1
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Ma Y, Guo W, Mou Q, Shao X, Lyu M, Garcia V, Kong L, Lewis W, Ward C, Yang Z, Pan X, Yi SS, Lu Y. Spatial imaging of glycoRNA in single cells with ARPLA. Nat Biotechnol 2024; 42:608-616. [PMID: 37217750 PMCID: PMC10663388 DOI: 10.1038/s41587-023-01801-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023]
Abstract
Little is known about the biological roles of glycosylated RNAs (glycoRNAs), a recently discovered class of glycosylated molecules, because of a lack of visualization methods. We report sialic acid aptamer and RNA in situ hybridization-mediated proximity ligation assay (ARPLA) to visualize glycoRNAs in single cells with high sensitivity and selectivity. The signal output of ARPLA occurs only when dual recognition of a glycan and an RNA triggers in situ ligation, followed by rolling circle amplification of a complementary DNA, which generates a fluorescent signal by binding fluorophore-labeled oligonucleotides. Using ARPLA, we detect spatial distributions of glycoRNAs on the cell surface and their colocalization with lipid rafts as well as the intracellular trafficking of glycoRNAs through SNARE protein-mediated secretory exocytosis. Studies in breast cell lines suggest that surface glycoRNA is inversely associated with tumor malignancy and metastasis. Investigation of the relationship between glycoRNAs and monocyte-endothelial cell interactions suggests that glycoRNAs may mediate cell-cell interactions during the immune response.
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Affiliation(s)
- Yuan Ma
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Weijie Guo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Quanbing Mou
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xiangli Shao
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Mingkuan Lyu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Valeria Garcia
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Linggen Kong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Whitney Lewis
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
| | - Carson Ward
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Zhenglin Yang
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA
| | - Xingxin Pan
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
| | - S Stephen Yi
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA
- Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, USA.
- Interdisciplinary Life Sciences Graduate Programs, The University of Texas at Austin, Austin, TX, USA.
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2
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Kotammagari TK, Saleh LY, Lönnberg T. Organometallic modification confers oligonucleotides new functionalities. Chem Commun (Camb) 2024; 60:3118-3128. [PMID: 38385213 DOI: 10.1039/d4cc00305e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
To improve their properties or to introduce entirely new functionalities, the intriguing scaffolds of nucleic acids have been decorated with various modifications, most recently also organometallic ones. While challenging to introduce, organometallic modifications offer the potential of expanding the field of application of metal-dependent functionalities to metal-deficient conditions, notably those of biological media. So far, organometallic moieties have been utilized as probes, labels and catalysts. This Feature Article summarizes recent efforts and predicts likely future developments in each of these lines of research.
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Affiliation(s)
- Tharun K Kotammagari
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Lange Yakubu Saleh
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland.
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3
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Majumdar B, Sarma D, Yu Y, Lozoya-Colinas A, Chaput JC. Increasing the functional density of threose nucleic acid. RSC Chem Biol 2024; 5:41-48. [PMID: 38179195 PMCID: PMC10763562 DOI: 10.1039/d3cb00159h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/18/2023] [Indexed: 01/06/2024] Open
Abstract
Chemical strategies that augment genetic polymers with amino acid residues that are overrepresented on the paratope surface of an antibody offer a promising route for enhancing the binding properties of nucleic acid aptamers. Here, we describe the chemical synthesis of α-l-threofuranosyl cytidine nucleoside triphosphate (tCTP) carrying either a benzyl or phenylpropyl side chain at the pyrimidine C-5 position. Polymerase recognition studies indicate that both substrates are readily incorporated into a full-length α-l-threofuranosyl nucleic acid (TNA) product by extension of a DNA primer-template duplex with an engineered TNA polymerase. Similar primer extension reactions performed using nucleoside triphosphate mixtures containing both C-5 modified tCTP and C-5 modified tUTP substrates enable the production of doubly modified TNA strands for a panel of 20 chemotype combinations. Kinetic measurements reveal faster on-rates (kon) and tighter binding affinity constants (Kd) for engineered versions of TNA aptamers carrying chemotypes at both pyrimidine positions as compared to their singly modified counterparts. These findings expand the chemical space of evolvable non-natural genetic polymers by offering a path for improving the quality of biologically stable TNA aptamers for future clinical applications.
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Affiliation(s)
- Biju Majumdar
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Daisy Sarma
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Yutong Yu
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - Adriana Lozoya-Colinas
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California Irvine CA 92697-3958 USA +1 949-824-8149
- Department of Chemistry, University of California Irvine CA 92697-3958 USA
- Department of Molecular Biology and Biochemistry, University of California Irvine CA 92697-3958 USA
- Department of Chemical and Biomolecular Engineering, University of California Irvine CA 92697-3958 USA
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4
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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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5
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Sabat N, Stämpfli A, Flamme M, Hanlon S, Bisagni S, Sladojevich F, Püntener K, Hollenstein M. Artificial nucleotide codons for enzymatic DNA synthesis. Chem Commun (Camb) 2023; 59:14547-14550. [PMID: 37987464 DOI: 10.1039/d3cc04933g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Herein, we report the high-yielding solid-phase synthesis of unmodified and chemically modified trinucleotide triphosphates (dN3TPs). These synthetic codons can be used for enzymatic DNA synthesis provided their scaffold is stabilized with phosphorothioate units. Enzymatic synthesis with three rather than one letter nucleotides will be useful to produce xenonucleic acids (XNAs) and for in vitro selection of modified functional nucleic acids.
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Affiliation(s)
- Nazarii Sabat
- 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.
| | - Andreas Stämpfli
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Marie Flamme
- 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.
| | - Steven Hanlon
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry & Catalysis, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - Serena Bisagni
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry & Catalysis, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - Filippo Sladojevich
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Kurt Püntener
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Chemistry & Catalysis, F. Hoffmann-La Roche Ltd, Basel 4070, Switzerland
| | - 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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6
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Lozoya-Colinas A, Yu Y, Chaput JC. Functionally Enhanced XNA Aptamers Discovered by Parallelized Library Screening. J Am Chem Soc 2023; 145:25789-25796. [PMID: 37962593 PMCID: PMC10690791 DOI: 10.1021/jacs.3c09497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
In vitro evolution strategies have been used for >30 years to generate nucleic acid aptamers against therapeutic targets of interest, including disease-associated proteins. However, this process requires many iterative cycles of selection and amplification, which severely restricts the number of target and library design combinations that can be explored in parallel. Here, we describe a single-round screening approach to aptamer discovery that relies on function-enhancing chemotypes to increase the distribution of high-affinity sequences in a random-sequence library. We demonstrate the success of de novo discovery by affinity selection of threomers against the receptor binding domain of the S1 protein from SARS-CoV-2. Detailed biochemical characterization of the enriched population identified threomers with binding affinity values that are comparable to aptamers produced by conventional SELEX. This work establishes a highly parallelizable path for querying diverse chemical repertoires and may offer a viable route for accelerating the discovery of therapeutic aptamers.
