1
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Yan S, Lu Z, Yang W, Xu J, Wang Y, Xiong W, Zhu R, Ren L, Chen Z, Wei Q, Liu SM, Feng T, Yuan B, Weng X, Du Y, Zhou X. Antibody-Free Fluorine-Assisted Metabolic Sequencing of RNA N4-Acetylcytidine. J Am Chem Soc 2023; 145:22232-22242. [PMID: 37772932 DOI: 10.1021/jacs.3c08483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
N4-Acetylcytidine (ac4C) has been found to affect a variety of cellular and biological processes. For a mechanistic understanding of the roles of ac4C in biology and disease, we present an antibody-free, fluorine-assisted metabolic sequencing method to detect RNA ac4C, called "FAM-seq". We successfully applied FAM-seq to profile ac4C landscapes in human 293T, HeLa, and MDA cell lines in parallel with the reported acRIP-seq method. By comparison with the classic ac4C antibody sequencing method, we found that FAM-seq is a convenient and reliable method for transcriptome-wide mapping of ac4C. Because this method holds promise for detecting nascent RNA ac4C modifications, we further investigated the role of ac4C in regulating chemotherapy drug resistance in chronic myeloid leukemia. The results indicated that drug development or combination therapy could be enhanced by appreciating the key role of ac4C modification in cancer therapy.
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Affiliation(s)
- Shen Yan
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Wei Yang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Yafen Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Wei Xiong
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Rongjie Zhu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Linao Ren
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Zhaoxin Chen
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Qi Wei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Song-Mei Liu
- Department of Clinical Laboratory, Center for Gene Diagnosis, and Program of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan 430071, Hubei, PR China
| | - Tian Feng
- School of Public Health, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Bifeng Yuan
- School of Public Health, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Yuhao Du
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Wuhan 430072, Hubei, PR China
- Department of Hematology, Zhongnan Hospital, Wuhan University, Wuhan 430072, Hubei, PR China
- Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, Hubei, PR China
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2
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Pradhan S, Apaydin S, Bucevičius J, Gerasimaitė R, Kostiuk G, Lukinavičius G. Sequence-specific DNA labelling for fluorescence microscopy. Biosens Bioelectron 2023; 230:115256. [PMID: 36989663 DOI: 10.1016/j.bios.2023.115256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 03/04/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023]
Abstract
The preservation of nucleus structure during microscopy imaging is a top priority for understanding chromatin organization, genome dynamics, and gene expression regulation. In this review, we summarize the sequence-specific DNA labelling methods that can be used for imaging in fixed and/or living cells without harsh treatment and DNA denaturation: (i) hairpin polyamides, (ii) triplex-forming oligonucleotides, (iii) dCas9 proteins, (iv) transcription activator-like effectors (TALEs) and (v) DNA methyltransferases (MTases). All these techniques are capable of identifying repetitive DNA loci and robust probes are available for telomeres and centromeres, but visualizing single-copy sequences is still challenging. In our futuristic vision, we see gradual replacement of the historically important fluorescence in situ hybridization (FISH) by less invasive and non-destructive methods compatible with live cell imaging. Combined with super-resolution fluorescence microscopy, these methods will open the possibility to look into unperturbed structure and dynamics of chromatin in living cells, tissues and whole organisms.
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3
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Cornelissen NV, Hoffmann A, Rentmeister A. DNA‐Methyltransferasen und AdoMet‐Analoga als Werkzeuge für die Molekularbiologie und Biotechnologie. CHEM-ING-TECH 2023. [DOI: 10.1002/cite.202200174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Nicolas V. Cornelissen
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Arne Hoffmann
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster Institut für Biochemie, Fachbereich Chemie und Pharmazie Corrensstraße 36 48149 Münster Deutschland
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4
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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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5
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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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6
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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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7
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Jalali E, Thorson JS. Enzyme-mediated bioorthogonal technologies: catalysts, chemoselective reactions and recent methyltransferase applications. Curr Opin Biotechnol 2021; 69:290-298. [PMID: 33901763 DOI: 10.1016/j.copbio.2021.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 02/24/2021] [Accepted: 02/26/2021] [Indexed: 12/28/2022]
Abstract
Transferases have emerged as among the best catalysts for enzyme-mediated bioorthogonal functional group installation to advance innovative in vitro, cell-based and in vivo chemical biology applications. This review introduces the key considerations for selecting enzyme catalysts and chemoselective reactions most amenable to bioorthogonal platform development and highlights relevant key technology development and applications for one ubiquitous transferase subclass - methyltransferases (MTs). Within this context, recent advances in MT-enabled bioorthogonal labeling/conjugation relevant to DNA, RNA, protein, and natural products (i.e. complex small molecule metabolites) are highlighted.
