 2019. [DOI: 10.1002/slct.201902940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nichanun Sirasunthorn
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Anuj Jailwala
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Anna Gerber
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Lindsay R. Comstock
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
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6
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Methyltransferase-Directed Labeling of Biomolecules and its Applications. Angew Chem Int Ed Engl 2017; 56:5182-5200. [PMID: 27943567 PMCID: PMC5502580 DOI: 10.1002/anie.201608625] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Indexed: 01/01/2023]
Abstract
Methyltransferases (MTases) form a large family of enzymes that methylate a diverse set of targets, ranging from the three major biopolymers to small molecules. Most of these MTases use the cofactor S-adenosyl-l-Methionine (AdoMet) as a methyl source. In recent years, there have been significant efforts toward the development of AdoMet analogues with the aim of transferring moieties other than simple methyl groups. Two major classes of AdoMet analogues currently exist: doubly-activated molecules and aziridine based molecules, each of which employs a different approach to achieve transalkylation rather than transmethylation. In this review, we discuss the various strategies for labelling and functionalizing biomolecules using AdoMet-dependent MTases and AdoMet analogues. We cover the synthetic routes to AdoMet analogues, their stability in biological environments and their application in transalkylation reactions. Finally, some perspectives are presented for the potential use of AdoMet analogues in biology research, (epi)genetics and nanotechnology.
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Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale BiologySchool of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM)Station 17CH-1015LausanneSwitzerland
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Robert K. Neely
- School of ChemistryUniversity of BirminghamEdgbastonBirminghamB15 2TTUK
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of ChemistryKU LeuvenCelestijnenlaan 200FB-3001HeverleeBelgium
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7
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Deen J, Vranken C, Leen V, Neely RK, Janssen KPF, Hofkens J. Die Methyltransferase-gesteuerte Markierung von Biomolekülen und ihre Anwendungen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201608625] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jochem Deen
- Laboratory of Nanoscale Biology; School of Engineering, EPFL, STI IBI-STI LBEN BM 5134 (Bâtiment BM); Station 17 CH-1015 Lausanne Schweiz
| | - Charlotte Vranken
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Volker Leen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Robert K. Neely
- School of Chemistry; University of Birmingham; Edgbaston Birmingham B15 2TT Großbritannien
| | - Kris P. F. Janssen
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
| | - Johan Hofkens
- Laboratory of Photochemistry and Spectroscopy, Department of Chemistry; KU Leuven; Celestijnenlaan 200F B-3001 Heverlee Belgien
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8
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Catcott KC, Yan J, Qu W, Wysocki VH, Zhou ZS. Identifying Unknown Enzyme-Substrate Pairs from the Cellular Milieu with Native Mass Spectrometry. Chembiochem 2017; 18:613-617. [PMID: 28140508 DOI: 10.1002/cbic.201600634] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Indexed: 01/22/2023]
Abstract
The enzyme-substrate complex is inherently transient, rendering its detection difficult. In our framework designed for bisubstrate systems-isotope-labeled, activity-based identification and tracking (IsoLAIT)-the common substrate, such as S-adenosyl-l-methionine (AdoMet) for methyltransferases, is replaced by an analogue (e.g., S-adenosyl-l-vinthionine) that, as a probe, creates a tightly bound [enzyme⋅substrate⋅probe] complex upon catalysis by thiopurine-S-methyltransferase (TPMT, EC 2.1.1.67). This persistent complex is then identified by native mass spectrometry from the cellular milieu without separation. Furthermore, the probe's isotope pattern flags even unknown substrates and enzymes. IsoLAIT is broadly applicable for other enzyme systems, particularly those catalyzing group transfer and with multiple substrates, such as glycosyltransferases and kinases.
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Affiliation(s)
- Kalli C Catcott
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Jing Yan
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Wanlu Qu
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
| | - Vicki H Wysocki
- Department of Chemistry and Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH, 43210, USA
| | - Zhaohui Sunny Zhou
- Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA.,Barnett Institute of Chemical and Biological Analysis, Northeastern University, 360 Huntington Avenue, Boston, MA, 02115, USA
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9
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Engineering and Directed Evolution of DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016. [PMID: 27826849 DOI: 10.1007/978-3-319-43624-1_18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
DNA methyltransferases (MTases) constitute an attractive target for protein engineering, thus opening the road to new ways of manipulating DNA in a unique and selective manner. Here, we review various aspects of MTase engineering, both methodological and conceptual, and also discuss future directions and challenges. Bacterial MTases that are part of restriction/modification (R/M) systems offer a convenient way for the selection of large gene libraries, both in vivo and in vitro. We review these selection methods, their strengths and weaknesses, and also the prospects for new selection approaches that will enable the directed evolution of mammalian DNA methyltransferases (Dnmts). We explore various properties of MTases that may be subject to engineering. These include engineering for higher stability and soluble expression (MTases, including bacterial ones, are prone to misfolding), engineering of the DNA target specificity, and engineering for the usage of S-adenosyl-L-methionine (AdoMet) analogs. Directed evolution of bacterial MTases also offers insights into how these enzymes readily evolve in nature, thus yielding MTases with a huge spectrum of DNA target specificities. Engineering for alternative cofactors, on the other hand, enables modification of DNA with various groups other than methyl and thus can be employed to map and redirect DNA epigenetic modifications.