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Affiliation(s)
- Adriana Lozoya-Colinas
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
| | - Yutong Yu
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697-3958, United States
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, Irvine, California 92697-3958, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3958, United States
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7
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Kuprikova N, Ondruš M, Bednárová L, Riopedre-Fernandez M, Slavětínská L, Sýkorová V, Hocek M. Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases. Nucleic Acids Res 2023; 51:11428-11438. [PMID: 37870471 PMCID: PMC10681718 DOI: 10.1093/nar/gkad893] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/06/2023] [Accepted: 10/04/2023] [Indexed: 10/24/2023] Open
Abstract
We designed and synthesized a set of four 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phosphate). The anion-linked dNTPs were used for enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase containing one, two, three, or four modified nucleotides. The polymerase was able to synthesize even long sequences of >100 modified nucleotides in a row by primer extension (PEX). We also successfully combined two anionic and two hydrophobic dNTPs bearing phenyl and indole moieties. In PCR, the combinations of one or two modified dNTPs gave exponential amplification, while most of the combinations of three or four modified dNTPs gave only linear amplification in asymmetric PCR. The hypermodified ONs were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies including hybridization, denaturation, CD spectroscopy and molecular modelling and dynamics suggest that the presence of anionic modifications in one strand decreases the stability of duplexes while still preserving the B-DNA conformation, whilst the DNA hypermodified in both strands adopts a different secondary structure.
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Affiliation(s)
- Natalia Kuprikova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Miguel Riopedre-Fernandez
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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8
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Troisi R, Balasco N, Autiero I, Vitagliano L, Sica F. Structural Insights into Protein-Aptamer Recognitions Emerged from Experimental and Computational Studies. Int J Mol Sci 2023; 24:16318. [PMID: 38003510 PMCID: PMC10671752 DOI: 10.3390/ijms242216318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
Aptamers are synthetic nucleic acids that are developed to target with high affinity and specificity chemical entities ranging from single ions to macromolecules and present a wide range of chemical and physical properties. Their ability to selectively bind proteins has made these compounds very attractive and versatile tools, in both basic and applied sciences, to such an extent that they are considered an appealing alternative to antibodies. Here, by exhaustively surveying the content of the Protein Data Bank (PDB), we review the structural aspects of the protein-aptamer recognition process. As a result of three decades of structural studies, we identified 144 PDB entries containing atomic-level information on protein-aptamer complexes. Interestingly, we found a remarkable increase in the number of determined structures in the last two years as a consequence of the effective application of the cryo-electron microscopy technique to these systems. In the present paper, particular attention is devoted to the articulated architectures that protein-aptamer complexes may exhibit. Moreover, the molecular mechanism of the binding process was analyzed by collecting all available information on the structural transitions that aptamers undergo, from their protein-unbound to the protein-bound state. The contribution of computational approaches in this area is also highlighted.
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Affiliation(s)
- Romualdo Troisi
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Nicole Balasco
- Institute of Molecular Biology and Pathology, CNR c/o Department of Chemistry, University of Rome Sapienza, 00185 Rome, Italy;
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, 80131 Naples, Italy;
| | - Filomena Sica
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy;
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9
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Jestřábová I, Poštová Slavětínská L, Hocek M. Arylethynyl- or Alkynyl-Linked Pyrimidine and 7-Deazapurine 2'-Deoxyribonucleoside 3'-Phosphoramidites for Chemical Synthesis of Hypermodified Hydrophobic Oligonucleotides. ACS OMEGA 2023; 8:39447-39453. [PMID: 37901526 PMCID: PMC10601081 DOI: 10.1021/acsomega.3c05202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
We designed and synthesized a set of 2'-deoxyribonucleoside 3'-phosphoramidites derived from 5-phenylethynyluracil, 5-(pentyn-1-yl)cytosine, 7-(indol-3-yl)ethynyl-7-deazaadenine, and 7-isopropylethynyl-7-deazaguanine. These nucleoside phosphoramidites were successfully used for automated solid-phase synthesis of oligonucleotides containing one or several modifications, including fully modified sequences where every nucleobase was displaying a modification, and their hybridization was studied. The phosphoramidite building blocks have potential for synthesis of hypermodified aptamers and other functional nucleic acid-based polymers, which sequence-specifically display amino acid-like hydrophobic substituents.
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Affiliation(s)
- Ivana Jestřábová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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10
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Kimoto M, Tan HP, Matsunaga KI, Binte Mohd Mislan NA, Kawai G, Hirao I. Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins. J Am Chem Soc 2023; 145:20432-20441. [PMID: 37677157 PMCID: PMC10515488 DOI: 10.1021/jacs.3c06122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/09/2023]
Abstract
XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.
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Affiliation(s)
- Michiko Kimoto
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Hui Pen Tan
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Ken-ichiro Matsunaga
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | | | - Gota Kawai
- Chiba
Institute of Technology (CIT), Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Ichiro Hirao
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
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11
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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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12
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Kim YJ, Shin JS, Lee KW, Eom HJ, Jo BG, Lee JW, Kim JH, Kim SY, Kang JH, Choi JW. Expression, Purification, and Characterization of Plasmodium vivax Lactate Dehydrogenase from Bacteria without Codon Optimization. Int J Mol Sci 2023; 24:11083. [PMID: 37446261 DOI: 10.3390/ijms241311083] [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: 05/30/2023] [Revised: 06/30/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Plasmodium vivax is the most widespread cause of malaria, especially in subtropical and temperate regions such as Asia-Pacific and America. P. vivax lactate dehydrogenase (PvLDH), an essential enzyme in the glycolytic pathway, is required for the development and reproduction of the parasite. Thus, LDH from these parasites has garnered attention as a diagnostic biomarker for malaria and as a potential molecular target for developing antimalarial drugs. In this study, we prepared a transformed Escherichia coli strain for the overexpression of PvLDH without codon optimization. We introduced this recombinant plasmid DNA prepared by insertion of the PvLDH gene in the pET-21a(+) expression vector, into the Rosetta(DE3), an E. coli strain suitable for eukaryotic protein expression. The time, temperature, and inducer concentration for PvLDH expression from this E. coli Rosetta(DE3), containing the original PvLDH gene, were optimized. We obtained PvLDH with a 31.0 mg/L yield and high purity (>95%) from this Rosetta(DE3) strain. The purified protein was characterized structurally and functionally. The PvLDH expressed and purified from transformed bacteria without codon optimization was successfully demonstrated to exhibit its potential tetramer structure and enzyme activity. These findings are expected to provide valuable insights for research on infectious diseases, metabolism, diagnostics, and therapeutics for malaria caused by P. vivax.
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Affiliation(s)
- Yeon-Jun Kim
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Jun-Seop Shin
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Kang Woo Lee
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Hyo-Ji Eom
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Byung Gwan Jo
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
| | - Jin Woo Lee
- College of Pharmacy, Duksung Women's University, Seoul 01369, Republic of Korea
| | - Jun Hyoung Kim
- Division of Infectious Diseases, Department of Internal Medicine, Chungbuk National University Hospital, Cheongju 28644, Republic of Korea
| | - So Yeon Kim
- Department of Dental Hygiene, Cheongju University, Cheongju 28503, Republic of Korea
| | - Jung Hoon Kang
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
| | - Jae-Won Choi
- Department of Biomedical Science, Cheongju University, Cheongju 28160, Republic of Korea
- Department of Biopharmaceutical Sciences, Cheongju University, Cheongju 28160, Republic of Korea
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13
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Mulholland C, Jestřábová I, Sett A, Ondruš M, Sýkorová V, Manzanares CL, Šimončík O, Muller P, Hocek M. The selection of a hydrophobic 7-phenylbutyl-7-deazaadenine-modified DNA aptamer with high binding affinity for the Heat Shock Protein 70. Commun Chem 2023; 6:65. [PMID: 37024672 PMCID: PMC10079658 DOI: 10.1038/s42004-023-00862-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Nucleic acids aptamers often fail to efficiently target some proteins because of the hydrophilic character of the natural nucleotides. Here we present hydrophobic 7-phenylbutyl-7-deaadenine-modified DNA aptamers against the Heat Shock Protein 70 that were selected via PEX and magnetic bead-based SELEX. After 9 rounds of selection, the pool was sequenced and a number of candidates were identified. Following initial screening, two modified aptamers were chemically synthesised in-house and their binding affinity analysed by two methods, bio-layer interferometry and fluorescent-plate-based binding assay. The binding affinities of the modified aptamers were compared with that of their natural counterparts. The resulting modified aptamers bound with higher affinity (low nanomolar range) to the Hsp70 than their natural sequence (>5 µM) and hence have potential for applications and further development towards Hsp70 diagnostics or even therapeutics.