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Affiliation(s)
- Elnaz Jalali
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States
| | - Jon S Thorson
- Department of Pharmaceutical Sciences, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States; Center for Pharmaceutical Research and Innovation, University of Kentucky College of Pharmacy, Lexington, KY 40536, United States.
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8
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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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9
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Yan XL, Xue XX, Deng XM, Jian YT, Luo J, Jiang MM, Zheng XJ. Chemiluminescence strategy induced by HRP-sandwich structure based on strand displacement for sensitive detection of DNA methyltransferase. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Huber TD, Clinger JA, Liu Y, Xu W, Miller MD, Phillips GN, Thorson JS. Methionine Adenosyltransferase Engineering to Enable Bioorthogonal Platforms for AdoMet-Utilizing Enzymes. ACS Chem Biol 2020; 15:695-705. [PMID: 32091873 DOI: 10.1021/acschembio.9b00943] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structural conservation among methyltransferases (MTs) and MT functional redundancy is a major challenge to the cellular study of individual MTs. As a first step toward the development of an alternative biorthogonal platform for MTs and other AdoMet-utilizing enzymes, we describe the evaluation of 38 human methionine adenosyltransferase II-α (hMAT2A) mutants in combination with 14 non-native methionine analogues to identify suitable bioorthogonal mutant/analogue pairings. Enabled by the development and implementation of a hMAT2A high-throughput (HT) assay, this study revealed hMAT2A K289L to afford a 160-fold inversion of the hMAT2A selectivity index for a non-native methionine analogue over the native substrate l-Met. Structure elucidation of K289L revealed the mutant to be folded normally with minor observed repacking within the modified substrate pocket. This study highlights the first example of exchanging l-Met terminal carboxylate/amine recognition elements within the hMAT2A active-site to enable non-native bioorthgonal substrate utilization. Additionally, several hMAT2A mutants and l-Met substrate analogues produced AdoMet analogue products with increased stability. As many AdoMet-producing (e.g., hMAT2A) and AdoMet-utlizing (e.g., MTs) enzymes adopt similar active-site strategies for substrate recognition, the proof of concept first generation hMAT2A engineering highlighted herein is expected to translate to a range of AdoMet-utilizing target enzymes.
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Affiliation(s)
- Tyler D. Huber
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | - Yang Liu
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
| | | | | | | | - Jon S. Thorson
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
- Center for Pharmaceutical Research and Innovation (CPRI), College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, Kentucky 40536-0596, United States
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11
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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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12
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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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13
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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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14
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Lauer MH, Vranken C, Deen J, Frederickx W, Vanderlinden W, Wand N, Leen V, Gehlen MH, Hofkens J, Neely RK. Methyltransferase-directed covalent coupling of fluorophores to DNA. Chem Sci 2017; 8:3804-3811. [PMID: 28580113 PMCID: PMC5436541 DOI: 10.1039/c6sc04229e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 03/13/2017] [Indexed: 12/25/2022] Open
Abstract
Highly efficient DNA labelling using an enzymatically-directed, strain-promoted azide–alkyne cycloaddition.
We report an assay for determining the number of fluorophores conjugated to single plasmid DNA molecules and apply this to compare the efficiency of fluorophore coupling strategies for covalent DNA labelling. We compare a copper-catalyzed azide–alkyne cycloaddition reaction, amine to N-hydroxysuccinimidyl ester coupling reaction and strain-promoted azide–alkyne cycloaddition reaction for fluorescent DNA labelling. We found increased labelling efficiency going from the amine to N-hydroxysuccinimidyl ester coupling reaction to the copper-catalyzed azide–alkyne cycloaddition and found the highest degree of DNA labelling with the strain-promoted azide–alkyne cycloaddition reaction. We also examined the effect of labelling on the DNA structure using atomic force microscopy. We observe no distortions or damage to the DNA that was labeled using the amine to N-hydroxysuccinimidyl ester and strain-promoted azide–alkyne cycloaddition coupling reactions. This was in contrast to the copper-catalyzed azide–alkyne cycloaddition reaction, which, despite the use of copper-coordinating ligands in the labelling mixture, leads to some structural DNA damage (single-stranded DNA breaks).
