1
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Lou J, Ancajas CF, Zhou Y, Lane NS, Reynolds TB, Best MD. Probing Glycerolipid Metabolism using a Caged Clickable Glycerol-3-Phosphate Probe. Chembiochem 2024:e202300853. [PMID: 38705850 DOI: 10.1002/cbic.202300853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/25/2024] [Accepted: 05/05/2024] [Indexed: 05/07/2024]
Abstract
In this study, we present the probe SATE-G3P-N3 as a novel tool for metabolic labeling of glycerolipids (GLs) to investigate lipid metabolism in yeast cells. By introducing a clickable azide handle onto the glycerol backbone, this probe enables general labeling of glycerolipids. Additionally, this probe contains a caged phosphate moiety at the glycerol sn-3 position to not only facilitate probe uptake by masking negative charge but also to bypass the phosphorylation step crucial for initiating phospholipid synthesis, thereby enhancing phospholipid labeling. The metabolic labeling activity of the probe was thoroughly assessed through cellular fluorescence microscopy, mass spectrometry (MS), and thin-layer chromatography (TLC) experiments. Fluorescence microscopy analysis demonstrated successful incorporation of the probe into yeast cells, with labeling predominantly localized at the plasma membrane. LCMS analysis confirmed metabolic labeling of various phospholipid species (PC, PS, PA, PI, and PG) and neutral lipids (MAG, DAG, and TAG), and GL labeling was corroborated by TLC. These results showcased the potential of the SATE-G3P-N3 probe in studying GL metabolism, offering a versatile and valuable approach to explore the intricate dynamics of lipids in yeast cells.
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Affiliation(s)
- Jinchao Lou
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Christelle F Ancajas
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Yue Zhou
- Department of Microbiology, University of Tennessee, Knoxville, 1311 Cumberland Avenue, Knoxville, TN, 337996, USA
| | - Nicolas S Lane
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Todd B Reynolds
- Department of Microbiology, University of Tennessee, Knoxville, 1311 Cumberland Avenue, Knoxville, TN, 337996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, Knoxville, 1420 Circle Drive, Knoxville, TN, 37996, USA
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2
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Hernández-López L, von Baeckmann C, Martínez-Esaín J, Cortés-Martínez A, Faraudo J, Caules C, Parella T, Maspoch D, Carné-Sánchez A. (Bio)Functionalisation of Metal-Organic Polyhedra by Using Click Chemistry. Chemistry 2023; 29:e202301945. [PMID: 37523177 DOI: 10.1002/chem.202301945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/24/2023] [Accepted: 07/30/2023] [Indexed: 08/01/2023]
Abstract
The surface chemistry of Metal-Organic Polyhedra (MOPs) is crucial to their physicochemical properties because it governs how they interact with external substances such as solvents, synthetic organic molecules, metal ions, and even biomolecules. Consequently, the advancement of synthetic methods that facilitate the incorporation of diverse functional groups onto MOP surfaces will significantly broaden the range of properties and potential applications for MOPs. This study describes the use of copper(I)-catalysed, azide-alkyne cycloaddition (CuAAC) click reactions to post-synthetically modify the surface of alkyne-functionalised cuboctahedral MOPs. To this end, a novel Rh(II)-based MOP with 24 available surface alkyne groups was synthesised. Each of the 24 alkyne groups on the surface of the "clickable" Rh-MOP can react with azide-containing molecules at room temperature, without compromising the integrity of the MOP. The wide substrate catalogue and orthogonal nature of CuAAC click chemistry was exploited to densely functionalise MOPs with diverse functional groups, including polymers, carboxylic and phosphonic acids, and even biotin moieties, which retained their recognition capabilities once anchored onto the surface of the MOP.
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Affiliation(s)
- Laura Hernández-López
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Departament de Química, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
| | - Cornelia von Baeckmann
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Departament de Química, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
| | - Jordi Martínez-Esaín
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Alba Cortés-Martínez
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Departament de Química, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
| | - Jordi Faraudo
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), 08193, Bellaterra, Spain
| | - Caterina Caules
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Departament de Química, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
| | - Teodor Parella
- Servei de Ressonància Magnètica Nuclear, Universitat Autònoma de Barcelona, Campus UAB, Bellaterra, 08193, Barcelona, Spain
| | - Daniel Maspoch
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Departament de Química, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Arnau Carné-Sánchez
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and The Barcelona Institute of Science and Technology, Campus UAB, Bellaterra, 08193, Barcelona, Spain
- Departament de Química, Facultat de Ciencies, Universitat Autonoma de Barcelona, 08193, Bellaterra, Spain
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3
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Kohn EM, Konovalov K, Gomez CA, Hoover GN, Yik AKH, Huang X, Martell JD. Terminal Alkyne-Modified DNA Aptamers with Enhanced Protein Binding Affinities. ACS Chem Biol 2023; 18:1976-1984. [PMID: 37531184 DOI: 10.1021/acschembio.3c00183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Nucleic acid-based receptors, known as aptamers, are relatively fast to discover and manufacture but lack the diverse functional groups of protein receptors (e.g., antibodies). The binding properties of DNA aptamers can be enhanced by attaching abiotic functional groups; for example, aromatic groups such as naphthalene slow dissociation from proteins. Although the terminal alkyne is a π-electron-rich functional group that has been used in small molecule drugs to enhance binding to proteins through noncovalent interactions, it remains unexplored for enhancing DNA aptamer binding affinity. Here, we demonstrate the utility of the terminal alkyne for improving the binding of DNA to proteins. We prepared a library of 256 terminal-alkyne-bearing variants of HD22, a DNA aptamer that binds the protein thrombin with nanomolar affinity. After a one-step thrombin-binding selection, a high-affinity aptamer containing two alkynes was discovered, exhibiting 3.2-fold tighter thrombin binding than the corresponding unmodified sequence. The tighter binding was attributable to a slower rate of dissociation from thrombin (5.2-fold slower than HD22). Molecular dynamics simulations with enhanced sampling by Replica Exchange with Solute Tempering (REST2) suggest that the π-electron-rich alkyne interacts with an asparagine side chain N-H group on thrombin, forming a noncovalent interaction that stabilizes the aptamer-protein interface. Overall, this work represents the first case of terminal alkynes enhancing the binding properties of an aptamer and underscores the utility of the terminal alkyne as an atom economical π-electron-rich functional group to enhance binding affinity with minimal steric perturbation.
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Affiliation(s)
- Eric M Kohn
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kirill Konovalov
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Christian A Gomez
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Gillian N Hoover
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Andrew Kai-Hei Yik
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Xuhui Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Theoretical Chemistry Institute, Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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4
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Chandankar SS, Kondhare D, Leonard P, Seela F. Purine DNA Constructs Designed to Expand the Genetic Code: Functionalization, Impact of Ionic Forms, and Molecular Recognition of 7-Deazaxanthine-7-Deazapurine-2,6-diamine Base Pairs and Their Purine Counterparts. J Org Chem 2023; 88:13149-13168. [PMID: 37669119 DOI: 10.1021/acs.joc.3c01370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Purine DNA represents an alternative pairing system formed by two purines in the base pair with the recognition elements of Watson-Crick DNA. Base functionalization of 7-deaza-2'-deoxyxanthosine with ethynyl and octadiynyl residues led to clickable side chain derivatives with short and long linker arms. As complementary bases, purine-2,6-diamine or 7-deazapurine-2,6-diamine 2'-deoxyribonucleosides were used. 7-Deaza-7-iodo-2'-deoxyxanthosine served as a starting material for Sonogashira cross-coupling and the p-nitrophenylethyl group for base protection. Phosphoramidite building blocks for DNA synthesis were prepared. Oligonucleotides containing single modifications or runs of three purine base pairs embedded in 12-mer Watson-Crick DNA were synthesized and hybridized with complementary strands with purine- or 7-deazapurine-2,6-diamine located opposite to the xanthine derivatives. The stability of base pairs was evaluated in a comparative study on the basis of DNA melting experiments and Tm values. As 7-deazaxanthine and xanthine nucleosides form anionic forms at neutral pH, duplex stability became pK-dependent, and the system with 7-deazapurine displayed a significant higher stability as that containing xanthine. Alkynyl side chains are well accommodated in the purine-purine helix. Click adducts with pyrene showed that short linker arms destabilize duplexes, whereas long linkers increase duplex stability. CD and fluorescence measurements provide further insights into purine-purine base pairing.