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10
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Vranken C, Fin A, Tufar P, Hofkens J, Burkart MD, Tor Y. Chemoenzymatic synthesis and utilization of a SAM analog with an isomorphic nucleobase. Org Biomol Chem 2016; 14:6189-92. [PMID: 27270873 DOI: 10.1039/c6ob00844e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
SalL, an enzyme that catalyzes the synthesis of SAM from l-methionine and 5'-chloro-5'-deoxyoadenosine, is shown to accept 5'-chloro-5'-deoxythienoadenosine as a substrate and facilitate the synthesis of a synthetic SAM analog with an unnatural nucleobase. This synthetic cofactor is demonstrated to replace SAM in the DNA methylation reaction with M.TaqI.
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Affiliation(s)
- C Vranken
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Heverlee, Belgium
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11
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Abstract
Chromatin is the universal template of genetic information in all eukaryotic organisms. Chemical modifications of the DNA-packaging histone proteins and the DNA bases are crucial signaling events in directing the use and readout of eukaryotic genomes. The enzymes that install and remove these chromatin modifications as well as the proteins that bind these marks govern information that goes beyond the sequence of DNA. Therefore, these so-called epigenetic regulators are intensively studied and represent promising drug targets in modern medicine. We summarize and discuss recent advances in the field of chemical biology that have provided chromatin research with sophisticated tools for investigating the composition, activity, and target sites of chromatin modifying enzymes and reader proteins.
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Affiliation(s)
- Wolfgang Fischle
- King Abdullah University of Science and Technology (KAUST), Environmental Epigenetics Program, Thuwal 23955-6900, Saudi Arabia
- Max Planck Institute for Biophysical Chemistry, Laboratory of Chromatin Biochemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty
Institute of Biochemistry (IFIB), University of Tübingen, Hoppe-Seyler-Str.
4, 72076 Tübingen, Germany
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12
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Abstract
S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.
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Affiliation(s)
- Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
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13
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Qu W, Catcott KC, Zhang K, Liu S, Guo JJ, Ma J, Pablo M, Glick J, Xiu Y, Kenton N, Ma X, Duclos RI, Zhou ZS. Capturing Unknown Substrates via in Situ Formation of Tightly Bound Bisubstrate Adducts: S-Adenosyl-vinthionine as a Functional Probe for AdoMet-Dependent Methyltransferases. J Am Chem Soc 2016; 138:2877-80. [DOI: 10.1021/jacs.5b05950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Kun Zhang
- School
of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | | | | | - Jisheng Ma
- School
of Pharmaceutical Science, Wenzhou Medical University, Wenzhou 325035, China
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14
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Tomkuvienė M, Kriukienė E, Klimašauskas S. DNA Labeling Using DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:511-535. [PMID: 27826850 PMCID: PMC11032744 DOI: 10.1007/978-3-319-43624-1_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA methyltransferases (MTases) uniquely combine the ability to recognize and covalently modify specific target sequences in DNA using the ubiquitous cofactor S-adenosyl-L-methionine (AdoMet). Although DNA methylation plays important roles in biological signaling, the transferred methyl group is a poor reporter and is highly inert to further biocompatible derivatization. To unlock the biotechnological power of these enzymes, two major types of cofactor AdoMet analogs were developed that permit targeted MTase-directed attachment of larger moieties containing functional or reporter groups onto DNA. One such approach (named sequence-specific methyltransferase-induced labeling, SMILing) uses reactive aziridine or N-mustard mimics of the cofactor AdoMet, which render targeted coupling of a whole cofactor molecule to the target DNA. The second approach (methyltransferase-directed transfer of activated groups, mTAG) uses AdoMet analogs with a sulfonium-bound extended side chain replacing the methyl group, which permits MTase-directed covalent transfer of the activated side chain alone. As the enlarged cofactors are not always compatible with the active sites of native MTases, steric engineering of the active site has been employed to optimize their alkyltransferase activity. In addition to the described cofactor analogs, recently discovered atypical reactions of DNA cytosine-5 MTases involving non-cofactor-like compounds can also be exploited for targeted derivatization and labeling of DNA. Altogether, these approaches offer new powerful tools for sequence-specific covalent DNA labeling, which not only pave the way to developing a variety of useful techniques in DNA research, diagnostics, and nanotechnologies but have already proven practical utility for optical DNA mapping and epigenome studies.