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Affiliation(s)
- Catherine Mulholland
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
| | - Ivana Jestřábová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Prague, 12843, Czech Republic
| | - Arghya Sett
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
| | - Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Prague, 12843, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
| | - C Lorena Manzanares
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13 Haus E, 81377, München, Germany
| | - Oliver Šimončík
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53, Brno, Czech Republic
| | - Petr Muller
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute (MMCI), Zluty Kopec 7, 656 53, Brno, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague 6, Prague, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague 2, Prague, 12843, Czech Republic.
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14
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Chen Z, Luo H, Gubu A, Yu S, Zhang H, Dai H, Zhang Y, Zhang B, Ma Y, Lu A, Zhang G. Chemically modified aptamers for improving binding affinity to the target proteins via enhanced non-covalent bonding. Front Cell Dev Biol 2023; 11:1091809. [PMID: 36910146 PMCID: PMC9996316 DOI: 10.3389/fcell.2023.1091809] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Nucleic acid aptamers are ssDNA or ssRNA fragments that specifically recognize targets. However, the pharmacodynamic properties of natural aptamers consisting of 4 naturally occurring nucleosides (A, G, C, T/U) are generally restricted for inferior binding affinity than the cognate antibodies. The development of high-affinity modification strategies has attracted extensive attention in aptamer applications. Chemically modified aptamers with stable three-dimensional shapes can tightly interact with the target proteins via enhanced non-covalent bonding, possibly resulting in hundreds of affinity enhancements. This review overviewed high-affinity modification strategies used in aptamers, including nucleobase modifications, fluorine modifications (2'-fluoro nucleic acid, 2'-fluoro arabino nucleic acid, 2',2'-difluoro nucleic acid), structural alteration modifications (locked nucleic acid, unlocked nucleic acid), phosphate modifications (phosphorothioates, phosphorodithioates), and extended alphabets. The review emphasized how these high-affinity modifications function in effect as the interactions with target proteins, thereby refining the pharmacodynamic properties of aptamers.
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Affiliation(s)
- Zefeng Chen
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Hang Luo
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Amu Gubu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Aptacure Therapeutics Limited, Kowloon, Hong Kong SAR, China
| | - Sifan Yu
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Huarui Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hong Dai
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Yihao Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Yuan Ma
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China.,Institute of Precision Medicine and Innovative Drug Discovery, HKBU Institute for Research and Continuing Education, Shenzhen, Hong Kong SAR, China
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15
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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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16
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Abstract
The systematic evolution of ligands by exponential enrichment (SELEX) enables the identification of ssDNA or RNA sequences binding to different target molecules, highly specific and with high affinity. In this chapter, we describe a selection strategy with ssDNA for a histidine-tagged protein that could be either performed hands-on manually or fully automated by an appropriate robotic selection platform.
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Affiliation(s)
- Stefan Breuers
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany.
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17
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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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18
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Zhang J, Xu Y, Chen M, Huang Y, Song T, Yang C, Yang Y, Song Y. Elucidating the Effect of Nanoscale Receptor-Binding Domain Organization on SARS-CoV-2 Infection and Immunity Activation with DNA Origami. J Am Chem Soc 2022; 144:21295-21303. [DOI: 10.1021/jacs.2c09229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Mingying Chen
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Ting Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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19
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Zhang J, Huang Y, Sun M, Song T, Wan S, Yang C, Song Y. Mechanosensing view of SARS-CoV-2 infection by a DNA nano-assembly. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101048. [PMID: 36157982 PMCID: PMC9490855 DOI: 10.1016/j.xcrp.2022.101048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/18/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
The mechanical force between a virus and its host cell plays a critical role in viral infection. However, characterization of the virus-cell mechanical force at the whole-virus level remains a challenge. Herein, we develop a platform in which the virus is anchored with multivalence-controlled aptamers to achieve transfer of the virus-cell mechanical force to a DNA tension gauge tether (Virus-TGT). When the TGT is ruptured, the complex of binding module-virus-cell is detached from the substrate, accompanied by decreased host cell-substrate adhesion, thus revealing the mechanical force between whole-virus and cell. Using Virus-TGT, direct evidence about the biomechanical force between SARS-CoV-2 and the host cell is obtained. The relative mechanical force gap (<10 pN) at the cellular level between the wild-type virus to cell and a variant virus to cell is measured, suggesting a possible positive correlation between virus-cell mechanical force and infectivity. Overall, this strategy provides a new perspective to probe the SARS-CoV-2 mechanical force.
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Affiliation(s)
- Jialu Zhang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yihao Huang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Miao Sun
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Ting Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shuang Wan
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yanling Song
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
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20
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Ondruš M, Sýkorová V, Hocek M. Traceless enzymatic synthesis of monodispersed hypermodified oligodeoxyribonucleotide polymers from RNA templates. Chem Commun (Camb) 2022; 58:11248-11251. [PMID: 36124894 DOI: 10.1039/d2cc03588j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new alternative for enzymatic synthesis of single-stranded hypermodified oligodeoxyribonucleotides displaying four different hydrophobic groups based on reverse transcription from RNA templates catalyzed by DNA polymerases using a set of base-modified dNTPs followed by digestion of RNA by RNases. Using mixed oligodeoxyribonucleotide primers containing a ribonucleotide at the 3'-end, RNase AT1 simultaneously digested the template and cleaved off the primer to release a fully modified oligonucleotide that can be further 3'-labelled with a fluorescent nucleotide using TdT. The resulting hypermodified oligonucleotides could find applications in selection of aptamers or other functional macromolecules.
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Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic. .,Dept. of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16000 Prague 6, Czech Republic. .,Dept. of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
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21
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Zhang L, Chu M, Ji C, Tan J, Yuan Q. Preparation, applications, and challenges of functional DNA nanomaterials. NANO RESEARCH 2022; 16:3895-3912. [PMID: 36065175 PMCID: PMC9430014 DOI: 10.1007/s12274-022-4793-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
As a carrier of genetic information, DNA is a versatile module for fabricating nanostructures and nanodevices. Functional molecules could be integrated into DNA by precise base complementary pairing, greatly expanding the functions of DNA nanomaterials. These functions endow DNA nanomaterials with great potential in the application of biomedical field. In recent years, functional DNA nanomaterials have been rapidly investigated and perfected. There have been reviews that classified DNA nanomaterials from the perspective of functions, while this review primarily focuses on the preparation methods of functional DNA nanomaterials. This review comprehensively introduces the preparation methods of DNA nanomaterials with functions such as molecular recognition, nanozyme catalysis, drug delivery, and biomedical material templates. Then, the latest application progress of functional DNA nanomaterials is systematically reviewed. Finally, current challenges and future prospects for functional DNA nanomaterials are discussed.