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Affiliation(s)
- Somnath Shivaji Chandankar
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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5
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Osawa T, Ren Q, Obika S. Development of Phosphoramidite Reagents for the Synthesis of Base-Labile Oligonucleotides Modified with a Linear Aminoalkyl and Amino-PEG Linker at the 3'-End. Molecules 2022; 27:molecules27238501. [PMID: 36500594 PMCID: PMC9736658 DOI: 10.3390/molecules27238501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/11/2022] Open
Abstract
Oligonucleotides with an amino linker at the 3'-end are useful for the preparation of conjugated oligonucleotides. However, chemically modified nucleosides, which are unstable under basic conditions, cannot be incorporated into oligonucleotides using the conventional method entailing the preparation of oligonucleotides bearing a 3'-amino linker. Therefore, we designed Fmoc-protected phosphoramidites for the synthesis of base-labile oligonucleotides modified with a 3'-amino linker. The resultant phosphoramidites were then successfully incorporated into oligonucleotides bearing a 3'-amino linker. Various basic solutions were investigated for protecting group removal. All the protecting groups were removed by treating the oligonucleotides with 40% aqueous methylamine at room temperature for 2 h. Thus, the deprotection time and temperature were significantly reduced compared to the conventional conditions (28% NH3 aq., 55 °C, 17 h). In addition, the oligonucleotide protecting groups could be removed using a mild base (e.g., 50 mM potassium carbonate methanol solution). Furthermore, base-labile oligonucleotides bearing an amino linker at the 3'-end were successfully synthesized using the developed phosphoramidite reagents, highlighting the utility of our strategy.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
| | - Qin Ren
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, Yamadaoka 1-6, Osaka 565-0871, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Yamadaoka 1-3, Osaka 565-0871, Japan
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Osaka 567-0085, Japan
- Correspondence: ; Tel.: +81-6-6879-8200
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6
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Gebhard J, Hirsch L, Schwechheimer C, Wagenknecht HA. Hybridization-Sensitive Fluorescent Probes for DNA and RNA by a Modular "Click" Approach. Bioconjug Chem 2022; 33:1634-1642. [PMID: 35995426 PMCID: PMC9501807 DOI: 10.1021/acs.bioconjchem.2c00241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Fluorescent DNA probes were prepared in a modular approach
using
the “click” post-synthetic modification strategy. The
new glycol-based module and DNA building block place just two carbons
between the phosphodiester bridges and anchor the dye by an additional
alkyne group. This creates a stereocenter in the middle of this artificial
nucleoside substitute. Both enantiomers and a variety of photostable
cyanine–styryl dyes as well as thiazole orange derivatives
were screened as “clicked” conjugates in different surrounding
DNA sequences. The combination of the (S)-configured
DNA anchor and the cyanylated cyanine–styryl dye shows the
highest fluorescence light-up effect of 9.2 and a brightness of approximately
11,000 M–1 cm–1. This hybridization
sensitivity and fluorescence readout were further developed utilizing
electron transfer and energy transfer processes. The combination of
the hybridization-sensitive DNA building block with the nucleotide
of 5-nitroindole as an electron acceptor and a quencher increases
the light-up effect to 20 with the DNA target and to 15 with the RNA
target. The fluorescence readout could significantly be enhanced to
values between 50 and 360 by the use of energy transfer to a second
DNA probe with commercially available dyes, like Cy3.5, Cy5, and Atto590,
as energy acceptors at the 5′-end. The latter binary probes
shift the fluorescent readout from the range of 500–550 nm
to the range of 610–670 nm. The optical properties make these
fluorescent DNA probes potentially useful for RNA imaging. Due to
the strong light-up effect, they will not require washing procedures
and will thus be suitable for live-cell imaging.
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Affiliation(s)
- Julian Gebhard
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Lara Hirsch
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Christian Schwechheimer
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 7631 Karlsruhe, Germany
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7
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Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG. Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J Am Chem Soc 2022; 144:10556-10569. [PMID: 35666775 DOI: 10.1021/jacs.2c03454] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.
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Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Heike M Kropp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Samra Ludmann
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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8
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Bagra N, Jain R. Synthesis of 4-(1,2,3-triazol-1-yl)-L-phenylalanines. SYNTHETIC COMMUN 2022. [DOI: 10.1080/00397911.2022.2077114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Nitin Bagra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Punjab, India
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9
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Ito Y, Hari Y. Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution. CHEM REC 2022; 22:e202100325. [PMID: 35119181 DOI: 10.1002/tcr.202100325] [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: 12/17/2021] [Revised: 01/21/2022] [Indexed: 11/11/2022]
Abstract
Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.
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Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima, 770-8514, Japan
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10
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Siegl J, Nikolin C, Phung NL, Thoms S, Blume C, Mayer G. Split-Combine Click-SELEX Reveals Ligands Recognizing the Transplant Rejection Biomarker CXCL9. ACS Chem Biol 2022; 17:129-137. [PMID: 35018777 DOI: 10.1021/acschembio.1c00789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Renal rejection is a major incidence in patients after kidney transplantation and associated with allograft scarring and function loss, especially in antibody-mediated rejection. Regular clinical monitoring of kidney-transplanted patients is thus necessary, but measuring donor-specific antibodies is not always predictive, and graft biopsies are time-consuming and costly and may come up with a histological result unsuspicious for rejection. Therefore, a noninvasive diagnostic approach to estimate an increased probability of kidney graft rejection by measuring specific biomarkers is highly desired. The chemokine CXCL9 is described as an early indicator of rejection. In this work, we identified clickmers and an aptamer by split-combine click-SELEX (systematic evolution of ligands by exponential enrichment) that bind CXLC9 with high affinity. The aptamers recognize native CXCL9 and maintain binding properties under urine conditions. These features render the molecules as potential binding and detector probes for developing point-of-care devices, e.g., lateral flow assays, enabling the noninvasive monitoring of CXCL9 in renal allograft patients.
