1
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Tellurium-Modified Nucleosides, Nucleotides, and Nucleic Acids with Potential Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238379. [PMID: 36500495 PMCID: PMC9737395 DOI: 10.3390/molecules27238379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022]
Abstract
Tellurium was successfully incorporated into proteins and applied to protein structure determination through X-ray crystallography. However, studies on tellurium modification of DNA and RNA are limited. This review highlights the recent development of Te-modified nucleosides, nucleotides, and nucleic acids, and summarizes the main synthetic approaches for the preparation of 5-PhTe, 2'-MeTe, and 2'-PhTe modifications. Those modifications are compatible with solid-phase synthesis and stable during Te-oligonucleotide purification. Moreover, the ideal electronic and atomic properties of tellurium for generating clear isomorphous signals give Te-modified DNA and RNA great potential applications in 3D crystal structure determination through X-ray diffraction. STM study also shows that Te-modified DNA has strong topographic and current peaks, which immediately suggests potential applications in nucleic acid direct imaging, nanomaterials, molecular electronics, and diagnostics. Theoretical studies indicate the potential application of Te-modified nucleosides in cancer therapy.
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2
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Pandya N, Rani R, Kumar V, Kumar A. Discovery of potent Guanidine derivative that selectively binds and stabilizes the human BCL-2 G-quadruplex DNA and downregulates the transcription. Gene 2022; 851:146975. [PMID: 36261091 DOI: 10.1016/j.gene.2022.146975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/26/2022] [Accepted: 10/11/2022] [Indexed: 12/09/2022]
Abstract
Small molecules that interact with quadruplexes offer a wide range of potential applications, including not just as medications but also as sensors for quadruplexes structures. The BCL-2 is a proto-oncogene that often gets mutated in lethal cancer and could be an interesting target for developing an anti-cancer drug. In the present study, we have employed various biophysical techniques such as fluorescence, CD, Isothermal calorimeter, gel retardation, and PCR stop assay, indicating that Guanidine derivatives GD-1 and GD-2 selectively interact with high affinity with BCL-2 G-quadruplex over other G-quadruplex DNA and duplex DNA. The most promising small molecule GD-1 increases the thermostability of the BCL-2 GQ structure by 12°C. Our biological experiments such as ROS generation, qRT-PCR, western blot, TFP based Reporter assay, show that the GD-1 ligand causes a synthetic lethal interaction by suppressing the expression BCL-2 genes via interaction and stabilization of its the promoter G-quadruplexes in HeLa cells and act as a potential anti-cancer agent.
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Affiliation(s)
- Nirali Pandya
- Department for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, Simrol, India
| | - Reshma Rani
- Department of Biotechnology, Amity University, Noida
| | - Vinit Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research
| | - Amit Kumar
- Department for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, Madhya Pradesh, 453552, Simrol, India.
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3
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Chen K, Gularek F, Liu B, Weinhold E, Keyser UF. Electrical DNA Sequence Mapping Using Oligodeoxynucleotide Labels and Nanopores. ACS NANO 2021; 15:2679-2685. [PMID: 33478224 PMCID: PMC7905879 DOI: 10.1021/acsnano.0c07947] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Identifying DNA species is crucial for diagnostics. For DNA identification, single-molecule DNA sequence mapping is an alternative to DNA sequencing toward fast point-of-care testing, which traditionally relies on targeting and labeling DNA sequences with fluorescent labels and readout using optical imaging methods. A nanopore is a promising sensor as a complement to optical mapping with advantages of electric measurement suitable for portable devices and potential for high resolution. Here, we demonstrate a high-resolution nanopore-based DNA sequence mapping by labeling specific short sequence motifs with oligodeoxynucleotides (ODNs) using DNA methyltransferase (MTase) and detecting them using nanopores. We successfully detected ODNs down to the size of 11 nucleotides without introducing extra reporters and resolved neighboring sites with a distance of 141 bp (∼48 nm) on a single DNA molecule. To accurately locate the sequence motif positions on DNA, a nanopore data analysis method is proposed by considering DNA velocity change through nanopores and using ensemble statistics to translate the time-dependent signals to the location information. Our platform enables high-resolution detection of small labels on DNA and high-accuracy localization of them for DNA species identification in an all-electrical format. The method presents an alternative to optical techniques relying on fluorescent labels and is promising for miniature-scale integration for diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Boyao Liu
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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4
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Majumdar S, Guha T, Barman F, Kundu R. A Basic Method for Hoechst (33258) Staining of Nuclei from Whole Root Tissues of Oryza sativa. NATIONAL ACADEMY SCIENCE LETTERS 2020. [DOI: 10.1007/s40009-019-00865-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Loukanov A, Nikolova S, Filipov C, Nakabayashi S. Metabolic labeling of Escherichia coli
genomic DNA with erythrosine-11-dUTP for functional imaging via correlative microscopy. Microsc Res Tech 2020; 83:937-944. [DOI: 10.1002/jemt.23487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/02/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Alexandre Loukanov
- Division of Strategic Research and Development, Graduate School of Science and Engineering; Saitama University; Saitama Japan
- Laboratory of Engineering NanoBiotechnology, Department of Engineering Geoecology; University of Mining and Geology “St. Ivan Rilski”; Sofia Bulgaria
| | - Svetla Nikolova
- Medical University-Sofia; University Hospital “Maichin Dom”, National Genetic Laboratory; Sofia Bulgaria
| | - Chavdar Filipov
- Faculty of Veterinary Medicine; University of Forestry, Sofia; Sofia Bulgaria
| | - Seiichiro Nakabayashi
- Division of Strategic Research and Development, Graduate School of Science and Engineering; Saitama University; Saitama Japan
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6
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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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7
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Goyvaerts V, Van Snick S, D'Huys L, Vitale R, Helmer Lauer M, Wang S, Leen V, Dehaen W, Hofkens J. Fluorescent SAM analogues for methyltransferase based DNA labeling. Chem Commun (Camb) 2020; 56:3317-3320. [DOI: 10.1039/c9cc08938a] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this work, the preparation of new S-adenosyl-l-methionine (SAM) analogues for sequence specific DNA labeling is evaluated. Fluorescent cofactors were synthesized and their applicability in methyltransferase based optical mapping is demonstrated.