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Affiliation(s)
- Milena Helmer Lauer
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium.,Institute of Chemistry of São Carlos , University of São Paulo , Brazil
| | - Charlotte Vranken
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Jochem Deen
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Wout Frederickx
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Willem Vanderlinden
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Nathaniel Wand
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK .
| | - Volker Leen
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Marcelo H Gehlen
- Institute of Chemistry of São Carlos , University of São Paulo , Brazil
| | - Johan Hofkens
- Department of Chemistry , KU Leuven , Celestijnenlaan , 3001 Heverlee , Belgium
| | - Robert K Neely
- School of Chemistry , University of Birmingham , Edgbaston , Birmingham B15 2TT , UK .
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15
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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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16
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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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17
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Egloff D, Oleinich IA, Zhao M, König SLB, Sigel RKO, Freisinger E. Sequence-Specific Post-Synthetic Oligonucleotide Labeling for Single-Molecule Fluorescence Applications. ACS Chem Biol 2016; 11:2558-67. [PMID: 27409145 DOI: 10.1021/acschembio.6b00343] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The sequence-specific fluorescence labeling of nucleic acids is a prerequisite for various methods including single-molecule Förster resonance energy transfer (smFRET) for the detailed study of nucleic acid folding and function. Such nucleic acid derivatives are commonly obtained by solid-phase methods; however, yields decrease rapidly with increasing length and restrict the practicability of this approach for long strands. Here, we report a new labeling strategy for the postsynthetic incorporation of a bioorthogonal group into single stranded regions of both DNA and RNA of unrestricted length. A 12-alkyne-etheno-adenine modification is sequence-selectively formed using DNA-templated synthesis, followed by conjugation of the fluorophore Cy3 via a copper-catalyzed azide-alkyne cycloaddition (CuAAC). Evaluation of the labeled strands in smFRET measurements shows that the strategy developed here has the potential to be used for the study of long functional nucleic acids by (single-molecule) fluorescence or other methods. To prove the universal use of the method, its application was successfully extended to the labeling of a short RNA single strand. As a proof-of-concept, also the labeling of a large RNA molecule in form of a 633 nucleotide long construct derived from the Saccharomyces cerevisiae group II intron Sc.ai5γ was performed, and covalent attachment of the Cy3 fluorophore was shown with gel electrophoresis.
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Affiliation(s)
- David Egloff
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Igor A. Oleinich
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Meng Zhao
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Sebastian L. B. König
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Roland K. O. Sigel
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
| | - Eva Freisinger
- Department of Chemistry, University of Zurich, Winterthurerstrasse
190, 8057 Zurich, Switzerland
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18
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Huber TD, Johnson BR, Zhang J, Thorson JS. AdoMet analog synthesis and utilization: current state of the art. Curr Opin Biotechnol 2016; 42:189-197. [PMID: 27506965 DOI: 10.1016/j.copbio.2016.07.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 07/14/2016] [Accepted: 07/15/2016] [Indexed: 11/25/2022]
Abstract
S-Adenosyl-l-methionine (AdoMet) is an essential enzyme cosubstrate in fundamental biology with an expanding range of biocatalytic and therapeutic applications. In recent years, technologies enabling the synthesis and utilization of novel functional AdoMet surrogates have rapidly advanced. Developments highlighted within this brief review include improved syntheses of AdoMet analogs, unique S-adenosyl-l-methionine isosteres with enhanced stability, and corresponding applications in epigenetics, proteomics and natural product/small molecule diversification ('alkylrandomization').
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Affiliation(s)
- Tyler D Huber
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States
| | - Brooke R Johnson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States
| | - Jianjun Zhang
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States
| | - Jon S Thorson
- Center for Pharmaceutical Research and Innovation, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, United States; Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, United States.