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Affiliation(s)
- Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Mengge Chu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 China
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22
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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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23
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Flamme M, Hanlon S, Marzuoli I, Püntener K, Sladojevich F, Hollenstein M. Evaluation of 3'-phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and XNA oligonucleotides. Commun Chem 2022; 5:68. [PMID: 36697944 PMCID: PMC9814670 DOI: 10.1038/s42004-022-00685-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/12/2022] [Indexed: 01/28/2023] Open
Abstract
Chemically modified oligonucleotides have advanced as important therapeutic tools as reflected by the recent advent of mRNA vaccines and the FDA-approval of various siRNA and antisense oligonucleotides. These sequences are typically accessed by solid-phase synthesis which despite numerous advantages is restricted to short sequences and displays a limited tolerance to functional groups. Controlled enzymatic synthesis is an emerging alternative synthetic methodology that circumvents the limitations of traditional solid-phase synthesis. So far, most approaches strived to improve controlled enzymatic synthesis of canonical DNA and no potential routes to access xenonucleic acids (XNAs) have been reported. In this context, we have investigated the possibility of using phosphate as a transient protecting group for controlled enzymatic synthesis of DNA and locked nucleic acid (LNA) oligonucleotides. Phosphate is ubiquitously employed in natural systems and we demonstrate that this group displays most characteristics required for controlled enzymatic synthesis. We have devised robust synthetic pathways leading to these challenging compounds and we have discovered a hitherto unknown phosphatase activity of various DNA polymerases. These findings open up directions for the design of protected DNA and XNA nucleoside triphosphates for controlled enzymatic synthesis of chemically modified nucleic acids.
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Affiliation(s)
- Marie Flamme
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de 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, Paris, France
| | - Steven Hanlon
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Irene Marzuoli
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Kurt Püntener
- grid.417570.00000 0004 0374 1269Pharmaceutical Devision, Synthetic Molecules Technical Development, F. Hoffmann-La Roche Ltd, 4070 Basel, Switzerland
| | - Filippo Sladojevich
- grid.417570.00000 0004 0374 1269Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Marcel Hollenstein
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université de 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, Paris, France
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24
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Chan KY, Kinghorn AB, Hollenstein M, Tanner JA. Chemical modifications for a next generation of nucleic acid aptamers. Chembiochem 2022; 23:e202200006. [PMID: 35416400 DOI: 10.1002/cbic.202200006] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/11/2022] [Indexed: 11/08/2022]
Abstract
In the past three decades, in vitro systematic evolution of ligands by exponential enrichment (SELEX) has yielded many aptamers for translational applications in both research and clinical settings. Despite their promise as an alternative to antibodies, the low success rate of SELEX (~ 30%) has been a major bottleneck that hampers the further development of aptamers. One hurdle is the lack of chemical diversity in nucleic acids. To address this, the aptamer chemical repertoire has been extended by introducing exotic chemical groups, which provide novel binding functionalities. This review will focus on how modified aptamers can be selected and evolved, with illustration of some successful examples. In particular, unique chemistries are exemplified. Various strategies of incorporating modified building blocks into the standard SELEX protocol are highlighted, with a comparison of the differences between pre-SELEX and post-SELEX modifications. Nucleic acid aptamers with extended functionality evolved from non-natural chemistries will open up new vistas for function and application of nucleic acids.
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Affiliation(s)
- Kwing Yeung Chan
- The University of Hong Kong, School of Biomedical Sciences, HONG KONG
| | | | | | - Julian Alexander Tanner
- The University of Hong Kong, School of Biomedical Sciences, 3/F Laboratory Block, 21 Sassoon Road, 000000, Pokfulam, HONG KONG
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25
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Nonenzymatic assembly of active chimeric ribozymes from aminoacylated RNA oligonucleotides. Proc Natl Acad Sci U S A 2022; 119:2116840119. [PMID: 35140183 PMCID: PMC8851484 DOI: 10.1073/pnas.2116840119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2022] [Indexed: 02/07/2023] Open
Abstract
The emergence of a primordial ribosome from the RNA world would have required access to aminoacylated RNA substrates. The spontaneous generation of such substrates without enzymes is inefficient, and it remains unclear how they could be selected for in a prebiotic milieu. In our study, we identify a possible role for aminoacylated RNA in ribozyme assembly, a longstanding problem in the origin-of-life research. We show that aminoacylation of short RNAs greatly accelerates their assembly into functional ribozymes by forming amino acid bridges in the phosphodiester backbone. Our work therefore addresses two key challenges within the origin-of-life field: we demonstrate assembly of functional ribozymes, and we identify a potential evolutionary benefit for RNA aminoacylation that is independent of coded peptide translation. Aminoacylated transfer RNAs, which harbor a covalent linkage between amino acids and RNA, are a universally conserved feature of life. Because they are essential substrates for ribosomal translation, aminoacylated oligonucleotides must have been present in the RNA world prior to the evolution of the ribosome. One possibility we are exploring is that the aminoacyl ester linkage served another function before being recruited for ribosomal protein synthesis. The nonenzymatic assembly of ribozymes from short RNA oligomers under realistic conditions remains a key challenge in demonstrating a plausible pathway from prebiotic chemistry to the RNA world. Here, we show that aminoacylated RNAs can undergo template-directed assembly into chimeric amino acid–RNA polymers that are active ribozymes. We demonstrate that such chimeric polymers can retain the enzymatic function of their all-RNA counterparts by generating chimeric hammerhead, RNA ligase, and aminoacyl transferase ribozymes. Amino acids with diverse side chains form linkages that are well tolerated within the RNA backbone and, in the case of an aminoacyl transferase, even in its catalytic center, potentially bringing novel functionalities to ribozyme catalysis. Our work suggests that aminoacylation chemistry may have played a role in primordial ribozyme assembly. Increasing the efficiency of this process provides an evolutionary rationale for the emergence of sequence and amino acid–specific aminoacyl-RNA synthetase ribozymes, which could then have generated the substrates for ribosomal protein synthesis.
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26
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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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27
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McKenzie LK, Flamme M, Felder PS, Karges J, Bonhomme F, Gandioso A, Malosse C, Gasser G, Hollenstein M. A ruthenium-oligonucleotide bioconjugated photosensitizing aptamer for cancer cell specific photodynamic therapy. RSC Chem Biol 2022; 3:85-95. [PMID: 35128412 PMCID: PMC8729177 DOI: 10.1039/d1cb00146a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/31/2021] [Indexed: 12/15/2022] Open
Abstract
Ruthenium complexes have emerged as a promising class of compounds for use as photosensitizers (PSs) in photodynamic therapy (PDT) due to their attractive photophysical properties and relative ease of chemical alteration. While promising, they generally are not inherently targeting to disease sites and may therefore be prone to side effects and require higher doses. Aptamers are short oligonucleotides that bind specific targets with high affinity. One such aptamer is AS1411, a nucleolin targeting, G-quadruplex forming, DNA aptamer. Here we present the first example of direct conjugation of a Ru(ii) polypyridyl complex-based PS to an aptamer and an assessment of its in vitro cancer cell specific photosensitization including discussion of the challenges faced.