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Affiliation(s)
- Vince Goyvaerts
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Sven Van Snick
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Laurens D'Huys
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Raffaele Vitale
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Milena Helmer Lauer
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Su Wang
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Volker Leen
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Wim Dehaen
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
| | - Johan Hofkens
- Laboratory of Molecular Imaging and Photonics
- Department of Chemistry
- KU Leuven
- 3001 Leuven
- Belgium
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8
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Chen K, Juhasz M, Gularek F, Weinhold E, Tian Y, Keyser UF, Bell NAW. Ionic Current-Based Mapping of Short Sequence Motifs in Single DNA Molecules Using Solid-State Nanopores. NANO LETTERS 2017; 17:5199-5205. [PMID: 28829136 PMCID: PMC5599873 DOI: 10.1021/acs.nanolett.7b01009] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Nanopore sensors show great potential for rapid, single-molecule determination of DNA sequence information. Here, we develop an ionic current-based method for determining the positions of short sequence motifs in double-stranded DNA molecules with solid-state nanopores. Using the DNA-methyltransferase M.TaqI and a biotinylated S-adenosyl-l-methionine cofactor analogue we create covalently attached biotin labels at 5'-TCGA-3' sequence motifs. Monovalent streptavidin is then added to bind to the biotinylated sites giving rise to additional current blockade signals when the DNA passes through a conical quartz nanopore. We determine the relationship between translocation time and position along the DNA contour and find a minimum resolvable distance between two labeled sites of ∼200 bp. We then characterize a variety of DNA molecules by determining the positions of bound streptavidin and show that two short genomes can be simultaneously detected in a mixture. Our method provides a simple, generic single-molecule detection platform enabling DNA characterization in an electrical format suited for portable devices for potential diagnostic applications.
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Affiliation(s)
- Kaikai Chen
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Matyas Juhasz
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Felix Gularek
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Elmar Weinhold
- Institute
of Organic Chemistry, RWTH Aachen University, Landoltweg 1, D-52056 Aachen, Germany
| | - Yu Tian
- State
Key Laboratory of Tribology, Tsinghua University, Beijing 100084, China
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail:
| | - Nicholas A. W. Bell
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, United Kingdom
- E-mail: . Fax: +44 (0)1223 337000
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9
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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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10
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Gilboa T, Torfstein C, Juhasz M, Grunwald A, Ebenstein Y, Weinhold E, Meller A. Single-Molecule DNA Methylation Quantification Using Electro-optical Sensing in Solid-State Nanopores. ACS NANO 2016; 10:8861-8870. [PMID: 27580095 DOI: 10.1021/acsnano.6b04748] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Detection of epigenetic markers, including 5-methylcytosine, is crucial due to their role in gene expression regulation and due to the mounting evidence of aberrant DNA methylation patterns in cancer biogenesis. Single-molecule methods to date have primarily been focused on hypermethylation detection; however, many oncogenes are hypomethylated during cancer development, presenting an important unmet biosensing challenge. To this end, we have developed a labeling and single-molecule quantification method for multiple unmethylated cytosine-guanine dinucleotides (CpGs). Our method involves a single-step covalent coupling of DNA with synthetic cofactor analogues using DNA methyltransferases (MTases) followed by molecule-by-molecule electro-optical nanopore detection and quantification with single or multiple colors. This sensing method yields a calibrated scale to directly quantify the number of unmethylated CpGs in the target sequences of each DNA molecule. Importantly, our method can be used to analyze ∼10 kbp long double-stranded DNA while circumventing PCR amplification or bisulfite conversion. Expanding this technique to use two colors, as demonstrated here, would enable sensing of multiple DNA MTases through orthogonal labeling/sensing of unmethylated CpGs (or other epigenetic modifications) associated with specific recognition sites. Our proof-of-principle study may permit sequence-specific, direct targeting of clinically relevant hypomethylated sites in the genome.