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Affiliation(s)
- Julia Siegl
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Str. 1, Bonn 53121, Germany
| | - Christoph Nikolin
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover 30625, Germany
| | - Ngoc Linh Phung
- Institute for Technical Chemistry, Leibniz University Hannover, Callinstr. 5, Hannover 30167, Germany
| | - Stefanie Thoms
- Institute for Technical Chemistry, Leibniz University Hannover, Callinstr. 5, Hannover 30167, Germany
| | - Cornelia Blume
- Institute for Technical Chemistry, Leibniz University Hannover, Callinstr. 5, Hannover 30167, Germany
| | - Günter Mayer
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, Gerhard-Domagk-Str. 1, Bonn 53121, Germany
- Center of Aptamer Research & Development (CARD), University of Bonn, Gerhard-Domagk-Str. 1, Bonn 53121, Germany
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11
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Siegl J, Plückthun O, Mayer G. Dependence of click-SELEX performance on the nature and average number of modified nucleotides. RSC Chem Biol 2022; 3:288-294. [PMID: 35359492 PMCID: PMC8905535 DOI: 10.1039/d2cb00012a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/17/2022] [Indexed: 11/21/2022] Open
Abstract
The click-SELEX procedure enables the identification of nucleobase-modified aptamers in which chemical entities are introduced by a copper(i)-catalysed alkyne-azide ‘click’ reaction. Here we report on the impact of modified nucleobases on PCR conditions and the average amount of modified nucleobases on click-SELEX performance. We demonstrate click-SELEX being strongly dependent on which and on how many modifications are used. However, when using C3-GFP the number of modifications did not impact the overall success of the selection procedure. The click-SELEX procedure enables the identification of nucleobase-modified aptamers in which chemical entities are introduced by a copper(i)-catalysed alkyne-azide ‘click’ reaction.![]()
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Affiliation(s)
- Julia Siegl
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Olga Plückthun
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
| | - Günter Mayer
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
- Center of Aptamer Research & Development (CARD), University of Bonn Gerhard-Domagk-Str. 1 53121 Bonn Germany
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12
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Oligonucleotide conjugation by tyrosine‐click reaction. European J Org Chem 2021. [DOI: 10.1002/ejoc.202101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Teng Y, Yang H, Li X, Wang Y, Yin D, Tian Y. A
Bioorthogonal‐Activated
Fluorescence
Turn‐On
Probe Based on
Nitrone‐Modified
1,
8‐Naphthalimide
for
Live‐Cell
Imaging. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yu Teng
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences 1st Xian Nong Tan Street Beijing 100050 China
| | - Hong Yang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences 1st Xian Nong Tan Street Beijing 100050 China
| | - Xiang Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences 1st Xian Nong Tan Street Beijing 100050 China
| | - Yongcheng Wang
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences 1st Xian Nong Tan Street Beijing 100050 China
| | - Dali Yin
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences 1st Xian Nong Tan Street Beijing 100050 China
| | - Yulin Tian
- State Key Laboratory of Bioactive Substances and Function of Natural Medicine, Beijing Key Laboratory of Active Substances Discovery and Drugability Evaluation, Institute of Materia Medica, Peking Union Medical College and Chinese Academy of Medical Sciences 1st Xian Nong Tan Street Beijing 100050 China
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14
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Patel M, Desai B, Sheth A, Dholakiya BZ, Naveen T. Recent Advances in Mono‐ and Difunctionalization of Unactivated Olefins. ASIAN J ORG CHEM 2021. [DOI: 10.1002/ajoc.202100666] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Monak Patel
- Department of Chemistry Sardar Vallabhbhai National Institute of Technology Gujarat–Surat 395 007 India
| | - Bhargav Desai
- Department of Chemistry Sardar Vallabhbhai National Institute of Technology Gujarat–Surat 395 007 India
| | - Aakash Sheth
- Department of Chemistry Sardar Vallabhbhai National Institute of Technology Gujarat–Surat 395 007 India
| | - Bharatkumar Z. Dholakiya
- Department of Chemistry Sardar Vallabhbhai National Institute of Technology Gujarat–Surat 395 007 India
| | - Togati Naveen
- Department of Chemistry Sardar Vallabhbhai National Institute of Technology Gujarat–Surat 395 007 India
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15
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Choi MH, Nguyen VT, Ravi Kumara GS, Seo YJ. RNA Polymerase-Mediated Stepwise RNA-Primed RNA Polymerization for Site-Specific Multiple Labeling into RNA: A Fluorescence Resonance Energy Transfer Probe Detects the Structural Change of an RNA G-Quadruplex. ACS Synth Biol 2021; 10:3139-3147. [PMID: 34762391 DOI: 10.1021/acssynbio.1c00418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this paper, we report a stepwise RNA-primed RNA polymerization method for the site-specific incorporation of multiple fluorescent moieties into RNA, mediated by an RNA polymerase. A screen of several RNA polymerases revealed that T7 RNA polymerase was the only one that functioned in the RNA-primed RNA polymerization. In the first fluorescence labeling step, a fluorescent rUthioTP residue was incorporated directly into the RNA using T7 RNA polymerase; the second fluorescence labeling step was performed using a post-labeling strategy: directly introducing an rUamiTP residue into RNA, using T7 RNA polymerase, and then reacting with ylidenemalononitrile enamine (P3). The whole process for the site-specific introduction of the multiple labeled moieties was performed through stepwise RNA-primed RNA polymerization. Interestingly, the resulting multiple-labeled RNA exhibited fluorescence resonance energy transfer (FRET) between the two fluorescent labels in the RNA. We optimized the FRET-breaking point in the RNA by changing of distance between the two fluorescent labels and then used this property for the detection of the structural change of the RNA. The FRET signal increased in intensity upon the transformation of the RNA from a single-strand structure to the G-quadruplex. This approach for site-specific FRET labeling into RNA using RNA polymerase suggests the possibility of performing other diverse site-specific modifications at predefined positions in RNA.
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Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
| | - Van Thang Nguyen
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City 700000, Vietnam
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
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16
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Rabah J, Yonkeu L, Wright K, Vallée A, Méallet-Renault R, Ha-Thi MH, Fatima A, Clavier G, Fensterbank H, Allard E. Synthesis of a dual clickable fullerene platform and construction of a dissymmetric BODIPY-[60]Fullerene-DistyrylBODIPY triad. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Gurawa A, Kumar M, Kashyap S. Selective Azidooxygenation of Alkenes Enabled by Photo-induced Radical Transfer Using Aryl-λ 3-azidoiodane Species. ACS OMEGA 2021; 6:26623-26639. [PMID: 34661016 PMCID: PMC8515593 DOI: 10.1021/acsomega.1c03991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/16/2021] [Indexed: 06/13/2023]
Abstract
The photolytic radical-induced vicinal azidooxygenation of synthetically important and diverse functionalized substrates including unactivated alkenes is reported. The photoredox-catalyst/additive-free protocol enables intermolecular oxyazidation by simultaneously incorporating two new functionalities; C-O and C-N across the C=C double bond in a selective manner. Mechanistic investigations reveal the intermediacy of the azidyl radical facilitated via the photolysis of λ3-azidoiodane species and cascade proceeding to generate an active carbon-centered radical. The late-stage transformations of azido- and oxy-moieties were amply highlighted by assembling high-value drug analogs and bioactive skeletons.
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18
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Depmeier H, Hoffmann E, Bornewasser L, Kath‐Schorr S. Strategies for Covalent Labeling of Long RNAs. Chembiochem 2021; 22:2826-2847. [PMID: 34043861 PMCID: PMC8518768 DOI: 10.1002/cbic.202100161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Indexed: 12/17/2022]
Abstract
The introduction of chemical modifications into long RNA molecules at specific positions for visualization, biophysical investigations, diagnostic and therapeutic applications still remains challenging. In this review, we present recent approaches for covalent internal labeling of long RNAs. Topics included are the assembly of large modified RNAs via enzymatic ligation of short synthetic oligonucleotides and synthetic biology approaches preparing site-specifically modified RNAs via in vitro transcription using an expanded genetic alphabet. Moreover, recent approaches to employ deoxyribozymes (DNAzymes) and ribozymes for RNA labeling and RNA methyltransferase based labeling strategies are presented. We discuss the potentials and limits of the individual methods, their applicability for RNAs with several hundred to thousands of nucleotides in length and indicate future directions in the field.