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Affiliation(s)
- Miglė Tomkuvienė
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10222, Lithuania
| | - Edita Kriukienė
- Institute of Biotechnology, Vilnius University, Vilnius, LT-10222, Lithuania
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15
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Kunkel F, Lurz R, Weinhold E. A 7-Deazaadenosylaziridine Cofactor for Sequence-Specific Labeling of DNA by the DNA Cytosine-C5 Methyltransferase M.HhaI. Molecules 2015; 20:20805-22. [PMID: 26610450 PMCID: PMC6332214 DOI: 10.3390/molecules201119723] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 11/03/2015] [Accepted: 11/10/2015] [Indexed: 12/30/2022] Open
Abstract
DNA methyltransferases (MTases) catalyze the transfer of the activated methyl group of the cofactor S-adenosyl-l-methionine (AdoMet or SAM) to the exocyclic amino groups of adenine or cytosine or the C5 ring atom of cytosine within specific DNA sequences. The DNA adenine-N6 MTase from Thermus aquaticus (M.TaqI) is also capable of coupling synthetic N-adenosylaziridine cofactor analogues to its target adenine within the double-stranded 5′-TCGA-3′ sequence. This M.TaqI-mediated coupling reaction was exploited to sequence-specifically deliver fluorophores and biotin to DNA using N-adenosylaziridine derivatives carrying reporter groups at the 8-position of the adenine ring. However, these 8-modified aziridine cofactors were poor substrates for the DNA cytosine-C5 MTase from Haemophilus haemolyticus (M.HhaI). Based on the crystal structure of M.HhaI in complex with a duplex oligodeoxynucleotide and the cofactor product, we synthesized a stable 7-deazaadenosylaziridine derivative with a biotin group attached to the 7-position via a flexible linker. This 7-modified aziridine cofactor can be efficiently used by M.HhaI for the direct, quantitative and sequence-specific delivery of biotin to the second cytosine within 5′-GCGC-3′ sequences in short duplex oligodeoxynucleotides and plasmid DNA. In addition, we demonstrate that biotinylation by M.HhaI depends on the methylation status of the target cytosine and, thus, could provide a method for cytosine-C5 DNA methylation detection in mammalian DNA.
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Affiliation(s)
- Falk Kunkel
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen D-52056, Germany.
| | - Rudi Lurz
- Max-Planck-Institute for Molecular Genetics, Ihnestrasse 73, Berlin D-14195, Germany.
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Landoltweg 1, Aachen D-52056, Germany.
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16
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Winz ML, Linder EC, André T, Becker J, Jäschke A. Nucleotidyl transferase assisted DNA labeling with different click chemistries. Nucleic Acids Res 2015; 43:e110. [PMID: 26013812 PMCID: PMC4787804 DOI: 10.1093/nar/gkv544] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 05/12/2015] [Indexed: 01/19/2023] Open
Abstract
Here, we present a simple, modular and efficient strategy that allows the 3′-terminal labeling of DNA, regardless of whether it has been chemically or enzymatically synthesized or isolated from natural sources. We first incorporate a range of modified nucleotides at the 3′-terminus, using terminal deoxynucleotidyl transferase. In the second step, we convert the incorporated nucleotides, using either of four highly efficient click chemistry-type reactions, namely copper-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, Staudinger ligation or Diels-Alder reaction with inverse electron demand. Moreover, we create internal modifications, making use of either ligation or primer extension, after the nucleotidyl transferase step, prior to the click reaction. We further study the influence of linker variants on the reactivity of azides in different click reactions. We find that different click reactions exhibit distinct substrate preferences, a fact that is often overlooked, but should be considered when labeling oligonucleotides or other biomolecules with click chemistry. Finally, our findings allowed us to extend our previously published RNA labeling strategy to the use of a different copper-free click chemistry, namely the Staudinger ligation.
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Affiliation(s)
- Marie-Luise Winz
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Eva Christina Linder
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Timon André
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Juliane Becker
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Andres Jäschke
- Heidelberg University, Institute of Pharmacy and Molecular Biotechnology, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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17
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Hymbaugh Bergman SJ, Comstock LR. N-mustard analogs of S-adenosyl-L-methionine as biochemical probes of protein arginine methylation. Bioorg Med Chem 2015; 23:5050-5055. [PMID: 26037613 DOI: 10.1016/j.bmc.2015.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/24/2015] [Accepted: 05/02/2015] [Indexed: 11/30/2022]
Abstract
Nucleosomes, the fundamental building blocks of eukaryotic chromatin, undergo post-synthetic modifications and play a major role in the regulation of transcriptional processes. Combinations of these modifications, including methylation, regulate chromatin structure, determining its different functional states and playing a central role in differentiation. The biological significance of cellular methylation, particularly on chromatin, is widely recognized, yet we know little about the mechanisms that link biological methylation events. To characterize and fully understand protein methylation, we describe here novel N-mustard analogs of S-adenosyl-l-methionine (SAM) as biochemical tools to better understand protein arginine methylation events using protein arginine methyltransferase 1 (PRMT1). Specifically, azide- and alkyne-functionalized N-mustard analogs serve as cofactor mimics of SAM and are enzymatically transferred to a model peptide substrate in a PRMT1-dependent fashion. Once incorporated, the resulting alkynes and azides can be modified through chemoselective ligations, including click chemistry and the Staudinger ligation. These results readily demonstrate the feasibility of utilizing N-mustard analogs as biochemical tools to site-specifically label substrates of PRMT1 and serve as an alternative approach to study protein methylation events.