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Affiliation(s)
- Luke K McKenzie
- Institut Pasteur, 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 https://research.pasteur.fr/en/team/bioorganic-chemistry-of-nucleic-acids/ +33 1 44 38 94 66
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Marie Flamme
- Institut Pasteur, 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 https://research.pasteur.fr/en/team/bioorganic-chemistry-of-nucleic-acids/ +33 1 44 38 94 66
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
- Université de Paris 12 rue de l'École de Médecine 75006 Paris France
| | - Patrick S Felder
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Johannes Karges
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Frederic Bonhomme
- Institut Pasteur, Department of Structural Biology and Chemistry, Unité de Chimie Biologique Epigénétique, UMR CNRS 3523 28 rue du Docteur Roux 75724 Paris Cedex 15 France
| | - Albert Gandioso
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Christian Malosse
- Institut Pasteur, Mass Spectrometry for Biology Unit 28 rue du Docteur Roux 75724 Paris Cedex 15 France
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology 75005 Paris France www.gassergroup.com +33 1 85 78 41 51
| | - Marcel Hollenstein
- Institut Pasteur, 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 https://research.pasteur.fr/en/team/bioorganic-chemistry-of-nucleic-acids/ +33 1 44 38 94 66
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28
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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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29
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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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30
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Hervey JRD, Freund N, Houlihan G, Dhaliwal G, Holliger P, Taylor AI. Efficient synthesis and replication of diverse sequence libraries composed of biostable nucleic acid analogues. RSC Chem Biol 2022; 3:1209-1215. [PMID: 36320888 PMCID: PMC9533476 DOI: 10.1039/d2cb00035k] [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] [Received: 02/09/2022] [Accepted: 04/15/2022] [Indexed: 11/10/2022] Open
Abstract
Functional nucleic acids can be evolved in vitro using cycles of selection and amplification, starting from diverse-sequence libraries, which are typically restricted to natural or partially-modified polymer chemistries. Here, we describe the efficient DNA-templated synthesis and reverse transcription of libraries entirely composed of serum nuclease resistant alternative nucleic acid chemistries validated in nucleic acid therapeutics; locked nucleic acid (LNA), 2′-O-methyl-RNA (2′OMe-RNA), or mixtures of the two. We evaluate yield and diversity of synthesised libraries and measure the aggregate error rate of a selection cycle. We find that in addition to pure 2′-O-methyl-RNA and LNA, several 2′OMe-RNA/LNA blends seem suitable and promising for discovery of biostable functional nucleic acids for biomedical applications. Blends of engineered polymerases enable efficient DNA-templated synthesis and reverse transcription of diverse-sequence oligonucleotide libraries composed of locked nucleic acid (LNA), 2′-O-methyl-RNA (2′OMe-RNA), or mixtures of the two.![]()
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Affiliation(s)
- John R. D. Hervey
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, CB2 0AW, UK
| | - Niklas Freund
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Gillian Houlihan
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Gurpreet Dhaliwal
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, CB2 0AW, UK
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alexander I. Taylor
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge, CB2 0AW, UK
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31
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Freund N, Fürst MJLJ, Holliger P. New chemistries and enzymes for synthetic genetics. Curr Opin Biotechnol 2021; 74:129-136. [PMID: 34883451 DOI: 10.1016/j.copbio.2021.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022]
Abstract
Beyond the natural nucleic acids DNA and RNA, nucleic acid chemistry has unlocked a whole universe of modifications to their canonical chemical structure, which can in various ways modify and enhance nucleic acid function and utility for applications in biotechnology and medicine. Unlike the natural modifications of tRNA and rRNA or the epigenetic modifications in mRNA and genomic DNA, these altered chemistries are not found in nature and therefore these molecules are referred to as xeno-nucleic acids (XNAs). In this review we aim to focus specifically on recent progress in a subsection of this vast field-synthetic genetics-concerned with encoded synthesis, reverse transcription, and evolution of XNAs.
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Affiliation(s)
- Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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32
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McCloskey CM, Li Q, Yik EJ, Chim N, Ngor AK, Medina E, Grubisic I, Co Ting Keh L, Poplin R, Chaput JC. Evolution of Functionally Enhanced α-l-Threofuranosyl Nucleic Acid Aptamers. ACS Synth Biol 2021; 10:3190-3199. [PMID: 34739228 DOI: 10.1021/acssynbio.1c00481] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Synthetic genetic polymers (xeno-nucleic acids, XNAs) have the potential to transition aptamers from laboratory tools to therapeutic agents, but additional functionality is needed to compete with antibodies. Here, we describe the evolution of a biologically stable artificial genetic system composed of α-l-threofuranosyl nucleic acid (TNA) that facilitates the production of backbone- and base-modified aptamers termed "threomers" that function as high quality protein capture reagents. Threomers were discovered against two prototypical protein targets implicated in human diseases through a combination of in vitro selection and next-generation sequencing using uracil nucleotides that are uniformly equipped with aromatic side chains commonly found in the paratope of antibody-antigen crystal structures. Kinetic measurements reveal that the side chain modifications are critical for generating threomers with slow off-rate binding kinetics. These findings expand the chemical space of evolvable non-natural genetic systems to include functional groups that enhance protein target binding by mimicking the structural properties of traditional antibodies.
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Affiliation(s)
| | | | | | | | | | | | - Ivan Grubisic
- X, The Moonshot Factory, Mountain View, California 94043, United States
| | - Lance Co Ting Keh
- X, The Moonshot Factory, Mountain View, California 94043, United States
| | - Ryan Poplin
- X, The Moonshot Factory, Mountain View, California 94043, United States
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33
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Li Q, Maola VA, Chim N, Hussain J, Lozoya-Colinas A, Chaput JC. Synthesis and Polymerase Recognition of Threose Nucleic Acid Triphosphates Equipped with Diverse Chemical Functionalities. J Am Chem Soc 2021; 143:17761-17768. [PMID: 34637287 DOI: 10.1021/jacs.1c08649] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Expanding the chemical space of evolvable non-natural genetic polymers (XNAs) to include functional groups that enhance protein target binding affinity offers a promising route to therapeutic aptamers with high biological stability. Here we describe the chemical synthesis and polymerase recognition of 10 chemically diverse functional groups introduced at the C-5 position of α-l-threofuranosyl uridine nucleoside triphosphate (tUTP). We show that the set of tUTP substrates is universally recognized by the laboratory-evolved polymerase Kod-RSGA. Insights into the mechanism of TNA synthesis were obtained from a high-resolution X-ray crystal structure of the postcatalytic complex bound to the primer-template duplex. A structural analysis reveals a large cavity in the enzyme active site that can accommodate the side chain of C-5-modified tUTP substrates. Our findings expand the chemical space of evolvable nucleic acid systems by providing a synthetic route to artificial genetic polymers that are uniformly modified with diversity-enhancing functional groups.
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34
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Alamudi SH, Kimoto M, Hirao I. Uptake mechanisms of cell-internalizing nucleic acid aptamers for applications as pharmacological agents. RSC Med Chem 2021; 12:1640-1649. [PMID: 34778766 PMCID: PMC8528270 DOI: 10.1039/d1md00199j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acid aptamers, also regarded as chemical antibodies, show potential as targeted therapeutic and delivery agents since they possess unique advantages over antibodies. Generated by an iterative selection and amplification process from oligonucleotide libraries using cultured cells, the aptamers bind to their target molecules expressed on the cell surface. Excitingly, most aptamers also demonstrate a cell-internalizing property in native living cells, allowing them to directly enter the cells via endocytosis depending on the target. In this review, we discuss selection methods in generating cell-internalizing aptamers via a cell-based selection process, along with their challenges and optimization strategies. We highlight the cellular uptake routes adopted by the aptamers and also their intracellular fate after the uptake, to give an overview of their mechanism of action for applications as promising pharmacological agents.