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Affiliation(s)
- Hannah Depmeier
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Eva Hoffmann
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Lisa Bornewasser
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
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19
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Convertible and Constrained Nucleotides: The 2'-Deoxyribose 5'-C-Functionalization Approach, a French Touch. Molecules 2021; 26:molecules26195925. [PMID: 34641475 PMCID: PMC8512084 DOI: 10.3390/molecules26195925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 09/21/2021] [Accepted: 09/27/2021] [Indexed: 11/17/2022] Open
Abstract
Many strategies have been developed to modulate the biological or biotechnical properties of oligonucleotides by introducing new chemical functionalities or by enhancing their affinity and specificity while restricting their conformational space. Among them, we review our approach consisting of modifications of the 5’-C-position of the nucleoside sugar. This allows the introduction of an additional chemical handle at any position on the nucleotide chain without disturbing the Watson–Crick base-pairing. We show that 5’-C bromo or propargyl convertible nucleotides (CvN) are accessible in pure diastereoisomeric form, either for nucleophilic displacement or for CuAAC conjugation. Alternatively, the 5’-carbon can be connected in a stereo-controlled manner to the phosphate moiety of the nucleotide chain to generate conformationally constrained nucleotides (CNA). These allow the precise control of the sugar/phosphate backbone torsional angles. The consequent modulation of the nucleic acid shape induces outstanding stabilization properties of duplex or hairpin structures in accordance with the preorganization concept. Some biological applications of these distorted oligonucleotides are also described. Effectively, the convertible and the constrained approaches have been merged to create constrained and convertible nucleotides (C2NA) providing unique tools to functionalize and stabilize nucleic acids.
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20
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Beukeaw D, Yotphan S. Copper‐Catalyzed Decarboxylative Cycloaddition of Alkynyl Carboxylic Acids and Sodium Azide with Epoxides and Ethers. ChemistrySelect 2021. [DOI: 10.1002/slct.202102494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Danupat Beukeaw
- Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand
| | - Sirilata Yotphan
- Department of Chemistry and Center of Excellence for Innovation in Chemistry Faculty of Science Mahidol University Rama VI Road Bangkok 10400 Thailand
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21
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Ren P, Li Q, Song T, Wang Z, Motokura K, Yang Y. Highly Efficient and Stable Atomically Dispersed Cu Catalyst for Azide‐Alkyne Cycloaddition Reaction. ChemCatChem 2021. [DOI: 10.1002/cctc.202100831] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Peng Ren
- CAS Key Laboratory of Bio-Based Materials Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Qingdao 266101 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Qinglin Li
- CAS Key Laboratory of Bio-Based Materials Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Qingdao 266101 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Tao Song
- CAS Key Laboratory of Bio-Based Materials Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Qingdao 266101 P. R. China
- Shandong Energy Institute Qingdao 266101 P. R. China
- Qingdao New Energy Shandong Laboratory Qingdao 266101 P. R. China
| | - Zhaozhan Wang
- CAS Key Laboratory of Bio-Based Materials Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Qingdao 266101 P. R. China
- Shandong Energy Institute Qingdao 266101 P. R. China
- Qingdao New Energy Shandong Laboratory Qingdao 266101 P. R. China
| | - Ken Motokura
- Department of Chemistry and Life Science Yokohama National University Yokohama 240-8501 Japan
| | - Yong Yang
- CAS Key Laboratory of Bio-Based Materials Qingdao Institute of Bioenergy and Bioprocess Technology Chinese Academy of Sciences Qingdao 266101 P. R. China
- Shandong Energy Institute Qingdao 266101 P. R. China
- Qingdao New Energy Shandong Laboratory Qingdao 266101 P. R. China
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22
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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23
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Wang Z, Niu J, Zhao C, Wang X, Ren J, Qu X. A Bimetallic Metal–Organic Framework Encapsulated with DNAzyme for Intracellular Drug Synthesis and Self‐Sufficient Gene Therapy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016442] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jingsheng Niu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Xiaohui Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization Changchun Institute of Applied Chemistry Chinese Academy of Sciences Changchun Jilin 130022 P. R. China
- University of Science and Technology of China Hefei Anhui 230026 P. R. China
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24
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Wang Z, Niu J, Zhao C, Wang X, Ren J, Qu X. A Bimetallic Metal-Organic Framework Encapsulated with DNAzyme for Intracellular Drug Synthesis and Self-Sufficient Gene Therapy. Angew Chem Int Ed Engl 2021; 60:12431-12437. [PMID: 33739589 DOI: 10.1002/anie.202016442] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 02/25/2021] [Indexed: 12/11/2022]
Abstract
Although chemotherapy is one of the most widely used cancer treatments, there are serious side effects, drug resistance, and secondary metastasis. To address these problems, herein we designed a bimetallic metal-organic framework (MOF) encapsulated with DNAzyme for co-triggered in situ cancer drug synthesis and DNAzyme-based gene therapy. Once in cancer cells, MOFs would disassemble and liberate copper ions, zinc ions, and DNAzyme under the acidic environment of lysosomes. Copper ions can catalyze the synthesis of the chemotherapeutic drug through copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction after being reduced to CuI ; zinc ions act as the cofactor to activate the cleavage activity of DNAzyme. The anticancer drug is synthesized intracellularly and can kill cancer cells on site to minimize side effects to normal organisms. The activated DNAzyme starts gene therapy to inhibit tumor proliferation and metastasis by targeting and cleaving oncogene substrates.
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Affiliation(s)
- Zhao Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jingsheng Niu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Chuanqi Zhao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaohui Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China.,University of Science and Technology of China, Hefei, Anhui, 230026, P. R. China
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25
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Wang J, Shang J, Xiang Y, Tong A. General Method for Post-Synthetic Modification of Oligonucleotides Based on Oxidative Amination of 4-Thio-2'-deoxyuridine. Bioconjug Chem 2021; 32:721-728. [PMID: 33730486 DOI: 10.1021/acs.bioconjchem.1c00016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functionalized oligonucleotides (ONs) are widely applied as target binding molecules for biosensing and regulators for gene expression. Numerous efforts have been focused on developing facile methods for preparing these useful ONs carrying diverse modifications. Herein, we present a general method for postsynthetic modification of ONs via oxidative amination of 4-thio-2'-deoxyuridine (4SdU). 4SdU-containing ON can be derived by both alkyl and aromatic amines. Using this approach, ONs are successfully attached with alkyne/azide, biotin and dansylamide moieties, and these as-prepared ONs possess the expected biorthogonal reactivity, streptavidin affinity and fluorescent property, respectively. Furthermore, we also directly install fluorophores to the ON nucleobase based on oxidative amination of 4SdU, and these fluorophores exhibit distinct luminescence behaviors before and after conjugation. We believe our method will be a versatile strategy for constructing various functionalized ONs used in a wide range of nucleic acid applications.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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26
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Moghadam SMM, Alibolandi M, Babaei M, Mosafer J, Saljooghi AS, Ramezani M. Fabrication of deferasirox-decorated aptamer-targeted superparamagnetic iron oxide nanoparticles (SPION) as a therapeutic and magnetic resonance imaging agent in cancer therapy. J Biol Inorg Chem 2021; 26:29-41. [PMID: 33156416 DOI: 10.1007/s00775-020-01834-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 10/22/2020] [Indexed: 02/07/2023]
Abstract
In the current study, the synthesis of a theranostic platform composed of superparamagnetic iron oxide nanoparticles (SPION)-deferasirox conjugates targeted with AS1411 DNA aptamer was reported. In this regard, SPION was amine-functionalized by (3-aminopropyl)trimethoxysilane (ATPMS), and then deferasirox was covalently conjugated onto its surface. Finally, to provide guided drug delivery to cancerous tissue, AS1411 aptamer was conjugated to the complex of SPION-deferasirox. The cellular toxicity assay on CHO, C-26 and AGS cell lines verified higher cellular toxicity of targeted complex in comparison with non-targeted one. The evaluation of in vivo tumor growth inhibitory effect in C26 tumor-bearing mice illustrated that the aptamer-targeted complex significantly enhanced the therapeutic outcome in comparison with both non-targeted complex and free drug. The diagnostic capability of the prepared platform was also evaluated implementing C26-tumor-bearing mice. Obtained data confirmed higher tumor accumulation and higher tumor residence time for targeted complex through MRI imaging due to the existence of SPION as a contrast agent in the core of the prepared complex. The prepared multimodal theranostic system provides a safe and effective platform for fighting against cancer.