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Affiliation(s)
| | - Lindsay R Comstock
- Wake Forest University, Department of Chemistry, Winston-Salem, NC 27106, United States.
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18
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Ramadan M, Bremner-Hay NK, Carlson SA, Comstock LR. Synthesis and evaluation of N6-substituted azide- and alkyne-bearing N-mustard analogs of S-adenosyl-l-methionine. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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19
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Lukinavičius G, Tomkuvienė M, Masevičius V, Klimašauskas S. Enhanced chemical stability of adomet analogues for improved methyltransferase-directed labeling of DNA. ACS Chem Biol 2013; 8:1134-9. [PMID: 23557731 DOI: 10.1021/cb300669x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Methyltransferases catalyze specific transfers of methyl groups from the ubiquitous cofactor S-adenosyl-l-methionine (AdoMet) to various nucleophilic positions in biopolymers like DNA, RNA, and proteins. We had previously described synthesis and application of AdoMet analogues carrying sulfonium-bound 4-substituted but-2-ynyl side chains for transfer by methyltransferases. Although useful in certain applications, these cofactor analogues exhibited short lifetimes in physiological buffers. Examination of the reaction kinetics and products showed that their fast inactivation followed a different pathway than observed for AdoMet and rather involved a pH-dependent addition of a water molecule to the side chain. This side reaction was eradicated by synthesis of a series of cofactor analogues in which the separation between an electronegative group and the triple bond was increased from one to three carbon units. The designed hex-2-ynyl moiety-based cofactor analogues with terminal amino, azide, or alkyne groups showed a markedly improved enzymatic transalkylation activity and proved well suitable for methyltransferase-directed sequence-specific labeling of DNA in vitro and in bacterial cell lysates.
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Affiliation(s)
| | - Miglė Tomkuvienė
- Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
| | - Viktoras Masevičius
- Institute of Biotechnology, Vilnius University, LT-02241 Vilnius, Lithuania
- Faculty of Chemistry, Vilnius University, LT-03225 Vilnius, Lithuania
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20
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Lukinavicius G, Lapinaite A, Urbanaviciute G, Gerasimaite R, Klimasauskas S. Engineering the DNA cytosine-5 methyltransferase reaction for sequence-specific labeling of DNA. Nucleic Acids Res 2012; 40:11594-602. [PMID: 23042683 PMCID: PMC3526304 DOI: 10.1093/nar/gks914] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
DNA methyltransferases catalyse the transfer of a methyl group from the ubiquitous cofactor S-adenosyl-L-methionine (AdoMet) onto specific target sites on DNA and play important roles in organisms from bacteria to humans. AdoMet analogs with extended propargylic side chains have been chemically produced for methyltransferase-directed transfer of activated groups (mTAG) onto DNA, although the efficiency of reactions with synthetic analogs remained low. We performed steric engineering of the cofactor pocket in a model DNA cytosine-5 methyltransferase (C5-MTase), M.HhaI, by systematic replacement of three non-essential positions, located in two conserved sequence motifs and in a variable region, with smaller residues. We found that double and triple replacements lead to a substantial improvement of the transalkylation activity, which manifests itself in a mild increase of cofactor binding affinity and a larger increase of the rate of alkyl transfer. These effects are accompanied with reduction of both the stability of the product DNA–M.HhaI–AdoHcy complex and the rate of methylation, permitting competitive mTAG labeling in the presence of AdoMet. Analogous replacements of two conserved residues in M.HpaII and M2.Eco31I also resulted in improved transalkylation activity attesting a general applicability of the homology-guided engineering to the C5-MTase family and expanding the repertoire of sequence-specific tools for covalent in vitro and ex vivo labeling of DNA.
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Affiliation(s)
- Grazvydas Lukinavicius
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, 02241 Vilnius, Lithuania
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21
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Du Y, Hendrick CE, Frye KS, Comstock LR. Fluorescent DNA labeling by N-mustard analogues of S-adenosyl-L-methionine. Chembiochem 2012; 13:2225-33. [PMID: 22961989 DOI: 10.1002/cbic.201200438] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Indexed: 12/30/2022]
Abstract
Azide and alkyne-functionalized N-mustard analogues of S-adenosyl-L-methionine have been synthesized and were demonstrated to undergo efficient methyltransferase-dependent DNA alkylation by M.TaqI and M.HhaI. Subsequent labeling of the DNA with a fluorophore was carried out using copper-catalyzed azide-alkyne cycloaddition chemistry and was visualized by fluorescence scanning. This work demonstrates the utility of functionalized N-mustard analogues as biochemical tools to study biological methylation and offers a facile way to site-selectively label substrates of DNA methyltransferases.