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19
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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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20
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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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21
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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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22
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Masevičius V, Nainytė M, Klimašauskas S. Synthesis of S-Adenosyl-L-Methionine Analogs with Extended Transferable Groups for Methyltransferase-Directed Labeling of DNA and RNA. ACTA ACUST UNITED AC 2016; 64:1.36.1-1.36.13. [PMID: 26967468 DOI: 10.1002/0471142700.nc0136s64] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
S-Adenosyl-L-methionine (AdoMet) is a ubiquitous methyl donor for a variety of biological methylation reactions catalyzed by methyltransferases (MTases). AdoMet analogs with extended propargylic chains replacing the sulfonium-bound methyl group can serve as surrogate cofactors for many DNA and RNA MTases enabling covalent deposition of these linear chains to their cognate targets sites in DNA or RNA. Here we describe synthetic procedures for the preparation of two representative examples of AdoMet analogs with a transferable hex-2-ynyl group carrying a terminal azide or amine functionality. Our approach is based on direct chemoselective alkylation of S-adenosyl-L-homocysteine at sulfur with corresponding nosylates under acidic conditions. We also describe synthetic routes to 6-substituted hex-2-yn-1-ols and their conversion to the corresponding nosylates. Using these protocols, synthetic AdoMet analogs can be prepared within 1 to 2 weeks.
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Affiliation(s)
- Viktoras Masevičius
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Faculty of Chemistry, Vilnius University, Vilnius, Lithuania
| | - Milda Nainytė
- Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,Faculty of Chemistry, Vilnius University, Vilnius, Lithuania
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23
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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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24
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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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25
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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26
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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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27
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Gillingham D, Shahid R. Catalysts for RNA and DNA modification. Curr Opin Chem Biol 2015; 25:110-4. [PMID: 25590584 DOI: 10.1016/j.cbpa.2014.12.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 12/11/2014] [Accepted: 12/15/2014] [Indexed: 11/18/2022]
Abstract
To study DNAs and RNAs it is often necessary to chemically modify them. Nature's strategy for nucleic acid modification is to use selective catalysts, and chemists have begun to emulate this conceptual approach. In this review we present a summary of catalytic approaches toward the construction of modified RNAs and DNAs and outline our opinions on where new research is needed.
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Affiliation(s)
| | - Ramla Shahid
- COMSATS Institute of Technology, Park Road, Islamabad, Pakistan
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28
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Hanz GM, Jung B, Giesbertz A, Juhasz M, Weinhold E. Sequence-specific labeling of nucleic acids and proteins with methyltransferases and cofactor analogues. J Vis Exp 2014:e52014. [PMID: 25490674 DOI: 10.3791/52014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
S-Adenosyl-l-methionine (AdoMet or SAM)-dependent methyltransferases (MTase) catalyze the transfer of the activated methyl group from AdoMet to specific positions in DNA, RNA, proteins and small biomolecules. This natural methylation reaction can be expanded to a wide variety of alkylation reactions using synthetic cofactor analogues. Replacement of the reactive sulfonium center of AdoMet with an aziridine ring leads to cofactors which can be coupled with DNA by various DNA MTases. These aziridine cofactors can be equipped with reporter groups at different positions of the adenine moiety and used for Sequence-specific Methyltransferase-Induced Labeling of DNA (SMILing DNA). As a typical example we give a protocol for biotinylation of pBR322 plasmid DNA at the 5'-ATCGAT-3' sequence with the DNA MTase M.BseCI and the aziridine cofactor 6BAz in one step. Extension of the activated methyl group with unsaturated alkyl groups results in another class of AdoMet analogues which are used for methyltransferase-directed Transfer of Activated Groups (mTAG). Since the extended side chains are activated by the sulfonium center and the unsaturated bond, these cofactors are called double-activated AdoMet analogues. These analogues not only function as cofactors for DNA MTases, like the aziridine cofactors, but also for RNA, protein and small molecule MTases. They are typically used for enzymatic modification of MTase substrates with unique functional groups which are labeled with reporter groups in a second chemical step. This is exemplified in a protocol for fluorescence labeling of histone H3 protein. A small propargyl group is transferred from the cofactor analogue SeAdoYn to the protein by the histone H3 lysine 4 (H3K4) MTase Set7/9 followed by click labeling of the alkynylated histone H3 with TAMRA azide. MTase-mediated labeling with cofactor analogues is an enabling technology for many exciting applications including identification and functional study of MTase substrates as well as DNA genotyping and methylation detection.