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Affiliation(s)
| | - Mona Alibolandi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Pharmaceutical Biotechnology, Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam Babaei
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jafar Mosafer
- Department of Medical Biotechnology, School of Paramedical Sciences, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
- Department of Radiology, 9 Day Educational Hospital, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Amir Sh Saljooghi
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, 91775-1436, Iran.
| | - Mohammad Ramezani
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Pharmaceutical Biotechnology, Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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27
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Chen X, Xiao F, He WM. Recent developments in the difunctionalization of alkenes with C–N bond formation. Org Chem Front 2021. [DOI: 10.1039/d1qo00375e] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Various alkene difunctionalization reactions involving nitridization, diamination, azidation, oxyamination, carboamination, aminohalogenation, and nitration are introduced in this review.
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Affiliation(s)
- Xiang Chen
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
| | - Fang Xiao
- Xiangya School of Public Health, Central South University, Changsha 410078, PR China
| | - Wei-Min He
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, 421001, China
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28
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Gharpure SJ, Naveen S, Chavan RS, Padmaja. Regioselective Synthesis of Halotriazoles and their Utility in Metal Catalyzed Coupling Reactions. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000973] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Santosh J. Gharpure
- Department of Chemistry Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Sudi Naveen
- Department of Chemistry Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Rupali S. Chavan
- Department of Chemistry Indian Institute of Technology Bombay 400076 Powai Mumbai India
| | - Padmaja
- Department of Chemistry Indian Institute of Technology Bombay 400076 Powai Mumbai India
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29
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Walunj MB, Srivatsan SG. Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides. Bioconjug Chem 2020; 31:2513-2521. [PMID: 33089687 PMCID: PMC7611128 DOI: 10.1021/acs.bioconjchem.0c00466] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the performance of such chemoselective nucleic labeling methods are less explored. Given that nucleic acids adopt complex structures, it is highly important to study the scope of the chemical modification method in the context of nucleic acid conformations. Here we report a systematic study on the effect of local conformation on the postsynthetic Suzuki-Miyaura functionalization of human telomeric (H-Telo) DNA repeat oligonucleotide (ON) sequences, which form multiple G-quadruplex (GQ) structures. 5-Iodo-2'-deoxyuridine (IdU)-modified H-Telo ONs were synthesized by the solid-phase method, and when subjected to Suzuki-Miyaura cross-coupling reaction, its efficiency was found to depend on the type of conformation and the position of IdU label in different loops of the GQ structure. IdU-labeled GQs gave better yields as compared to single-stranded random coil structures. However, the IdU-labeled duplex under different ionic conditions did not undergo the coupling reaction. Further, using this method, we directly installed an environment-sensitive fluorescent probe, which photophysically reported the formation as well as distinguished different GQ topologies of telomeric repeat. Collectively, this systematic study underscores the influence of nucleic acid conformation, which has to be taken into account when establishing postsynthetic chemoselective functionalization strategies.
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Affiliation(s)
- Manisha B. Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Seergazhi G. Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, India
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30
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Gray MD, Deore PS, Chung AJ, Van Riesen AJ, Manderville RA, Prabhakar PS, Wetmore SD. Lighting Up the Thrombin-Binding Aptamer G-Quadruplex with an Internal Cyanine-Indole-Quinolinium Nucleobase Surrogate. Direct Fluorescent Intensity Readout for Thrombin Binding without Topology Switching. Bioconjug Chem 2020; 31:2596-2606. [PMID: 33156614 DOI: 10.1021/acs.bioconjchem.0c00530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorescent nucleobases represent an important class of molecular reporters of nucleic acid interactions. In this work, the advantages of utilizing a noncanonical fluorescent nucleobase surrogate for monitoring thrombin binding by the 15-mer thrombin binding aptamer (TBA) is presented. TBA folds into an antiparallel G-quadruplex (GQ) with loop thymidine (T) residues interacting directly with the protein in the thrombin-TBA complex. In the free GQ, T3 is solvent-exposed and does not form canonical base-pairs within the antiparallel GQ motif. Upon thrombin binding, T3 interacts directly with a hydrophobic protein binding pocket. Replacing T3 with a cyanine-indole-quinolinium (4QI) hemicyanine dye tethered to an acyclic 1,2-propanediol linker is shown to have minimal impact on GQ stability and structure with the internal 4QI displaying a 40-fold increase in emission intensity at 586 nm (excitation 508 nm) compared to the free dye in solution. Molecular dynamics (MD) simulations demonstrate that the 4QI label π-stacks with T4 and T13 within the antiparallel GQ fold, which is supported by strong energy transfer (ET) fluorescence from the GQ (donor) to the 4QI label (acceptor). Thrombin binding to 4QI-TBA diminishes π-stacking interactions between 4QI and the GQ structure to cause a turn-off emission intensity response with an apparent dissociation constant (Kd) of 650 nM and a limit of detection (LoD) of 150 nM. These features highlight the utility of internal noncanonical fluorescent surrogates for monitoring protein binding by GQ-folding aptamers in the absence of DNA topology switching.
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Affiliation(s)
- Micaela D Gray
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Prashant S Deore
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Andrew J Chung
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Abigail J Van Riesen
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard A Manderville
- Department of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Preethi Seelam Prabhakar
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada T1K 3M4
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31
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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32
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Ancajas CF, Ricks TJ, Best MD. Metabolic labeling of glycerophospholipids via clickable analogs derivatized at the lipid headgroup. Chem Phys Lipids 2020; 232:104971. [PMID: 32898510 PMCID: PMC7606648 DOI: 10.1016/j.chemphyslip.2020.104971] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 09/01/2020] [Indexed: 02/09/2023]
Abstract
Metabolic labeling, in which substrate analogs containing diminutive tags can infiltrate biosynthetic pathways and generate labeled products in cells, has led to dramatic advancements in the means by which complex biomolecules can be detected and biological processes can be elucidated. Within this realm, metabolic labeling of lipid products, particularly in a manner that is headgroup-specific, brings about a number of technical challenges including the complexity of lipid metabolic pathways as well as the simplicity of biosynthetic precursors to headgroup functionality. As such, only a handful of strategies for metabolic labeling of lipids have thus far been reported. However, these approaches provide enticing examples of how strategic modifications to substrate structures, particularly by introducing clickable moieties, can enable the hijacking of lipid biosynthesis. Furthermore, early work in this field has led to an explosion in diverse applications by which these techniques have been exploited to answer key biological questions or detect and track various lipid-containing biological entities. In this article, we review these efforts and emphasize recent advancements in the development and application of lipid metabolic labeling strategies.
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Affiliation(s)
- Christelle F Ancajas
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Tanei J Ricks
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA.