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Affiliation(s)
- Yuhao Du
- Department of Chemistry, Wake Forest University, 1834 Wake Forest Road, Winston-Salem, NC 27106, USA
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22
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Mai V, Comstock LR. Synthesis of an azide-bearing N-mustard analogue of S-adenosyl-L-methionine. J Org Chem 2011; 76:10319-24. [PMID: 22050725 DOI: 10.1021/jo2019637] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of an azide-bearing N-mustard S-adenosyl-L-methionine (SAM) analogue, 8-azido-5'-(diaminobutyric acid)-N-iodoethyl-5'-deoxyadenosine, has been accomplished in 10 steps from commercially available 2',3'-isopropylidene adenosine. Critical to this success was executing C8 azidation prior to derivatizing the 5'-position of the ribose sugar and the late stage alkylation of the 5' amino group with bromoethanol, which was necessitated by the reactivity of the aryl azide moiety. The azide-bearing N-mustard is envisioned as a useful biochemical tool by which to probe DNA and protein methylation patterns.
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Affiliation(s)
- Van Mai
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109, USA
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23
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van Berkel SS, van Eldijk MB, van Hest JCM. Staudinger ligation as a method for bioconjugation. Angew Chem Int Ed Engl 2011; 50:8806-27. [PMID: 21887733 DOI: 10.1002/anie.201008102] [Citation(s) in RCA: 206] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Indexed: 11/11/2022]
Abstract
In 1919 the German chemist Hermann Staudinger was the first to describe the reaction between an azide and a phosphine. It was not until recently, however, that Bertozzi and co-workers recognized the potential of this reaction as a method for bioconjugation and transformed it into the so-called Staudinger ligation. The bio-orthogonal character of both the azide and the phosphine functions has resulted in the Staudinger ligation finding numerous applications in various complex biological systems. For example, the Staudinger ligation has been utilized to label glycans, lipids, DNA, and proteins. Moreover, the Staudinger ligation has been used as a synthetic method to construct glycopeptides, microarrays, and functional biopolymers. In the emerging field of bio-orthogonal ligation strategies, the Staudinger ligation has set a high standard to which most of the new techniques are often compared. This Review summarizes recent developments and new applications of the Staudinger ligation.
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Affiliation(s)
- Sander S van Berkel
- Department of Bioorganic Chemistry, Radboud University Nijmegen, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands
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24
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van Berkel SS, van Eldijk MB, van Hest JCM. Staudinger-Ligation als Methode zur Biokonjugation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201008102] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Abstract
Sequence-specific DNA modification is of significance for applications in bio- and nano-technology, medical diagnostics and fundamental life sciences research. Preferentially, labelling should be performed covalently, which avoids doubts about label dissociation from the DNA under various conditions. Several methods to label native DNA have been developed in the last two decades. Triple-helix-forming oligodeoxynucleotides and hairpin polyamides that bind DNA sequences specifically in the major and minor groove respectively were used as targeting devices for subsequent covalent labelling. In addition, enzyme-directed labelling approaches utilizing nicking endonucleases in combination with DNA polymerases or DNA methyltransferases have been employed. This review summarizes various techniques useful for functionalization of long native DNA.
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Neely RK, Deen J, Hofkens J. Optical mapping of DNA: Single-molecule-based methods for mapping genomes. Biopolymers 2011; 95:298-311. [DOI: 10.1002/bip.21579] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/09/2022]
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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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Sletten E, Bertozzi C. Bioorthogonale Chemie - oder: in einem Meer aus Funktionalität nach Selektivität fischen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900942] [Citation(s) in RCA: 522] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Townsend AP, Roth S, Williams HEL, Stylianou E, Thomas NR. New S-Adenosyl-l-methionine Analogues: Synthesis and Reactivity Studies. Org Lett 2009; 11:2976-9. [DOI: 10.1021/ol9009859] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrew P. Townsend
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, United Kingdom, and School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Stefanie Roth
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, United Kingdom, and School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Huw E. L. Williams
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, United Kingdom, and School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Eleni Stylianou
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, United Kingdom, and School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
| | - Neil R. Thomas
- University of Nottingham, School of Chemistry, Centre for Biomolecular Sciences, University Park, Nottingham, NG7 2RD, United Kingdom, and School of Biomedical Sciences, University of Nottingham Medical School, Queen’s Medical Centre, Nottingham NG7 2UH, United Kingdom
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Sletten EM, Bertozzi CR. Bioorthogonal chemistry: fishing for selectivity in a sea of functionality. Angew Chem Int Ed Engl 2009; 48:6974-98. [PMID: 19714693 PMCID: PMC2864149 DOI: 10.1002/anie.200900942] [Citation(s) in RCA: 2338] [Impact Index Per Article: 155.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The study of biomolecules in their native environments is a challenging task because of the vast complexity of cellular systems. Technologies developed in the last few years for the selective modification of biological species in living systems have yielded new insights into cellular processes. Key to these new techniques are bioorthogonal chemical reactions, whose components must react rapidly and selectively with each other under physiological conditions in the presence of the plethora of functionality necessary to sustain life. Herein we describe the bioorthogonal chemical reactions developed to date and how they can be used to study biomolecules.
