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Shanmugasundaram M, Senthilvelan A, Kore AR. An efficient green synthesis of UNA-nucleoside-5′-triphosphates: a versatile synthon for RNA modification with broad therapeutic potential. RESULTS IN CHEMISTRY 2023. [DOI: 10.1016/j.rechem.2023.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023] Open
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Nakamura M, Yoshioka H, Takada T. Conformational Switching of Pyrenes Associated on Hairpin Loop Region by DNA B‐Z Transition. ChemistrySelect 2022. [DOI: 10.1002/slct.202200696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Hibiki Yoshioka
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry University of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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Santorelli A, Gothelf K. Conjugation of chemical handles and functional moieties to DNA during solid phase synthesis with sulfonyl azides. Nucleic Acids Res 2022; 50:7235-7246. [PMID: 35801866 PMCID: PMC9303310 DOI: 10.1093/nar/gkac566] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/15/2022] [Accepted: 06/28/2022] [Indexed: 11/24/2022] Open
Abstract
Labelling of oligonucleotides with dyes, targeting ligands, and other moieties has become ever more essential in life-sciences. Conventionally, modifications are introduced to oligonucleotides during solid phase synthesis by special phosphoramidites functionalised with a chemical handle or the desired functional group. In this work, we present a facile and inexpensive method to introduce modifications to oligonucleotides without the need for special phosphoramidites. Sulfonyl azides are applied to react with one or more selected phosphite intermediates during solid phase synthesis. We have prepared 11 sulfonyl azides with different chemical handles such as amine, azide, alkyne, and thiol, and we have further introduced functionalities such as pyrene, other dyes, photo-switchable azobenzenes, and a steroid. The method is compatible with current phosphoramidite-based automated oligonucleotide synthesis and serves as a simple alternative to the unstable and expensive special phosphoramidites currently used for conjugation to oligonucleotides.
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Affiliation(s)
- Angel Santorelli
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
| | - Kurt V Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Central Denmark Region, 8000, Denmark
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The role of Nucleic Acid Mimics (NAMs) on FISH-based techniques and applications for microbial detection. Microbiol Res 2022; 262:127086. [PMID: 35700584 DOI: 10.1016/j.micres.2022.127086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful tool that for more than 30 years has allowed to detect and quantify microorganisms as well as to study their spatial distribution in three-dimensional structured environments such as biofilms. Throughout these years, FISH has been improved in order to face some of its earlier limitations and to adapt to new research objectives. One of these improvements is related to the emergence of Nucleic Acid Mimics (NAMs), which are now employed as alternatives to the DNA and RNA probes that have been classically used in FISH. NAMs such as peptide and locked nucleic acids (PNA and LNA) have provided enhanced sensitivity and specificity to the FISH technique, as well as higher flexibility in terms of applications. In this review, we aim to cover the state-of-the-art of the different NAMs and explore their possible applications in FISH, providing a general overview of the technique advancement in the last decades.
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Nakamura M, Takada T, Yamana K. Controlling Pyrene Association in DNA Duplexes by B‐ to Z‐DNA Transitions. Chembiochem 2019; 20:2949-2954. [DOI: 10.1002/cbic.201900350] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Tadao Takada
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
| | - Kazushige Yamana
- Department of Applied ChemistryUniversity of Hyogo 2167 Shosha Himeji Hyogo 671–2280 Japan
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Nakamura M, Matsui Y, Takada T, Yamana K. Chromophore Arrays Constructed in the Major Groove of DNA Duplexes Using a Post-Synthetic Strategy. ChemistrySelect 2019. [DOI: 10.1002/slct.201803464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Mitsunobu Nakamura
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Yuki Matsui
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Tadao Takada
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; University of Hyogo; 2167 Shosha, Himeji Hyogo 671-2280 Japan
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Paulsen B, Fredriksen KA, Petersen D, Maes L, Matheeussen A, Naemi AO, Scheie AA, Simm R, Ma R, Wan B, Franzblau S, Gundersen LL. Synthesis and antimicrobial activities of N 6-hydroxyagelasine analogs and revision of the structure of ageloximes. Bioorg Med Chem 2019; 27:620-629. [PMID: 30638761 DOI: 10.1016/j.bmc.2019.01.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 12/20/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022]
Abstract
(+)-N6-Hydroxyagelasine D, the enantiomer of the proposed structure of (-)-ageloxime D, as well as N6-hydroxyagelasine analogs were synthesized by selective N-7 alkylation of N6-[tert-butyl(dimethyl)silyloxy]-9-methyl-9H-purin-6-amine in order to install the terpenoid side chain, followed by fluoride mediated removal of the TBDMS-protecting group. N6-Hydroxyagelasine D and the analog carrying a geranylgeranyl side chain displayed profound antimicrobial activities against several pathogenic bacteria and protozoa and inhibited bacterial biofilm formation. However these compounds were also toxic towards mammalian fibroblast cells (MRC-5). The spectral data of N6-hydroxyagelasine D did not match those reported for ageloxime D before. Hence, a revised structure of ageloxime D was proposed. Basic hydrolysis of agelasine D gave (+)-N-[4-amino-6-(methylamino)pyrimidin-5-yl]-N-copalylformamide, a compound with spectral data in full agreement with those reported for (-)-ageloxime D.
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Affiliation(s)
- Britt Paulsen
- Department of Chemistry, University of Oslo, P.O.Box 1033, Blindern, 0315 Oslo, Norway
| | - Kim Alex Fredriksen
- Department of Chemistry, University of Oslo, P.O.Box 1033, Blindern, 0315 Oslo, Norway
| | - Dirk Petersen
- Department of Chemistry, University of Oslo, P.O.Box 1033, Blindern, 0315 Oslo, Norway
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Wilrijk, Belgium
| | - An Matheeussen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), University of Antwerp, Wilrijk, Belgium
| | - Ali-Oddin Naemi
- Institute of Oral Biology, University of Oslo, P.O. Box 1052, Blindern, 0316 Oslo, Norway
| | - Anne Aamdal Scheie
- Institute of Oral Biology, University of Oslo, P.O. Box 1052, Blindern, 0316 Oslo, Norway
| | - Roger Simm
- Institute of Oral Biology, University of Oslo, P.O. Box 1052, Blindern, 0316 Oslo, Norway
| | - Rui Ma
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL, USA
| | - Baojie Wan
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL, USA
| | - Scott Franzblau
- Institute for Tuberculosis Research, University of Illinois at Chicago, 833 S. Wood St., Chicago, IL, USA
| | - Lise-Lotte Gundersen
- Department of Chemistry, University of Oslo, P.O.Box 1033, Blindern, 0315 Oslo, Norway.
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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