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33
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Fehlau M, Kaspar F, Hellendahl KF, Schollmeyer J, Neubauer P, Wagner A. Modular Enzymatic Cascade Synthesis of Nucleotides Using a (d)ATP Regeneration System. Front Bioeng Biotechnol 2020; 8:854. [PMID: 32903716 PMCID: PMC7438870 DOI: 10.3389/fbioe.2020.00854] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 07/02/2020] [Indexed: 12/14/2022] Open
Abstract
Nucleoside-5'-triphosphates (NTPs) and their analogs are building blocks of DNA and are important compounds in both pharmaceutical and molecular biology applications. Currently, commercially available base or sugar modified NTPs are mainly synthesized chemically. Since the chemical production of NTPs is time-consuming and generally inefficient, alternative approaches are under development. Here we present a simple, efficient and generalizable enzymatic synthesis method for the conversion of nucleosides to NTPs. Our one-pot method is modular, applicable to a wide range of natural and modified nucleotide products and accesses NTPs directly from cheap nucleoside precursors. Nucleoside kinases, nucleoside monophosphate (NMP) kinases and a nucleoside diphosphate (NDP) kinase were applied as biocatalysts. Enzymes with different substrate specificities were combined to produce derivatives of adenosine and cytidine triphosphate with conversions of 4 to 26%. The implementation of a (deoxy)ATP recycling system resulted in a significant increase in the conversion to all NTP products, furnishing 4 different NTPs in quantitative conversion. Natural (deoxy)NTPs were synthesized with 60 to >99% conversion and sugar- and base-modified NTPs were produced with 69 to >99% and 27 to 75% conversion, respectively. The presented method is suitable for the efficient synthesis of a wide range of natural and modified NTPs in a sustainable one-pot process.
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Affiliation(s)
- Maryke Fehlau
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
| | - Felix Kaspar
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
| | - Katja F Hellendahl
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany
| | - Julia Schollmeyer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
| | - Peter Neubauer
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany
| | - Anke Wagner
- Chair of Bioprocess Engineering, Institute of Biotechnology, Faculty III Process Sciences, Technische Universität Berlin, Berlin, Germany.,BioNukleo GmbH, Berlin, Germany
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34
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Rodríguez J, Martínez-Calvo M. Transition-Metal-Mediated Modification of Biomolecules. Chemistry 2020; 26:9792-9813. [PMID: 32602145 DOI: 10.1002/chem.202001287] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 06/25/2020] [Indexed: 01/15/2023]
Abstract
The site-selective modification of biomolecules has grown spectacularly in recent years. The presence of a large number of functional groups in a biomolecule makes its chemo- and regioselective modification a challenging goal. In this context, transition-metal-mediated reactions are emerging as a powerful tool owing to their unique reactivity and good functional group compatibility, allowing highly efficient and selective bioconjugation reactions that operate under mild conditions. This Minireview focuses on the current state of organometallic chemistry for bioconjugation, highlighting the potential of transition metals for the development of chemoselective and site-specific methods for functionalization of peptides, proteins and nucleic acids. The importance of the selection of ligands attached to the transition metal for conferring the desired chemoselectivity will be highlighted.
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Affiliation(s)
- Jessica Rodríguez
- Laboratoire Hétérochimie Fondamentale et Appliquée, Université Paul Sabatier/CNRS UMR 5069, 118 Route de Narbonne, 31062, Toulouse Cedex 09, France
| | - Miguel Martínez-Calvo
- Centro de Investigaciones Científicas Avanzadas (CICA), AE CICA-INIBIC, Departamento de Química, Facultade de Ciencias, Universidade da Coruña, Campus de Elviña, 15071 A, Coruña, Galicia, Spain
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35
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Raddaoui N, Croce S, Geiger F, Borodavka A, Möckl L, Stazzoni S, Viverge B, Bräuchle C, Frischmuth T, Engelke H, Carell T. Supersensitive Multifluorophore RNA-FISH for Early Virus Detection and Flow-FISH by Using Click Chemistry. Chembiochem 2020; 21:2214-2218. [PMID: 32187837 PMCID: PMC7496099 DOI: 10.1002/cbic.202000081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/11/2020] [Indexed: 01/25/2023]
Abstract
The reliable detection of transcription events through the quantification of the corresponding mRNA is of paramount importance for the diagnostics of infections and diseases. The quantification and localization analysis of the transcripts of a particular gene allows disease states to be characterized more directly compared to an analysis on the transcriptome wide level. This is particularly needed for the early detection of virus infections as now required for emergent viral diseases, e. g. Covid-19. In situ mRNA analysis, however, is a formidable challenge and currently performed with sets of single-fluorophore-containing oligonucleotide probes that hybridize to the mRNA in question. Often a large number of probe strands (>30) are required to get a reliable signal. The more oligonucleotide probes are used, however, the higher the potential off-target binding effects that create background noise. Here, we used click chemistry and alkyne-modified DNA oligonucleotides to prepare multiple-fluorophore-containing probes. We found that these multiple-dye probes allow reliable detection and direct visualization of mRNA with only a very small number (5-10) of probe strands. The new method enabled the in situ detection of viral transcripts as early as 4 hours after infection.
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Affiliation(s)
- Nada Raddaoui
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Stefano Croce
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
- Baseclick GmbHFloriansbogen 2–482061Neuried (MünchenGermany
| | - Florian Geiger
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Alexander Borodavka
- Astbury Centre for Structural Molecular BiologySchool of Molecular and Cellular Biology, University of LeedsLeedsLS2 9JTUK
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QWUK
| | - Leonhard Möckl
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Samuele Stazzoni
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Bastien Viverge
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Christoph Bräuchle
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | | | - Hanna Engelke
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
| | - Thomas Carell
- Department of ChemistryLudwig-Maximilians-Universität MünchenButenandtstraße 5–1381377MunichGermany
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36
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Ganz D, Harijan D, Wagenknecht HA. Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry. RSC Chem Biol 2020; 1:86-97. [PMID: 34458750 PMCID: PMC8341813 DOI: 10.1039/d0cb00047g] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 05/27/2020] [Indexed: 12/18/2022] Open
Abstract
Labelling of nucleic acids as biologically important cellular components is a crucial prerequisite for the visualization and understanding of biological processes. Efficient bioorthogonal chemistry and in particular cycloadditions fullfill the requirements for cellular applications. The broadly applied Cu(i)-catalyzed azide-alkyne cycloaddition (CuAAC), however, is limited to labellings in vitro and in fixed cells due to the cytotoxicity of copper salts. Currently, there are three types of copper-free cycloadditions used for nucleic acid labelling in the cellular environment: (i) the ring-strain promoted azide-alkyne cycloaddition (SPAAC), (ii) the "photoclick" 1,3-dipolar cycloadditions, and (iii) the Diels-Alder reactions with inverse electron demand (iEDDA). We review only those building blocks for chemical synthesis on solid phase of DNA and RNA and for enzymatic DNA and RNA preparation, which were applied for labelling of DNA and RNA in situ or in vivo, i.e. in the cellular environment, in fixed or in living cells, by the use of bioorthogonal cycloaddition chemistry. Additionally, we review the current status of orthogonal dual and triple labelling of DNA and RNA in vitro to demonstrate their potential for future applications in situ or in vivo.
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Affiliation(s)
- Dorothée Ganz
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Dennis Harijan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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37
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Krell K, Harijan D, Ganz D, Doll L, Wagenknecht HA. Postsynthetic Modifications of DNA and RNA by Means of Copper-Free Cycloadditions as Bioorthogonal Reactions. Bioconjug Chem 2020; 31:990-1011. [DOI: 10.1021/acs.bioconjchem.0c00072] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Katja Krell
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dennis Harijan
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Dorothée Ganz
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Larissa Doll
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute for Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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38
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Yamashita S, Nishida K, Osawa T, Nakanishi A, Ito Y, Hari Y. Synthesis of Oligonucleotides Containing 2'- N-alkylaminocarbonyl-2'-amino-LNA (2'-urea-LNA) Moieties Using Post-Synthetic Modification Strategy. Molecules 2020; 25:molecules25020346. [PMID: 31952133 PMCID: PMC7024358 DOI: 10.3390/molecules25020346] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/10/2020] [Accepted: 01/14/2020] [Indexed: 11/16/2022] Open
Abstract
The post-synthetic modification of an oligonucleotide is a powerful strategy for the synthesis of various analogs of the oligonucleotide, aiming to achieve the desired functions. In this study, we synthesized the thymidine phosphoramidite of 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA, which was introduced into oligonucleotides. Oligonucleotides containing a 2′-N-pentafluorophenoxycarbonyl-2′-amino-LNA unit could be isolated under ultra-mild deprotection conditions (50 mM K2CO3 in MeOH at room temperature for 4 h). Moreover, by treatment with various amines as a post-synthetic modification, the oligonucleotides were successfully converted into the corresponding 2′-N-alkylaminocarbonyl-2′-amino-LNA (2′-urea-LNA) derivatives. The duplex- and triplex-forming abilities of the synthesized oligonucleotides were evaluated by UV-melting experiments, which showed that 2′-urea-LNAs could stabilize the nucleic acid complexes, similar to the proto-type, 2′-amino-LNA. Thus, 2′-urea-LNAs could be promising units for the modification of oligonucleotides; the design of a substituent on urea may aid the formation of useful oligonucleotides. In addition, pentafluorophenoxycarbonyl, an amino moiety, acted as a precursor of the substituted urea, which may be applicable to the synthesis of oligonucleotide conjugates.