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Affiliation(s)
- Samira Husen Alamudi
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
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35
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Tapp M, Dennis P, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9043-9052. [PMID: 34279112 DOI: 10.1021/acs.langmuir.1c01053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.
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Affiliation(s)
| | - Patrick Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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36
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Hammill ML, Salim L, Tsubaki K, Varley AJ, Kitamura M, Okauchi T, Desaulniers JP. Building siRNAs with Cubes: Synthesis and Evaluation of Cubane-Modified siRNAs. Chembiochem 2021; 22:2981-2985. [PMID: 34319643 DOI: 10.1002/cbic.202100334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/27/2021] [Indexed: 11/10/2022]
Abstract
Cubane molecules hold great potential for medicinal chemistry applications due to their inherent stability and low toxicity. In this study, we report the synthesis of a cubane derivative phosphoramidite for the incorporation of cubane into small interfering RNAs (siRNAs). Synthetic siRNAs rely on chemical modifications to improve their pharmacokinetic profiles. However, they are still able to mediate sequence-specific gene silencing via the endogenous RNA interference pathway. We designed a library of siRNAs bearing cubane at different positions within the sense and antisense strands. All siRNAs showed excellent gene-silencing activity, with IC50 values ranging from 45.4 to 305 pM. Incorporating the cubane modification in both the sense and antisense strand led to viable duplexes with good biological activity. To the best of our knowledge, this is the first report of siRNAs bearing a cubane derivative within the backbone.
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Affiliation(s)
- Matthew L Hammill
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
| | - Lidya Salim
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
| | - Kouta Tsubaki
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada.,Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Andrew J Varley
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
| | - Mitsuru Kitamura
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Graduate School of Engineering, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata, Kitakyushu, 804-8550, Japan
| | - Jean-Paul Desaulniers
- Faculty of Science, University of Ontario Institute of Technology, 2000 Simcoe Street North, Oshawa, Ontario, L1G 0C5, Canada
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37
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Navien TN, Yeoh TS, Anna A, Tang TH, Citartan M. Aptamers isolated against mosquito-borne pathogens. World J Microbiol Biotechnol 2021; 37:131. [PMID: 34240263 DOI: 10.1007/s11274-021-03097-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/21/2021] [Indexed: 11/27/2022]
Abstract
Mosquito-borne diseases are a major threat to public health. The shortcomings of diagnostic tools, especially those that are antibody-based, have been blamed in part for the rising annual morbidity and mortality caused by these diseases. Antibodies harbor a number of disadvantages that can be clearly addressed by aptamers as the more promising molecular recognition elements. Aptamers are defined as single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit high binding affinity and specificity against a wide variety of target molecules based on their unique structural conformations. A number of aptamers were developed against mosquito-borne pathogens such as Dengue virus, Zika virus, Chikungunya virus, Plasmodium parasite, Francisella tularensis, Japanese encephalitis virus, Venezuelan equine encephalitis virus, Rift Valley fever virus and Yellow fever virus. Intrigued by these achievements, we carry out a comprehensive overview of the aptamers developed against these mosquito-borne infectious agents. Characteristics of the aptamers and their roles in diagnostic, therapeutic as well as other applications are emphasized.
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Affiliation(s)
- Tholasi Nadhan Navien
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Tzi Shien Yeoh
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
| | - Andrew Anna
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia
- Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak (UNIMAS), 94300, Kota Samarahan, Sarawak, Malaysia
| | - Thean-Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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38
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Lo Y, Cheung YW, Wang L, Lee M, Figueroa-Miranda G, Liang S, Mayer D, Tanner JA. An electrochemical aptamer-based biosensor targeting Plasmodium falciparum histidine-rich protein II for malaria diagnosis. Biosens Bioelectron 2021; 192:113472. [PMID: 34271397 DOI: 10.1016/j.bios.2021.113472] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/18/2021] [Accepted: 06/28/2021] [Indexed: 11/29/2022]
Abstract
Malaria is an infectious disease caused by parasitic protozoans from the genus Plasmodium, with the species P. falciparum causing the highest number of deaths worldwide. Rapid diagnostic tests (RDTs) have become critical in the management of malaria, but current RDTs that detect P. falciparum are primarily antibody-based, which can have drawbacks in cost and robustness. Here, we report the development of an electrochemical aptamer-based (E-AB) biosensing alternative. Through selective evolution of ligands by exponential enrichment, we identify DNA aptamers that bind specifically to P. falciparum histidine-rich protein II (PfHRP2). The aptamer is modified with a methylene blue reporter and attached to a gold sensor surface for square-wave voltammetry interrogation. Through this method we are able to quantify PfHRP2 in human serum with an LOD of 3.73 nM. We further demonstrate the biosensor is stable in serum buffers and reusable for multiple detection rounds. These findings provide a promising alternative to conventional PfHRP2 detection for malaria diagnosis, while also expanding the capabilities of E-AB biosensors.
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Affiliation(s)
- Young Lo
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Yee-Wai Cheung
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Lin Wang
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Megan Lee
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gabriela Figueroa-Miranda
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Shaolin Liang
- "Mobile Health" Ministry of Education-China Mobile Joint Laboratory, Xiangya Hospital, Central South University, Changsha, China; School of Medicine, Northwest University, Xi'an, China
| | - Dirk Mayer
- Institute of Biological Information Processing, Bioelectronics (IBI-3), Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Julian Alexander Tanner
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Advanced Biomedical Instrumentation Centre, Hong Kong Science Park, Shatin, New Territories, Hong Kong (SAR), Hong Kong, China.
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39
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Freage L, Boykoff N, Mallikaratchy P. Utility of Multivalent Aptamers to Develop Nanoscale DNA Devices against Surface Receptors. ACS OMEGA 2021; 6:12382-12391. [PMID: 34056390 PMCID: PMC8154169 DOI: 10.1021/acsomega.1c01513] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
DNA nanotechnology is undergoing rapid progress in the assembly of functional devices with biological relevance. In particular, currently, the research attention is more focused on the application of nanodevices at the interface of chemistry and biology, on the cell membrane where protein receptors communicate with the extracellular environment. This review explores the use of multivalent nucleic acid ligands termed aptamers in the design of DNA-based nanodevices to probe cellular interactions followed by a perspective on the untapped utility of XNA and UBP nanotechnology in designing functional nanomaterials with broader structural space.
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Affiliation(s)
- Lina Freage
- Department
of Chemistry, Lehman College, The City University
of New York, 250 Bedford Park Boulevard, Bronx, New York 10468, United
States
| | - Natalie Boykoff
- Ph.D.
Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Prabodhika Mallikaratchy
- Department
of Chemistry, Lehman College, The City University
of New York, 250 Bedford Park Boulevard, Bronx, New York 10468, United
States
- Ph.D.
Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Ph.D.