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Affiliation(s)
- Tal Gilboa
- Department of Biomedical Engineering, The Technion-Israel Institute of Technology , Haifa, 32000 Israel
| | - Chen Torfstein
- Department of Biomedical Engineering, The Technion-Israel Institute of Technology , Haifa, 32000 Israel
| | - Matyas Juhasz
- Institute of Organic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Assaf Grunwald
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv, 6997801 Israel
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University , Tel Aviv, 6997801 Israel
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Amit Meller
- Department of Biomedical Engineering, The Technion-Israel Institute of Technology , Haifa, 32000 Israel
- Department of Biomedical Engineering, Boston University , Boston, Massachusetts 02215, United States
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11
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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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12
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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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13
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Tengg M, Stecher H, Offner L, Plasch K, Anderl F, Weber H, Schwab H, Gruber-Khadjawi M. Methyltransferases: Green Catalysts for Friedel-Crafts Alkylations. ChemCatChem 2016. [DOI: 10.1002/cctc.201501306] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Martin Tengg
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Petersgasse 14 8010 Graz Austria
| | - Harald Stecher
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Lisa Offner
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Katharina Plasch
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Felix Anderl
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Hansjörg Weber
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
| | - Helmut Schwab
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Molecular Biotechnology; Graz University of Technology; Petersgasse 14 8010 Graz Austria
| | - Mandana Gruber-Khadjawi
- ACIB, Austrian Centre of Industrial Biotechnology GmbH; Petersgasse 14 8010 Graz Austria
- Institute of Organic Chemistry; Graz University of Technology; Stremayrgasse 9 8010 Graz Austria
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14
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Grunwald A, Dahan M, Giesbertz A, Nilsson A, Nyberg LK, Weinhold E, Ambjörnsson T, Westerlund F, Ebenstein Y. Bacteriophage strain typing by rapid single molecule analysis. Nucleic Acids Res 2015; 43:e117. [PMID: 26019180 PMCID: PMC4605287 DOI: 10.1093/nar/gkv563] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/14/2015] [Accepted: 05/15/2015] [Indexed: 01/12/2023] Open
Abstract
Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.
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Affiliation(s)
- Assaf Grunwald
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Moran Dahan
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Anna Giesbertz
- Institute of Organic Chemistry, RWTH Aachen University, Aachen D-52056 Germany
| | - Adam Nilsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund 223 62, Sweden
| | - Lena K Nyberg
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Elmar Weinhold
- Institute of Organic Chemistry, RWTH Aachen University, Aachen D-52056 Germany
| | - Tobias Ambjörnsson
- Department of Astronomy and Theoretical Physics, Lund University, Lund 223 62, Sweden
| | - Fredrik Westerlund
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel
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15
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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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Dong Y, Liu D, Yang Z. A brief review of methods for terminal functionalization of DNA. Methods 2014; 67:116-22. [DOI: 10.1016/j.ymeth.2013.11.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/06/2013] [Accepted: 11/12/2013] [Indexed: 12/29/2022] Open
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Beyond sequencing: optical mapping of DNA in the age of nanotechnology and nanoscopy. Curr Opin Biotechnol 2013; 24:690-8. [DOI: 10.1016/j.copbio.2013.01.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Revised: 01/20/2013] [Accepted: 01/22/2013] [Indexed: 12/25/2022]
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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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Luzzietti N, Knappe S, Richter I, Seidel R. Nicking enzyme-based internal labeling of DNA at multiple loci. Nat Protoc 2012; 7:643-53. [PMID: 22402634 DOI: 10.1038/nprot.2012.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The labeling of biomolecules has become standard practice in molecular biosciences. Modifications are used for detection, sorting and isolation of small molecules, complexes and entire cells. We have recently reported a method for introducing internal chemical and structural modifications into kbp-sized DNA target substrates that are frequently used in single-molecule experiments. It makes use of nicking enzymes that create single-stranded DNA gaps, which can be subsequently filled with labeled oligonucleotides. Here we provide a detailed protocol and further expand this method. We show that modifications can be introduced at distant loci within one molecule in a simple one-pot reaction. In addition, we achieve labeling on both strands at a specific locus, as demonstrated by Förster resonance energy transfer (FRET) experiments. The protocol requires an initial cloning of the target substrate (3-5 d), whereas the labeling itself takes 4-6 h. More elaborate purification and verification of label incorporation requires 2 h for each method.
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Affiliation(s)
- Nicholas Luzzietti
- Biotechnology Center, Dresden University of Technology, Dresden, Germany
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