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Pichon M, Hollenstein M. Controlled enzymatic synthesis of oligonucleotides. Commun Chem 2024; 7:138. [PMID: 38890393 PMCID: PMC11189433 DOI: 10.1038/s42004-024-01216-0] [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: 02/16/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.
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Affiliation(s)
- Maëva Pichon
- 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
| | - 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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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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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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Seiler LK, Phung NL, Nikolin C, Immenschuh S, Erck C, Kaufeld J, Haller H, Falk CS, Jonczyk R, Lindner P, Thoms S, Siegl J, Mayer G, Feederle R, Blume CA. An Antibody-Aptamer-Hybrid Lateral Flow Assay for Detection of CXCL9 in Antibody-Mediated Rejection after Kidney Transplantation. Diagnostics (Basel) 2022; 12:diagnostics12020308. [PMID: 35204399 PMCID: PMC8871475 DOI: 10.3390/diagnostics12020308] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/04/2023] Open
Abstract
Chronic antibody-mediated rejection (AMR) is a key limiting factor for the clinical outcome of a kidney transplantation (Ktx), where early diagnosis and therapeutic intervention is needed. This study describes the identification of the biomarker CXC-motif chemokine ligand (CXCL) 9 as an indicator for AMR and presents a new aptamer-antibody-hybrid lateral flow assay (hybrid-LFA) for detection in urine. Biomarker evaluation included two independent cohorts of kidney transplant recipients (KTRs) from a protocol biopsy program and used subgroup comparisons according to BANFF-classifications. Plasma, urine and biopsy lysate samples were analyzed with a Luminex-based multiplex assay. The CXCL9-specific hybrid-LFA was developed based upon a specific rat antibody immobilized on a nitrocellulose-membrane and the coupling of a CXCL9-binding aptamer to gold nanoparticles. LFA performance was assessed according to receiver operating characteristic (ROC) analysis. Among 15 high-scored biomarkers according to a neural network analysis, significantly higher levels of CXCL9 were found in plasma and urine and biopsy lysates of KTRs with biopsy-proven AMR. The newly developed hybrid-LFA reached a sensitivity and specificity of 71% and an AUC of 0.79 for CXCL9. This point-of-care-test (POCT) improves early diagnosis-making in AMR after Ktx, especially in KTRs with undetermined status of donor-specific HLA-antibodies.
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Affiliation(s)
- Lisa K. Seiler
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (L.K.S.); (N.L.P.); (R.J.); (P.L.); (S.T.)
| | - Ngoc Linh Phung
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (L.K.S.); (N.L.P.); (R.J.); (P.L.); (S.T.)
| | - Christoph Nikolin
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, 30625 Hannover, Germany; (C.N.); (S.I.)
| | - Stephan Immenschuh
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, 30625 Hannover, Germany; (C.N.); (S.I.)
| | - Christian Erck
- Helmholtz Centre for Infection Research, Cellular Proteome Research Group, 38124 Braunschweig, Germany;
| | - Jessica Kaufeld
- Department of Nephrology and Hypertension, Hannover Medical School, 30625 Hannover, Germany; (J.K.); (H.H.)
| | - Hermann Haller
- Department of Nephrology and Hypertension, Hannover Medical School, 30625 Hannover, Germany; (J.K.); (H.H.)
| | - Christine S. Falk
- Institute for Transplant Immunology, Hannover Medical School, 30625 Hannover, Germany;
| | - Rebecca Jonczyk
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (L.K.S.); (N.L.P.); (R.J.); (P.L.); (S.T.)
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (L.K.S.); (N.L.P.); (R.J.); (P.L.); (S.T.)
| | - Stefanie Thoms
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (L.K.S.); (N.L.P.); (R.J.); (P.L.); (S.T.)
| | - Julia Siegl
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121 Bonn, Germany; (J.S.); (G.M.)
- Center of Aptamer Research & Development (CARD), University of Bonn, 53121 Bonn, Germany
| | - Günter Mayer
- Chemical Biology & Chemical Genetics, Life and Medical Sciences (LIMES) Institute, University of Bonn, 53121 Bonn, Germany; (J.S.); (G.M.)
- Center of Aptamer Research & Development (CARD), University of Bonn, 53121 Bonn, Germany
| | - Regina Feederle
- Monoclonal Antibody Core Facility, Institute for Diabetes and Obesity, Helmholtz-Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany;
| | - Cornelia A. Blume
- Institute of Technical Chemistry, Leibniz University Hannover, 30167 Hannover, Germany; (L.K.S.); (N.L.P.); (R.J.); (P.L.); (S.T.)
- Correspondence:
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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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