Program in Molecular, Cellular and Developmental Biology, The Graduate Center of the City University of New
York, 365 Fifth Avenue, New York, New York 10016, United States
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40
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Kodr D, Yenice CP, Simonova A, Saftić DP, Pohl R, Sýkorová V, Ortiz M, Havran L, Fojta M, Lesnikowski ZJ, O'Sullivan CK, Hocek M. Carborane- or Metallacarborane-Linked Nucleotides for Redox Labeling. Orthogonal Multipotential Coding of all Four DNA Bases for Electrochemical Analysis and Sequencing. J Am Chem Soc 2021; 143:7124-7134. [PMID: 33929195 DOI: 10.1021/jacs.1c02222] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report a series of 2'-deoxyribonucleoside triphosphates bearing dicarba-nido-undecaborate ([C2B9H11]1-), [3,3'-iron-bis(1,2-dicarbollide)]- (FESAN, [Fe(C2B9H11)2]2-) or [3,3'-cobalt-bis(1,2-dicarbollide)]- (COSAN, [Co(C2B9H11)2]2-) groups prepared either through the Sonogashira cross-coupling or the CuAAC click reaction. The modified dNXTPs were substrates for KOD XL DNA polymerase in enzymatic synthesis of modified DNA through primer extension (PEX). The nido-carborane- and FESAN-modified nucleotides gave analytically useful oxidation signals in square-wave voltammetry and were used for redox labeling of DNA. The redox-modified DNA probes were prepared by PEX using tailed primers and were hybridized to electrode (gold or glassy carbon) containing capture oligonucleotides. The combination of nido-carborane- and FESAN-linked nucleotides with 7-ferrocenylethynyl-7-deaza-dATP and 7-deaza-dGTP allowed polymerase synthesis of DNA fully modified at all four nucleobases, and each of the redox labels gave four differentiable and ratiometric signals in voltammetry. Thus, the combination of these four redox labels constitutes the first fully orthogonal redox coding of all four canonical nucleobases, which can be used for determination of nucleobase composition of short DNA stretches in one simple PEX experiment with electrochemical readout.
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Affiliation(s)
- David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Cansu Pinar Yenice
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
| | - Dijana Pavlović Saftić
- Laboratory of Medicinal Chemistry, Institute of Medical Biology PAS, Lodowa 106, 92-232 Łódź, Poland
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic
| | - Mayreli Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain
| | - Ludĕk Havran
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Miroslav Fojta
- Institute of Biophysics, Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| | - Zbigniew J Lesnikowski
- Laboratory of Medicinal Chemistry, Institute of Medical Biology PAS, Lodowa 106, 92-232 Łódź, Poland
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007 Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010, Barcelona, Spain
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, Prague-2 12843, Czech Republic
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41
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Flamme M, Figazzolo C, Gasser G, Hollenstein M. Enzymatic construction of metal-mediated nucleic acid base pairs. Metallomics 2021; 13:6206861. [PMID: 33791776 DOI: 10.1093/mtomcs/mfab016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 12/14/2022]
Abstract
Artificial metal base pairs have become increasingly important in nucleic acids chemistry due to their high thermal stability, water solubility, orthogonality to natural base pairs, and low cost of production. These interesting properties combined with ease of chemical and enzymatic synthesis have prompted their use in several practical applications, including the construction of nanomolecular devices, ions sensors, and metal nanowires. Chemical synthesis of metal base pairs is highly efficient and enables the rapid screening of novel metal base pair candidates. However, chemical synthesis is limited to rather short oligonucleotides and requires rather important synthetic efforts. Herein, we discuss recent progress made for the enzymatic construction of metal base pairs that can alleviate some of these limitations. First, we highlight the possibility of generating metal base pairs using canonical nucleotides and then describe how modified nucleotides can be used in this context. We also provide a description of the main analytical techniques used for the analysis of the nature and the formation of metal base pairs together with relevant examples of their applications.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, 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.,Université de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Chiara Figazzolo
- Institut Pasteur, 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.,Université de Paris, 12 rue de l'École de Médecine, 75006 Paris, France.,Centre de Recherches Interdisciplinaires CRI, 8 rue Charles V, 75004 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
| | - Marcel Hollenstein
- Institut Pasteur, 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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42
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Randomly positioned gold nanoparticles as fluorescence enhancers in apta-immunosensor for malaria test. Mikrochim Acta 2021; 188:88. [PMID: 33594523 PMCID: PMC7886758 DOI: 10.1007/s00604-021-04746-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/03/2021] [Indexed: 12/13/2022]
Abstract
A plasmon-enhanced fluorescence-based antibody-aptamer biosensor - consisting of gold nanoparticles randomly immobilized onto a glass substrate via electrostatic self-assembly - is described for specific detection of proteins in whole blood. Analyte recognition is realized through a sandwich scheme with a capture bioreceptor layer of antibodies - covalently immobilized onto the gold nanoparticle surface in upright orientation and close-packed configuration by photochemical immobilization technique (PIT) - and a top bioreceptor layer of fluorescently labelled aptamers. Such a sandwich configuration warrants not only extremely high specificity, but also an ideal fluorophore-nanostructure distance (approximately 10-15 nm) for achieving strong fluorescence amplification. For a specific application, we tested the biosensor performance in a case study for the detection of malaria-related marker Plasmodium falciparum lactate dehydrogenase (PfLDH). The proposed biosensor can specifically detect PfLDH in spiked whole blood down to 10 pM (0.3 ng/mL) without any sample pretreatment. The combination of simple and scalable fabrication, potentially high-throughput analysis, and excellent sensing performance provides a new approach to biosensing with significant advantages compared to conventional fluorescence immunoassays.
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43
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Radakovic A, Wright TH, Lelyveld VS, Szostak JW. A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry. Biochemistry 2021; 60:477-488. [PMID: 33523633 PMCID: PMC9634692 DOI: 10.1021/acs.biochem.0c00943] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Aminoacylated tRNAs
are the substrates for ribosomal protein synthesis
in all branches of life, implying an ancient origin for aminoacylation
chemistry. In the 1970s, Orgel and colleagues reported potentially
prebiotic routes to aminoacylated nucleotides and their RNA-templated
condensation to form amino acid-bridged dinucleotides. However, it
is unclear whether such reactions would have aided or impeded non-enzymatic
RNA replication. Determining whether aminoacylated RNAs could have
been advantageous in evolution prior to the emergence of protein synthesis
remains a key challenge. We therefore tested the ability of aminoacylated
RNA to participate in both templated primer extension and ligation
reactions. We find that at low magnesium concentrations that favor
fatty acid-based protocells, these reactions proceed orders of magnitude
more rapidly than when initiated from the cis-diol
of unmodified RNA. We further demonstrate that amino acid-bridged
RNAs can act as templates in a subsequent round of copying. Our results
suggest that aminoacylation facilitated non-enzymatic RNA replication,
thus outlining a potentially primordial functional link between aminoacylation
chemistry and RNA replication.
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Affiliation(s)
- Aleksandar Radakovic
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tom H Wright
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Victor S Lelyveld
- Howard Hughes Medical Institute, Department of Molecular Biology, and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Jack W Szostak
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
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44
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Chudinov AV, Vasiliskov VA, Kuznetsova VE, Lapa SA, Kolganova NA, Timofeev EN. Mononucleotide repeat expansions with non-natural polymerase substrates. Sci Rep 2021; 11:2423. [PMID: 33510377 PMCID: PMC7844250 DOI: 10.1038/s41598-021-82150-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/15/2021] [Indexed: 12/25/2022] Open
Abstract
Replicative strand slippage is a biological phenomenon, ubiquitous among different organisms. However, slippage events are also relevant to non-natural replication models utilizing synthetic polymerase substrates. Strand slippage may notably affect the outcome of the primer extension reaction with repetitive templates in the presence of non-natural nucleoside triphosphates. In the current paper, we studied the ability of Taq, Vent (exo-), and Deep Vent (exo-) polymerases to produce truncated, full size, or expanded modified strands utilizing non-natural 2′-deoxyuridine nucleotide analogues and different variants of the homopolymer template. Our data suggest that the slippage of the primer strand is dependent on the duplex fluttering, incorporation efficiency for a particular polymerase-dNTP pair, rate of non-templated base addition, and presence of competing nucleotides.