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Affiliation(s)
- Gisela Maria Hanz
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Britta Jung
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Anna Giesbertz
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Matyas Juhasz
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University
| | - Elmar Weinhold
- Institute of Organic Chemistry, Department of Chemistry, RWTH Aachen University;
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29
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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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30
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Thomsen M, Vogensen SB, Buchardt J, Burkart MD, Clausen RP. Chemoenzymatic synthesis and in situ application of S-adenosyl-L-methionine analogs. Org Biomol Chem 2014; 11:7606-10. [PMID: 24100405 DOI: 10.1039/c3ob41702f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analogs of S-adenosyl-L-methionine (SAM) are increasingly applied to the methyltransferase (MT) catalysed modification of biomolecules including proteins, nucleic acids, and small molecules. However, SAM and its analogs suffer from an inherent instability, and their chemical synthesis is challenged by low yields and difficulties in stereoisomer isolation and inhibition. Here we report the chemoenzymatic synthesis of a series of SAM analogs using wild-type (wt) and point mutants of two recently identified halogenases, SalL and FDAS. Molecular modelling studies are used to guide the rational design of mutants, and the enzymatic conversion of L-Met and other analogs into SAM analogs is demonstrated. We also apply this in situ enzymatic synthesis to the modification of a small peptide substrate by protein arginine methyltransferase 1 (PRMT1). This technique offers an attractive alternative to chemical synthesis and can be applied in situ to overcome stability and activity issues.
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Affiliation(s)
- Marie Thomsen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100, Copenhagen, Denmark.
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31
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Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
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Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
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32
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Struck AW, Thompson ML, Wong LS, Micklefield J. S-Adenosyl-Methionine-Dependent Methyltransferases: Highly Versatile Enzymes in Biocatalysis, Biosynthesis and Other Biotechnological Applications. Chembiochem 2012. [DOI: 10.1002/cbic.201200556] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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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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34
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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35
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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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36
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Zohar H, Muller SJ. Labeling DNA for single-molecule experiments: methods of labeling internal specific sequences on double-stranded DNA. NANOSCALE 2011; 3:3027-39. [PMID: 21734993 PMCID: PMC3322637 DOI: 10.1039/c1nr10280j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
This review is a practical guide for experimentalists interested in specifically labeling internal sequences on double-stranded (ds) DNA molecules for single-molecule experiments. We describe six labeling approaches demonstrated in a single-molecule context and discuss the merits and drawbacks of each approach with particular attention to the amount of specialized training and reagents required. By evaluating each approach according to criteria relevant to single-molecule experiments, including labeling yield and compatibility with cofactors such as Mg(2+), we provide a simple reference for selecting a labeling method for given experimental constraints. Intended for non-specialists seeking accessible solutions to DNA labeling challenges, the approaches outlined emphasize simplicity, robustness, suitability for use by non-biologists, and utility in diverse single-molecule experiments.
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Affiliation(s)
- Hagar Zohar
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA 94720, USA
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37
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Wang R, Zheng W, Yu H, Deng H, Luo M. Labeling substrates of protein arginine methyltransferase with engineered enzymes and matched S-adenosyl-L-methionine analogues. J Am Chem Soc 2011; 133:7648-51. [PMID: 21539310 PMCID: PMC3104021 DOI: 10.1021/ja2006719] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Elucidating physiological and pathogenic functions of protein methyltransferases (PMTs) relies on knowing their substrate profiles. S-adenosyl-L-methionine (SAM) is the sole methyl-donor cofactor of PMTs. Recently, SAM analogues have emerged as novel small-molecule tools to efficiently label PMT substrates. Here we reported the development of a clickable SAM analogue cofactor, 4-propargyloxy-but-2-enyl SAM, and its implementation to label substrates of human protein arginine methyltransferase 1 (PRMT1). In the system, the SAM analogue cofactor, coupled with matched PRMT1 mutants rather than native PRMT1, was shown to label PRMT1 substrates. The transferable 4-propargyloxy-but-2-enyl moiety of the SAM analogue further allowed corresponding modified substrates to be characterized through a subsequent click chemical ligation with an azido-based probe. The SAM analogue, in combination with a rational protein-engineering approach, thus shows potential to label and identify PMT targets in the context of a complex cellular mixture.