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Affiliation(s)
- Shoko Yamashita
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Kodai Nishida
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Takashi Osawa
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Japan
| | - Ayumi Nakanishi
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan
- Correspondence:
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39
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Maiti S, Roy N, Babu LT, Moharana P, Athira CC, Darsana Sreedhar E, De S, Ashok Kumar SK, Paira P. Cu(ii), Ir(i) and CuO nanocatalyzed mild synthesis of luminescent symmetrical and unsymmetrical bis(triazolylmethyl)quinoxalines: biocompatibility, cytotoxicity, live cell imaging and biomolecular interaction. NEW J CHEM 2020. [DOI: 10.1039/c9nj03131f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A microwave induced Cu(ii) and Ir(i) catalysed click reaction for the synthesis of anticancer symmetrical and unsymmetrical triazoles.
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Affiliation(s)
- Santanu Maiti
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
| | - Nilmadhab Roy
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
| | | | - Prithvi Moharana
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
| | - C. C. Athira
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
| | | | - Sourav De
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
| | - S. K. Ashok Kumar
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
| | - Priyankar Paira
- Department of Chemistry
- School of Advanced Sciences
- VIT
- Vellore-632014
- India
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40
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Bian KJ, Wang CY, Huang YL, Xu YH, Wang XS. Remote azidation of C(sp3)–H bonds to synthesize δ-azido sulfonamidesviairon-catalyzed radical relay. Org Biomol Chem 2020; 18:5354-5358. [DOI: 10.1039/d0ob00964d] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A selective remote C–H azidation was developed with an iron catalyst playing dual roles as a radical initiator and terminator.
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Affiliation(s)
- Kang-Jie Bian
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry
- Center for Excellence in Molecular Synthesis of CAS
- University of Science and Technology of China
- Hefei
- China
| | - Cheng-Yu Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry
- Center for Excellence in Molecular Synthesis of CAS
- University of Science and Technology of China
- Hefei
- China
| | - Yu-Ling Huang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry
- Center for Excellence in Molecular Synthesis of CAS
- University of Science and Technology of China
- Hefei
- China
| | - Yi-Hao Xu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry
- Center for Excellence in Molecular Synthesis of CAS
- University of Science and Technology of China
- Hefei
- China
| | - Xi-Sheng Wang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Chemistry
- Center for Excellence in Molecular Synthesis of CAS
- University of Science and Technology of China
- Hefei
- China
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41
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Gordon CKL, Wu D, Pusuluri A, Feagin TA, Csordas AT, Eisenstein MS, Hawker CJ, Niu J, Soh HT. Click-Particle Display for Base-Modified Aptamer Discovery. ACS Chem Biol 2019; 14:2652-2662. [PMID: 31532184 PMCID: PMC6929039 DOI: 10.1021/acschembio.9b00587] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Base-modified aptamers
that incorporate non-natural chemical moieties
can achieve greatly improved affinity and specificity relative to
natural DNA or RNA aptamers. However, conventional methods for generating
base-modified aptamers require considerable expertise and resources.
In this work, we have accelerated and generalized the process of generating
base-modified aptamers by combining a click-chemistry strategy with
a fluorescence-activated cell sorting (FACS)-based screening methodology
that measures the affinity and specificity of individual aptamers
at a throughput of ∼107 per hour. Our “click-particle
display (PD)” strategy offers many advantages. First, almost
any chemical modification can be introduced with a commercially available
polymerase. Second, click-PD can screen vast numbers of individual
aptamers on the basis of quantitative on- and off-target binding measurements
to simultaneously achieve high affinity and specificity. Finally,
the increasing availability of FACS instrumentation in academia and
industry allows for easy adoption of click-PD in a broader scientific
community. Using click-PD, we generated a boronic acid-modified aptamer
with ∼1 μM affinity for epinephrine, a target for which
no aptamer has been reported to date. We subsequently generated a
mannose-modified aptamer with nanomolar affinity for the lectin concanavalin
A (Con A). The strong affinity of both aptamers is fundamentally dependent
upon the presence of chemical modifications, and we show that their
removal essentially eliminates aptamer binding. Importantly, our Con
A aptamer exhibited exceptional specificity, with minimal binding
to other structurally similar lectins. Finally, we show that our aptamer
has remarkable biological activity. Indeed, this aptamer is the most
potent inhibitor of Con A-mediated hemagglutination reported to date.
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Affiliation(s)
| | | | | | | | | | | | | | - Jia Niu
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Hyongsok Tom Soh
- Chan Zuckerberg Biohub, San Francisco, California 94158, United States
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42
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Zhou L, Wang T, Bai Y, Li Y, Qiu J, Yu W, Zhang S. Dual-amplified strategy for ultrasensitive electrochemical biosensor based on click chemistry-mediated enzyme-assisted target recycling and functionalized fullerene nanoparticles in the detection of microRNA-141. Biosens Bioelectron 2019; 150:111964. [PMID: 31929092 DOI: 10.1016/j.bios.2019.111964] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/10/2019] [Accepted: 12/12/2019] [Indexed: 12/21/2022]
Abstract
Rapid and efficient detection of tumor marker at the early stages is one of the crucial challenges in cancer diagnostics and therapy. In this study, an ultrasensitive electrochemical biosensor was fabricated by dual-amplified strategy for the detection of ultra-trace microRNA-141 (miRNA-141). Firstly, two split sequences contained G-quadruplex were connected by click chemistry-mediated nucleic acid strands self-assembly and the obtained complete G-quadruplex was complementary with miRNA-141 to formed DNA-RNA hybrid duplexes. Subsequently, the formed DNA-RNA hybrid duplexes were specifically recognized by duplex-specific nuclease (DSN), and the DNA part of the duplexes were cleaved and the miRNA-141 were released to trigger next cycle, which acquired a primal signal amplification by enzyme-assisted target recycling (EATR). Moreover, amino and thiol group multi-labeled functionalized fullerene nanoparticles (FC60) with a larger surface active sites and better biocompatibility, were designed rationally to modify the Au electrodes, which produced multiply-enhanced amplified signal. This dual-amplified sensing system exhibited a remarkable analytical performance for the detection of miRNA-141 in concentrations ranging from 0.1 pM to 100 nM and the detection limit of 7.78 fM was obtained. Compared with the biosensor with single amplification strategy such as EATR, this electrochemical biosensor based on dual-amplified strategy exhibited an excellent discrimination capability and higher analytical performance. Therefore, this electrochemical biosensor might hold a great potential for further applications in biomedical research and early clinical diagnosis.