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Affiliation(s)
- Ellen M. Sletten
- Department of Chemistry, University of California, Berkeley, CA 94720 (USA)
| | - Carolyn R. Bertozzi
- Departments of Chemistry and Molecular and Cell Biology and Howard Hughes Medical Institute, University of California and The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 (USA), Fax: (+1)510-643-2628
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31
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Weisbrod SH, Marx A. Novel strategies for the site-specific covalent labelling of nucleic acids. Chem Commun (Camb) 2008:5675-85. [PMID: 19009049 DOI: 10.1039/b809528k] [Citation(s) in RCA: 181] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
To broaden the scope of applications in DNA nano- and biotechnology, material science, diagnostics and molecular recognition the functionalization of DNA is of utmost importance. In the last decade many new methods have been developed to achieve this goal. Apart from the direct chemical synthesis of modified DNA by automated phosphoramidite chemistry incorporation of labelled triphosphates and the post-synthetic labelling approach evolved as valuable methods. New bioorthogonal reactions as Diels-Alder, click and Staudinger ligations pushed forward the post-synthetic approach as new insights into DNA polymerase substrate specificity allowed generation and amplification of labelled DNA strands. These novel developments are summarized herein.
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Affiliation(s)
- Samuel H Weisbrod
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, 78457, Konstanz, Germany
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32
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Kiviniemi A, Virta P, Lönnberg H. Utilization of intrachain 4'-C-azidomethylthymidine for preparation of oligodeoxyribonucleotide conjugates by click chemistry in solution and on a solid support. Bioconjug Chem 2008; 19:1726-34. [PMID: 18671421 DOI: 10.1021/bc800221p] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
4'-C-Azidomethylthymidine 3'-(H-phosphonate) monomer (10) was synthesized in high yield and three such monomers were incorporated by the H-phosphonate coupling into a 15-mer oligodeoxyribonucleotide. The unmodified 2'-deoxynucleosides could be coupled by either the H-phosphonate or phosphoramidite chemistry, indicating that the Staudinger reaction between the azido group and the phosphoramidite reagent severely hampered the coupling only when it took place intramolecularly. After chain assembly, three alkynyl group bearing ligands, viz., propargyl 2,3,4,6-tetra-O-acetyl-alpha-D-mannopyranoside (2), N-{4-[N-(trifluoroacetyl)aminomethyl]benzyl}-4-pentynamide (3) and N (1), N (3), N (2')-tris(trifluoroacetyl)-N (6')-(4-pentynoyl)neamine (4), were conjugated to the azido groups of the oligonucleotide by click chemistry both on a solid support and in solution. The products were deprotected by conventional ammonolysis and purified by HPLC chromatography. Melting temperature studies revealed that the mannose conjugated oligonucleotides formed more stable duplexes with 2'-O-methyl RNA than with DNA strand. With 2'-O-methyl RNA, a slight destabilization compared to an unmodified sequence was observed at low ionic strength, while at high salt content, the manno-conjugation was stabilizing.
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Affiliation(s)
- Anu Kiviniemi
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland.
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33
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Schmidt FHG, Hüben M, Gider B, Renault F, Teulade-Fichou MP, Weinhold E. Sequence-specific Methyltransferase-Induced Labelling (SMILing) of plasmid DNA for studying cell transfection. Bioorg Med Chem 2008; 16:40-8. [DOI: 10.1016/j.bmc.2007.04.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2006] [Revised: 11/10/2006] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
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Link AJ, Vink MKS, Tirrell DA. Preparation of the functionalizable methionine surrogate azidohomoalanine via copper-catalyzed diazo transfer. Nat Protoc 2007; 2:1879-83. [PMID: 17703198 DOI: 10.1038/nprot.2007.268] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The azide functional group has assumed a prominent role in chemical biology efforts in recent years. Azides may be readily introduced into proteins upon replacement of methionine residues with the non-canonical amino acid azidohomoalanine (AHA). This protocol describes a synthetic route to AHA based on the copper-catalyzed conversion of amines to azides. An alternate protocol for the preparation of AHA is presented in a companion paper. The synthesis and purification of AHA via the route described herein can be completed in 3-4 days.
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Affiliation(s)
- A James Link
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91106, USA.