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Affiliation(s)
- Rui Wang
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
| | - Weihong Zheng
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
| | - Haiqiang Yu
- Proteomics Resource Center, Rockefeller University, New York, NY 10065
| | - Haiteng Deng
- Proteomics Resource Center, Rockefeller University, New York, NY 10065
- School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Minkui Luo
- Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065
- Program of Pharmacology, Weill Graduate School of Medical Science, Cornell University, New York, NY 10021
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38
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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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39
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Motorin Y, Burhenne J, Teimer R, Koynov K, Willnow S, Weinhold E, Helm M. Expanding the chemical scope of RNA:methyltransferases to site-specific alkynylation of RNA for click labeling. Nucleic Acids Res 2010; 39:1943-52. [PMID: 21037259 PMCID: PMC3061074 DOI: 10.1093/nar/gkq825] [Citation(s) in RCA: 109] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
This work identifies the combination of enzymatic transfer and click labeling as an efficient method for the site-specific tagging of RNA molecules for biophysical studies. A double-activated analog of the ubiquitous co-substrate S-adenosyl-l-methionine was employed to enzymatically transfer a five carbon chain containing a terminal alkynyl moiety onto RNA. The tRNA:methyltransferase Trm1 transferred the extended alkynyl moiety to its natural target, the N2 of guanosine 26 in tRNAPhe. LC/MS and LC/MS/MS techniques were used to detect and characterize the modified nucleoside as well as its cycloaddition product with a fluorescent azide. The latter resulted from a labeling reaction via Cu(I)-catalyzed azide-alkyne 1,3-cycloaddition click chemistry, producing site-specifically labeled RNA whose suitability for single molecule fluorescence experiments was verified in fluorescence correlation spectroscopy experiments.
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Affiliation(s)
- Yuri Motorin
- Institute of Pharmacy and Molecular Biotechnology, Heidelberg University, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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40
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Dalhoff C, Hüben M, Lenz T, Poot P, Nordhoff E, Köster H, Weinhold E. Synthesis of S-Adenosyl-L-homocysteine Capture Compounds for Selective Photoinduced Isolation of Methyltransferases. Chembiochem 2010; 11:256-65. [DOI: 10.1002/cbic.200900349] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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41
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Ottink OM, Nelissen FH, Derks Y, Wijmenga SS, Heus HA. Enzymatic stereospecific preparation of fluorescent S-adenosyl-l-methionine analogs. Anal Biochem 2010; 396:280-3. [DOI: 10.1016/j.ab.2009.09.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Revised: 08/24/2009] [Accepted: 09/09/2009] [Indexed: 10/20/2022]
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42
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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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43
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Braun G, Diechtierow M, Wilkinson S, Schmidt F, Hüben M, Weinhold E, Reich NO. Enzyme-directed positioning of nanoparticles on large DNA templates. Bioconjug Chem 2007; 19:476-9. [PMID: 18088085 DOI: 10.1021/bc700275h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method to position nanoparticles onto DNA with high resolution using an enzyme-based approach is described. This provides a convenient route to assemble multiple nanoparticles (e.g., Au and CdSe) to specific positions with a high level of control and expandability to more complex assemblies. Atomic force microscopy is used to analyze the nanostructures, which have potential interest for biosensor, optical waveguide, molecular electronics, and energy transfer studies.