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Affiliation(s)
- Lili Zhou
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China; Department of Clinical Laboratory, People's Hospital of Changshou Chongqing, Chongqing, 401220, PR China.
| | - Ting Wang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China; Department of Clinical Laboratory, The Central Hospital of Fuling Chongqing, Chongqing, 408099, PR China
| | - Yan Bai
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China; Department of Clinical Laboratory, People's Hospital of Changshou Chongqing, Chongqing, 401220, PR China
| | - Yi Li
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Juhui Qiu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, PR China
| | - Wen Yu
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Sheng Zhang
- School of Economics and Management, Chongqing University of Posts and Telecommunications, Chongqing, 400065, PR China
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43
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Rao DS, Reddy TR, Gurawa A, Kumar M, Kashyap S. Photoswitchable Regiodivergent Azidation of Olefins with Sulfonium Iodate(I) Reagent. Org Lett 2019; 21:9990-9994. [DOI: 10.1021/acs.orglett.9b03910] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Dodla S. Rao
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology (MNIT), Jaipur 302017, India
| | - Thurpu R. Reddy
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology (MNIT), Jaipur 302017, India
| | - Aakanksha Gurawa
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology (MNIT), Jaipur 302017, India
| | - Manoj Kumar
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology (MNIT), Jaipur 302017, India
| | - Sudhir Kashyap
- Carbohydrate Chemistry Research Laboratory (CCRL), Department of Chemistry, Malaviya National Institute of Technology (MNIT), Jaipur 302017, India
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44
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Noël M, Clément-Blanc C, Meyer A, Vasseur JJ, Morvan F. Solid Supports for the Synthesis of 3'-Aminooxy Deoxy- or Ribo-oligonucleotides and Their 3'-Conjugation by Oxime Ligation. J Org Chem 2019; 84:14854-14860. [PMID: 31615211 DOI: 10.1021/acs.joc.9b00848] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mono- and triethylene glycol aminooxy derivatives were reacted with levulinic acid, protected with dimethoxytrityl, and immobilized on solid support. The resulting solid supports were used for elongation of oligonucleotides. Then, a mild ammonia treatment was applied to remove the oligonucleotide protecting groups, followed by a treatment with 50 mM methoxyamine at pH 4.2, releasing the 3'-aminooxy oligonucleotides by an oxime exchange reaction. The resulting 3'-aminooxy deoxy- or ribo-oligonucleotides were conjugated to various ketones and aldehydes with high efficiency by oxime ligation.
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Affiliation(s)
- Mathieu Noël
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - Céline Clément-Blanc
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
| | - François Morvan
- Institut des Biomolécules Max Mousseron , Université de Montpellier, CNRS, ENSCM , Montpellier 34090 , France
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45
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Ivancová I, Leone DL, Hocek M. Reactive modifications of DNA nucleobases for labelling, bioconjugations, and cross-linking. Curr Opin Chem Biol 2019; 52:136-144. [DOI: 10.1016/j.cbpa.2019.07.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 06/26/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
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46
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Chen Y, Li L, He X, Li Z. Four-Component Reactions for the Synthesis of Perfluoroalkyl Isoxazoles. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03189] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Yuanjin Chen
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Liangkui Li
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Xiao He
- Department of Chemistry, Renmin University of China, Beijing 100872, China
| | - Zhiping Li
- Department of Chemistry, Renmin University of China, Beijing 100872, China
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47
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Rosenthal M, Pfeiffer F, Mayer G. Eine rezeptorgeleitete Designstrategie zur Identifikation von Clickmeren. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201903479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Malte Rosenthal
- Life and Medical Sciences InstitutUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Franziska Pfeiffer
- Life and Medical Sciences InstitutUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
| | - Günter Mayer
- Life and Medical Sciences InstitutUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
- Center of Aptamer Research and DevelopmentUniversität Bonn Gerhard-Domagk-Straße 1 53121 Bonn Deutschland
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48
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Escudier JM, Payrastre C, Gerland B, Tarrat N. Convertible and conformationally constrained nucleic acids (C 2NAs). Org Biomol Chem 2019; 17:6386-6397. [PMID: 31210235 DOI: 10.1039/c9ob01150a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We introduce the concept of Convertible and Constrained Nucleic Acids (C2NAs). By means of the synthesis of a stereocontrolled N-propargyl dioxo-1,3,2-oxaza-phosphorinane as an internucleotidic linkage, the torsional angles α and β can adopt either the canonical (g-, t) set of values able to increase DNA duplex stability or the non-canonical (g+, t) set that stabilized the hairpin structure when installed within the loop moiety. With an appended propargyl function on the nitrogen atom of the six-membered ring, the copper catalysed Huisgen's cycloaddition (CuAAC click chemistry) allows for the introduction of new functionalities at any location on the nucleic acid chain while maintaining the properties brought by the geometrical constraint and the neutral internucleotidic linkage.
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Affiliation(s)
- Jean-Marc Escudier
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Corinne Payrastre
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Béatrice Gerland
- Laboratoire de Synthèse et Physico-Chimie de Molécules d'Intérêt Biologique, UMR CNRS 5068, Université Paul Sabatier, 118 route de Narbonne, 31062 Toulouse, France.
| | - Nathalie Tarrat
- CEMES, Université de Toulouse, CNRS, 29 rue Jeanne Marvig, Toulouse 31055, France
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49
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Onizuka K, Miyashita T, Chikuni T, Ozawa M, Abe H, Nagatsugi F. Structural optimization of pseudorotaxane-forming oligonucleotides for efficient and stable complex formation. Nucleic Acids Res 2019; 46:8710-8719. [PMID: 30260454 PMCID: PMC6158610 DOI: 10.1093/nar/gky744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 08/06/2018] [Indexed: 01/15/2023] Open
Abstract
Interlocked structures, such as rotaxane and catenane, combine both static and dynamic properties. To expand their unique properties into the chemical biology field, a spontaneous formation method of the interlocked structures with the target would be ideal. We have previously developed a pseudorotaxane-forming oligo DNA (prfODN) to spontaneously form topological DNA/RNA architectures. In this study, we report the structural optimization of prfODNs for the efficient and stable complex formation. The optimized prfODNs efficiently formed pseudorotaxane structures with a DNA or RNA target, and the yield for the RNA target reached 85% in 5 min. In addition, the optimized prfODNs could form the pseudorotaxane structure with a smaller ring size and the structure significantly increased the kinetic stability. Furthermore, the catenane structure was successfully formed with the optimized prfODNs to provide the conclusive evidence for the formation of the threaded structure. This information will be valuable for developing new chemical methods using functional nucleic acids for antisense oligo nucleotides and DNA/RNA nanotechnology.
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Affiliation(s)
- Kazumitsu Onizuka
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Takuya Miyashita
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Tomoko Chikuni
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Mamiko Ozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Fumi Nagatsugi
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
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50
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Rosenthal M, Pfeiffer F, Mayer G. A Receptor-Guided Design Strategy for Ligand Identification. Angew Chem Int Ed Engl 2019; 58:10752-10755. [PMID: 31050104 DOI: 10.1002/anie.201903479] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Indexed: 01/08/2023]
Abstract
Biomedical sciences require effective tools to manipulate, detect, and study biological phenomena. Oligo(deoxy)nucleotide ligands represent such tools, but the current strategies to generate them are restricted. Their limited availability is insufficient to address the broad range of targets related to biomedical research. Exemplified by targeting the hydrophobic molecule (-)-Δ9 -tetrahydrocannabinol (THC), we report a receptor-guided design (RGD) strategy to generate chemically modified oligodeoxynucleotide libraries for the tailored selection of clickmers.
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Affiliation(s)
- Malte Rosenthal
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Franziska Pfeiffer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany.,Center of Aptamer Research and Development, University of Bonn, Gerhard-Domagk-Strasse 1, 53121, Bonn, Germany
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