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35
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Baskin J, Bertozzi C. Bioorthogonal Click Chemistry: Covalent Labeling in Living Systems. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/qsar.200740086] [Citation(s) in RCA: 245] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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36
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Pljevaljcić G, Schmidt F, Scheidig AJ, Lurz R, Weinhold E. Quantitative Labeling of Long Plasmid DNA with Nanometer Precision. Chembiochem 2007; 8:1516-9. [PMID: 17654629 DOI: 10.1002/cbic.200700294] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Goran Pljevaljcić
- Present address: Department of Molecular Biology, MB19, The Scripps Research Institute, 10550 N. Torrey Pines Rd. La Jolla, CA 92037, USA
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37
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Klimasauskas S, Weinhold E. A new tool for biotechnology: AdoMet-dependent methyltransferases. Trends Biotechnol 2007; 25:99-104. [PMID: 17254657 DOI: 10.1016/j.tibtech.2007.01.006] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2006] [Revised: 11/15/2006] [Accepted: 01/12/2007] [Indexed: 11/26/2022]
Abstract
AdoMet-dependent methyltransferases catalyze highly specific methyl group transfers from the ubiquitous cofactor S-adenosyl-L-methionine to a multitude of biological targets in the cell. Recently, DNA methyltransferases have been used for the sequence-specific, covalent attachment of larger chemical groups to plasmid and bacteriophage DNA using two classes of synthetic AdoMet analogs. These synthetic cofactors, in combination with the myriad AdoMet-dependent methyltransferases available in nature, provide new molecular tools for precise, targeted functionalization and labeling of large natural DNAs and, in all likelihood, RNAs and proteins. This paves the way for numerous novel applications in the functional analysis of biological methylation, biotechnology and medical diagnostics.
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Affiliation(s)
- Saulius Klimasauskas
- Laboratory of Biological DNA Modification, Institute of Biotechnology, LT-02241 Vilnius, Lithuania.
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38
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Abstract
The Staudinger ligation provides a means to form an amide bond between a phosphinothioester and azide. This reaction holds promise for the ligation of peptides en route to the total chemical synthesis of proteins. (Diphenylphosphino)methanethiol is the most efficacious of known reagents for mediating the Staudinger ligation of peptides, providing high (> 90%) isolated yields for equimolar couplings in which a glycine residue is at the nascent junction. Surprisingly, the yields are lower (< 50%) for non-glycyl couplings due to an aza-Wittig reaction that diverts the reaction toward a phosphonamide byproduct. Here, the partitioning of the reaction toward Staudinger ligation (and away from the aza-Wittig reaction) is shown to increase with increasing electron density on phosphorus. This electron density can be tuned either by installing functional groups on the phenyl substituents of (diphenylphosphino)methanethiol or by changing the polarity of the solvent. Installing p-methoxy groups and using a solvent of low polarity (such as toluene or dioxane) provide especially high (> 80%) isolated yields for the ligation of two non-glycyl residues. These conditions retain the high chemoselectivity of the reaction and do not lead to a substantial change in reaction rate. The traceless Staudinger ligation is now poised to enable the iterative ligation of peptides with little regard for their sequence, as well as the synthesis of amide bonds for other purposes.
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Affiliation(s)
| | - Annie Tam
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, WI 53706
- Department of Biochemistry, University of Wisconsin–Madison, Madison, WI 53706
- Corresponding author. Department of Biochemistry, University of Wisconsin–Madison, 433 Babcock Drive, Madison, WI 53706-1544; E-mail:
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Bräse S, Gil C, Knepper K, Zimmermann V. Organic azides: an exploding diversity of a unique class of compounds. Angew Chem Int Ed Engl 2006; 44:5188-240. [PMID: 16100733 DOI: 10.1002/anie.200400657] [Citation(s) in RCA: 1626] [Impact Index Per Article: 90.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Since the discovery of organic azides by Peter Griess more than 140 years ago, numerous syntheses of these energy-rich molecules have been developed. In more recent times in particular, completely new perspectives have been developed for their use in peptide chemistry, combinatorial chemistry, and heterocyclic synthesis. Organic azides have assumed an important position at the interface between chemistry, biology, medicine, and materials science. In this Review, the fundamental characteristics of azide chemistry and current developments are presented. The focus will be placed on cycloadditions (Huisgen reaction), aza ylide chemistry, and the synthesis of heterocycles. Further reactions such as the aza-Wittig reaction, the Sundberg rearrangement, the Staudinger ligation, the Boyer and Boyer-Aubé rearrangements, the Curtius rearrangement, the Schmidt rearrangement, and the Hemetsberger rearrangement bear witness to the versatility of modern azide chemistry.
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Affiliation(s)
- Stefan Bräse
- Institut für Organische Chemie, Universität Karlsruhe TH, Germany.
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40
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Weller RL, Rajski SR. Design, synthesis, and preliminary biological evaluation of a DNA methyltransferase-directed alkylating agent. Chembiochem 2006; 7:243-5. [PMID: 16365907 DOI: 10.1002/cbic.200500362] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Rachel L Weller
- University of Wisconsin-Madison, Department of Chemistry, Madison, WI 53706, USA
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41
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Zhang C, Weller RL, Thorson JS, Rajski SR. Natural Product Diversification Using a Non-natural Cofactor Analogue of S-Adenosyl-l-methionine. J Am Chem Soc 2006; 128:2760-1. [PMID: 16506729 DOI: 10.1021/ja056231t] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adenosine analogues bearing either 5'-aziridine or 5'-N-mustard electrophiles are methyltransferase-dependent DNA alkylating agents. We present here a novel synthetic cofactor bearing a pendant 5'-amino acid N-mustard. Unlike previously studied synthetic cofactors, this material is very efficiently used by the natural product biosynthetic enzyme rebeccamycin methyltransferase (RebM) to generate a number of new rebeccamycin analogues. These data promote the notion that natural product methyltransferases can be used with non-natural cofactors to enhance the molecular diversity of natural product analogues for drug discovery. To our knowledge, this is the first documentation of a biological methyltransferase, other than DNA methyltransferases, that can exploit such synthetic cofactors.