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Affiliation(s)
- Gary Braun
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, USA
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44
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Wilkinson S, Diechtierow M, Estabrook RA, Schmidt F, Hüben M, Weinhold E, Reich NO. Molecular scale architecture: engineered three- and four-way junctions. Bioconjug Chem 2007; 19:470-5. [PMID: 18069780 DOI: 10.1021/bc700270k] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Biomolecular self-assembly provides a basis for the bottom-up construction of useful and diverse nanoscale architectures. DNA is commonly used to create these assemblies and is often exploited as a lattice or an array. Although geometrically rigid and highly predictable, these sheets of repetitive constructs often lack the ability to be enzymatically manipulated or elongated by standard biochemical techniques. Here, we describe two approaches for the construction of position-controlled, molecular-scale, discrete, three- and four-way DNA junctions. The first approach for constructing these junctions relies on the use of nonmigrating cruciforms generated from synthetic oligonucleotides to which large, biologically generated, double-stranded DNA segments are enzymatically ligated. The second approach utilitizes the DNA methyltransferase-based SMILing (sequence-specific methyltransferase-induced labeling of DNA) method to site-specifically incorporate a biotin within biologically derived DNA. Streptavidin is then used to form junctions between unique DNA strands. The resultant assemblies have precise and predetermined connections with lengths that can be varied by enzymatic or hybridization techniques, or geometrically controlled with standard DNA functionalization methods. These junctions are positioned with single nucleotide resolution on large, micrometer-length templates. Both approaches generate DNA assemblies which are fully compatible with standard recombinant methods and thus provide a novel basis for nanoengineering applications.
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Affiliation(s)
- Stephanie Wilkinson
- Department of Chemistry and Biochemistry, University of California at Santa Barbara, California 93106-9510, USA
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45
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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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46
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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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47
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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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48
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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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49
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Comstock LR, Rajski SR. Conversion of DNA methyltransferases into azidonucleosidyl transferases via synthetic cofactors. Nucleic Acids Res 2005; 33:1644-52. [PMID: 15778434 PMCID: PMC1067524 DOI: 10.1093/nar/gki306] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2005] [Revised: 02/26/2005] [Accepted: 02/26/2005] [Indexed: 11/21/2022] Open
Abstract
Aziridine-based cofactor mimics have been synthesized and are shown to undergo methyltransferase-dependent DNA alkylation. Notably, each cofactor mimic possesses an azide functionality, to which can be attached an assortment of unnatural groups following methyltransferase-dependent DNA delivery. DNA duplexes modified with these cofactor mimics are capable of undergoing the Staudinger ligation with phosphines tethered to biological functionalities following enzymatic modification. This methodology provides a new tool by which to selectively modify DNA in a methyltransferase-dependent way. The conversion of biological methyltransferases into azidonucleosidyl transferases demonstrated here also holds tremendous promise as a means of identifying, as yet, unknown substrates of methylation.
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Affiliation(s)
- Lindsay R. Comstock
- School of Pharmacy, University of Wisconsin-Madison777 Highland Ave., Madison, WI 53705, USA
| | - Scott R. Rajski
- School of Pharmacy, University of Wisconsin-Madison777 Highland Ave., Madison, WI 53705, USA
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50
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Merkienė E, Klimašauskas S. Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase. Nucleic Acids Res 2005; 33:307-15. [PMID: 15653631 PMCID: PMC546160 DOI: 10.1093/nar/gki175] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
DNA methylation plays important roles via regulation of numerous cellular mechanisms in diverse organisms, including humans. The paradigm bacterial methyltransferase (MTase) HhaI (M.HhaI) catalyzes the transfer of a methyl group from the cofactor S-adenosyl-l-methionine (AdoMet) onto the target cytosine in DNA, yielding 5-methylcytosine and S-adenosyl-l-homocysteine (AdoHcy). The turnover rate (kcat) of M.HhaI, and the other two cytosine-5 MTases examined, is limited by a step subsequent to methyl transfer; however, no such step has so far been identified. To elucidate the role of cofactor interactions during catalysis, eight mutants of Trp41, which is located in the cofactor binding pocket, were constructed and characterized. The mutants show full proficiency in DNA binding and base-flipping, and little variation is observed in the apparent methyl transfer rate kchem as determined by rapid-quench experiments using immobilized fluorescent-labeled DNA. However, the Trp41 replacements with short side chains substantially perturb cofactor binding (100-fold higher KDAdoMet and KMAdoMet) leading to a faster turnover of the enzyme (10-fold higher kcat). Our analysis indicates that the rate-limiting breakdown of a long-lived ternary product complex is initiated by the dissociation of AdoHcy or the opening of the catalytic loop in the enzyme.
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Affiliation(s)
| | - Saulius Klimašauskas
- To whom correspondence should be addressed. Tel: +370 5 260 2114; Fax: +370 5 260 2116;
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