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Niogret G, Bouvier-Müller A, Figazzolo C, Joyce JM, Bonhomme F, England P, Mayboroda O, Pellarin R, Gasser G, Tucker JHR, Tanner JA, Savage GP, Hollenstein M. Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis. Chembiochem 2024; 25:e202300539. [PMID: 37837257 DOI: 10.1002/cbic.202300539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/09/2023] [Accepted: 10/13/2023] [Indexed: 10/15/2023]
Abstract
Chemical modification of aptamers is an important step to improve their performance and stability in biological media. This can be performed either during their identification (mod-SELEX) or after the in vitro selection process (post-SELEX). In order to reduce the complexity and workload of the post-SELEX modification of aptamers, we have evaluated the possibility of improving a previously reported, chemically modified aptamer by combining enzymatic synthesis and nucleotides bearing bioisosteres of the parent cubane side-chains or substituted cubane moieties. This method lowers the synthetic burden often associated with post-SELEX approaches and allowed to identify one additional sequence that maintains binding to the PvLDH target protein, albeit with reduced specificity. In addition, while bioisosteres often improve the potency of small molecule drugs, this does not extend to chemically modified aptamers. Overall, this versatile method can be applied for the post-SELEX modification of other aptamers and functional nucleic acids.
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Affiliation(s)
- Germain Niogret
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28, rue du Docteur Roux, 75015, Paris, France
| | - Alix Bouvier-Müller
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Chiara Figazzolo
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Jack M Joyce
- CSIRO Manufacturing, Clayton, VIC, 3168, Australia
- School of Chemistry, University of Sydney, Sydney, NSW, 2006, Australia
| | - Frédéric Bonhomme
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Unité de Chimie Biologique Epigénétique UMR CNRS 3523, 28, rue du Docteur Roux, CEDEX 15, 75724, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, C2RT, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Olena Mayboroda
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28, rue du Docteur Roux, 75015, Paris, France
| | - Riccardo Pellarin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR 3528, 28, rue du Docteur Roux, 75015, Paris, France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005, Paris, France
| | - James H R Tucker
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | - Julian A Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, Hong Kong SAR, China
| | | | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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Rabiee N, Chen S, Ahmadi S, Veedu RN. Aptamer-engineered (nano)materials for theranostic applications. Theranostics 2023; 13:5183-5206. [PMID: 37908725 PMCID: PMC10614690 DOI: 10.7150/thno.85419] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/09/2023] [Indexed: 11/02/2023] Open
Abstract
A diverse array of organic and inorganic materials, including nanomaterials, has been extensively employed in multifunctional biomedical applications. These applications encompass drug/gene delivery, tissue engineering, biosensors, photodynamic and photothermal therapy, and combinatorial sciences. Surface and bulk engineering of these materials, by incorporating biomolecules and aptamers, offers several advantages such as decreased cytotoxicity, improved stability, enhanced selectivity/sensitivity toward specific targets, and expanded multifunctional capabilities. In this comprehensive review, we specifically focus on aptamer-modified engineered materials for diverse biomedical applications. We delve into their mechanisms, advantages, and challenges, and provide an in-depth analysis of relevant literature references. This critical evaluation aims to enhance the scientific community's understanding of this field and inspire new ideas for future research endeavors.
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Affiliation(s)
- Navid Rabiee
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
| | - Sepideh Ahmadi
- Student Research Committee, Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Rakesh N. Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia
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Lakshman MK. Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents, and Beyond. CHEM REC 2023; 23:e202200182. [PMID: 36166699 DOI: 10.1002/tcr.202200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/26/2022] [Indexed: 01/24/2023]
Abstract
Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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Enzymatic Synthesis of Vancomycin-Modified DNA. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248927. [PMID: 36558056 PMCID: PMC9782525 DOI: 10.3390/molecules27248927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Many potent antibiotics fail to treat bacterial infections due to emergence of drug-resistant strains. This surge of antimicrobial resistance (AMR) calls in for the development of alternative strategies and methods for the development of drugs with restored bactericidal activities. In this context, we surmised that identifying aptamers using nucleotides connected to antibiotics will lead to chemically modified aptameric species capable of restoring the original binding activity of the drugs and hence produce active antibiotic species that could be used to combat AMR. Here, we report the synthesis of a modified nucleoside triphosphate equipped with a vancomycin moiety on the nucleobase. We demonstrate that this nucleotide analogue is suitable for polymerase-mediated synthesis of modified DNA and, importantly, highlight its compatibility with the SELEX methodology. These results pave the way for bacterial-SELEX for the identification of vancomycin-modified aptamers.
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Flamme M, Katkevica D, Pajuste K, Katkevics M, Sabat N, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Benzoyl and pivaloyl as efficient protecting groups for controlled enzymatic synthesis of DNA and XNA oligonucleotides. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202200384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marie Flamme
- Institut Pasteur Structrual Biology and Chemistry FRANCE
| | - Dace Katkevica
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Karlis Pajuste
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis: Latvijas Organiskas sintezes instituts Chemistry LATVIA
| | - Nazarii Sabat
- Institut Pasteur Structural Biology and Chemistry FRANCE
| | - Steven Hanlon
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | - Irene Marzuoli
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | - Kurt Püntener
- Hoffmann-La Roche Ltd Synthetic Molecules Technical Development SWITZERLAND
| | | | - Marcel Hollenstein
- Institut Pasteur Department of Structural Biology and Chemistry 28 Rue du Dr. Roux 75015 Paris FRANCE
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Figazzolo C, Ma Y, Tucker JHR, Hollenstein M. Ferrocene as a potential electrochemical reporting surrogate of abasic sites in DNA. Org Biomol Chem 2022; 20:8125-8135. [DOI: 10.1039/d2ob01540d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We have evaluated the possibility of replacing abasic sites with ferrocene for enzymatic synthesis of canonical and modified DNA.
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Affiliation(s)
- Chiara Figazzolo
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Learning Planet Institute, 8, rue Charles V, 75004 Paris, France
| | - Yifeng Ma
- School of Chemistry, University of Birmingham, Birmingham, B15 2TT, UK
| | | | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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