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Affiliation(s)
- Changsheng Zhang
- Laboratory for Biosynthetic Chemistry, University of Wisconsin National Cooperative Drug Discovery Group, Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
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Abstract
Dissecting complex cellular processes requires the ability to track biomolecules as they function within their native habitat. Although genetically encoded tags such as GFP are widely used to monitor discrete proteins, they can cause significant perturbations to a protein's structure and have no direct extension to other classes of biomolecules such as glycans, lipids, nucleic acids and secondary metabolites. In recent years, an alternative tool for tagging biomolecules has emerged from the chemical biology community--the bioorthogonal chemical reporter. In a prototypical experiment, a unique chemical motif, often as small as a single functional group, is incorporated into the target biomolecule using the cell's own biosynthetic machinery. The chemical reporter is then covalently modified in a highly selective fashion with an exogenously delivered probe. This review highlights the development of bioorthogonal chemical reporters and reactions and their application in living systems.
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Affiliation(s)
- Jennifer A Prescher
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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43
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Abstract
We demonstrate here that MTase-modified DNA can undergo the Staudinger ligation with triarylphosphines derivatized with phenanthroline. Presentation of these duplexes with Cu(II) and 3-mercaptopropionic acid leads to strand scission proximal to the MTase recognition site. By virtue of their ability to use a synthetic azide-bearing cofactor, M.TaqI and M.HhaI produce a DNA lesion that induces scission 5' to the base modified by the enzyme. This chemistry represents a new approach by which regions of DNA methylation can be rapidly identified on the basis of DNA damage.
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Affiliation(s)
- Lindsay R Comstock
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
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44
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Laughlin ST, Agard NJ, Baskin JM, Carrico IS, Chang PV, Ganguli AS, Hangauer MJ, Lo A, Prescher JA, Bertozzi CR. Metabolic Labeling of Glycans with Azido Sugars for Visualization and Glycoproteomics. Methods Enzymol 2006; 415:230-50. [PMID: 17116478 DOI: 10.1016/s0076-6879(06)15015-6] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The staggering complexity of glycans renders their analysis extraordinarily difficult, particularly in living systems. A recently developed technology, termed metabolic oligosaccharide engineering, enables glycan labeling with probes for visualization in cells and living animals, and enrichment of specific glycoconjugate types for proteomic analysis. This technology involves metabolic labeling of glycans with a specifically reactive, abiotic functional group, the azide. Azido sugars are fed to cells and integrated by the glycan biosynthetic machinery into various glycoconjugates. The azido sugars are then covalently tagged, either ex vivo or in vivo, using one of two azide-specific chemistries: the Staudinger ligation, or the strain-promoted [3+2] cycloaddition. These reactions can be used to tag glycans with imaging probes or epitope tags, thus enabling the visualization or enrichment of glycoconjugates. Applications to noninvasive imaging and glycoproteomic analyses are discussed.
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Affiliation(s)
- Scott T Laughlin
- Department of Chemistry, Howard Hughes Medical Institute, University of California, Berkeley, USA
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Bräse S, Gil C, Knepper K, Zimmermann V. Organische Azide - explodierende Vielfalt bei einer einzigartigen Substanzklasse. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200400657] [Citation(s) in RCA: 346] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Petersen SG, Rajski SR. o-Nitrobenzenesulfonamides in Nucleoside Synthesis: Efficient 5‘-Aziridination of Adenosine. J Org Chem 2005; 70:5833-9. [PMID: 16018675 DOI: 10.1021/jo050205w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
5'-Aziridinoadenylates of the form 1 and a related nitrogen mustard variant have been constructed using a novel variation of the Mitsunobu reaction. Such molecules allow conversion of biological methyltransferases into nucleoside transferases, thus providing powerful tools for investigating S-adenosyl-l-methionine (SAM)-dependent methylation. We present here a highly effective synthesis of such molecules that is amenable to aziridine diversification as well as elaboration of the base moiety so as to afford "bumped" cofactor mimics compatible with "hole"-bearing mutant proteins.
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Affiliation(s)
- Scott G Petersen
- The School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705-2222, USA
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Abstract
[reaction: see text]. Biological methylation plays a vital role in regulatory mechanisms of gene transcription. Methylation of both promoter sequences within the genome, as well as protein substrates, has a profound impact upon gene transcription. Yet, few tools exist by which to identify sites of biological methylation in complex biological mixtures. We have generated a novel adenosine-derived N-mustard that serves as an efficient synthetic cofactor and allows for subsequent "click" chemistry involving the modified nucleic acid substrate.
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Affiliation(s)
- Rachel L Weller
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53705, USA
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