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Affiliation(s)
- Alexander V Chudinov
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Vadim A Vasiliskov
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Viktoriya E Kuznetsova
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Sergey A Lapa
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Natalia A Kolganova
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991
| | - Edward N Timofeev
- W. A. Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Vavilov St. 32, Moscow, Russia, 119991.
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45
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McKenzie LK, El-Khoury R, Thorpe JD, Damha MJ, Hollenstein M. Recent progress in non-native nucleic acid modifications. Chem Soc Rev 2021; 50:5126-5164. [DOI: 10.1039/d0cs01430c] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
While Nature harnesses RNA and DNA to store, read and write genetic information, the inherent programmability, synthetic accessibility and wide functionality of these nucleic acids make them attractive tools for use in a vast array of applications.
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Affiliation(s)
- Luke K. McKenzie
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
| | | | | | | | - Marcel Hollenstein
- Institut Pasteur
- Department of Structural Biology and Chemistry
- Laboratory for Bioorganic Chemistry of Nucleic Acids
- CNRS UMR3523
- 75724 Paris Cedex 15
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46
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Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Nucleic Acids Res 2020; 48:11982-11993. [PMID: 33152081 PMCID: PMC7708046 DOI: 10.1093/nar/gkaa999] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/08/2020] [Accepted: 10/13/2020] [Indexed: 12/13/2022] Open
Abstract
A set of modified 2′-deoxyribonucleoside triphosphates (dNTPs) bearing a linear or branched alkane, indole or phenyl group linked through ethynyl or alkyl spacer were synthesized and used as substrates for polymerase synthesis of hypermodified DNA by primer extension (PEX). Using the alkyl-linked dNTPs, the polymerase synthesized up to 22-mer fully modified oligonucleotide (ON), whereas using the ethynyl-linked dNTPs, the enzyme was able to synthesize even long sequences of >100 modified nucleotides in a row. In PCR, the combinations of all four modified dNTPs showed only linear amplification. Asymmetric PCR or PEX with separation or digestion of the template strand can be used for synthesis of hypermodified single-stranded ONs, which are monodispersed polymers displaying four different substituents on DNA backbone in sequence-specific manner. The fully modified ONs hybridized with complementary strands and modified DNA duplexes were found to exist in B-type conformation (B- or C-DNA) according to CD spectral analysis. The modified DNA can be replicated with high fidelity to natural DNA through PCR and sequenced. Therefore, this approach has a promising potential in generation and selection of hypermodified aptamers and other functional polymers.
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Affiliation(s)
- Marek Ondruš
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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47
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Ultrasensitive antibody-aptamer plasmonic biosensor for malaria biomarker detection in whole blood. Nat Commun 2020; 11:6134. [PMID: 33262332 PMCID: PMC7708447 DOI: 10.1038/s41467-020-19755-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 10/08/2020] [Indexed: 12/19/2022] Open
Abstract
Development of plasmonic biosensors combining reliability and ease of use is still a challenge. Gold nanoparticle arrays made by block copolymer micelle nanolithography (BCMN) stand out for their scalability, cost-effectiveness and tunable plasmonic properties, making them ideal substrates for fluorescence enhancement. Here, we describe a plasmon-enhanced fluorescence immunosensor for the specific and ultrasensitive detection of Plasmodium falciparum lactate dehydrogenase (PfLDH)—a malaria marker—in whole blood. Analyte recognition is realized by oriented antibodies immobilized in a close-packed configuration via the photochemical immobilization technique (PIT), with a top bioreceptor of nucleic acid aptamers recognizing a different surface of PfLDH in a sandwich conformation. The combination of BCMN and PIT enabled maximum control over the nanoparticle size and lattice constant as well as the distance of the fluorophore from the sensing surface. The device achieved a limit of detection smaller than 1 pg/mL (<30 fM) with very high specificity without any sample pretreatment. This limit of detection is several orders of magnitude lower than that found in malaria rapid diagnostic tests or even commercial ELISA kits. Thanks to its overall dimensions, ease of use and high-throughput analysis, the device can be used as a substrate in automated multi-well plate readers and improve the efficiency of conventional fluorescence immunoassays. Reliable plasmonic biosensors with high throughput and ease of use are highly sought after. Here, the authors report a plasmon-enhanced fluorescence antibody-aptamer biosensor based on a gold nanoparticle array, and demonstrate its use for effective specific detection of a malaria marker, at femtomolar level, in whole blood.
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48
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Tran BT, Kim J, Ahn DR. Systemic delivery of aptamer-drug conjugates for cancer therapy using enzymatically generated self-assembled DNA nanoparticles. NANOSCALE 2020; 12:22945-22951. [PMID: 33188383 DOI: 10.1039/d0nr05652a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Aptamer-drug conjugates (ApDCs) are promising anticancer therapeutics with cancer cell specificity. However, versatile in vivo applications of ApDCs are hampered by their limited serum stability and inability to reach the tumour upon systemic administration. Here, we describe DNA nanoparticles of ApDCs as a platform for tumour-targeted systemic delivery of ApDCs. DNA nanoparticles of approximately 75 nm size were fabricated by self-assembly of a polymerised floxuridine (FUdR)-incorporated AS1411 aptamer produced via rolling circle amplification. The DNA nanoparticles of ApDCs showed highly efficient cancer cell uptake, enhanced serum stability, and tumour-targeted accumulation. These properties could be successfully utilised for tumour-specific apoptotic damage by ApDCs, leading to significant suppression of tumour growth without considerable systemic toxicity. Molecular analysis revealed that the enhanced anticancer potency was due to the synergic effect induced by the simultaneous activation of p53 by AS1411 and the inhibition of thymidylate synthase by FUdR, respectively, both of which were generated from the DNA nanoparticles. We therefore expect that the DNA nanoparticles of ApDCs can be a promising platform for tumour-targeted delivery of various nucleoside-incorporated ApDCs to treat cancer.
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Affiliation(s)
- Binh Thanh Tran
- Division of Biomedical Science and Technology, KIST School, Korea University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul 02792, Korea
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Flamme M, Röthlisberger P, Levi-Acobas F, Chawla M, Oliva R, Cavallo L, Gasser G, Marlière P, Herdewijn P, Hollenstein M. Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate. ACS Chem Biol 2020; 15:2872-2884. [PMID: 33090769 DOI: 10.1021/acschembio.0c00396] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, 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
- Université Paris Descartes, Sorbonne Paris Cité, 12 rue de l’École de Médecine, 75006 Paris, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Pascal Röthlisberger
- Institut Pasteur, 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
| | - Fabienne Levi-Acobas
- Institut Pasteur, 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
| | - Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, 80143, Naples, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, Kaust Catalysis Center, Thuwal, 23955-6900 Saudi Arabia
| | - Gilles Gasser
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Philippe Marlière
- University of Paris Saclay, CNRS, iSSB, UEVE, Genopole, 5 Rue Henri Desbrueres, 91030 Evry, France
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat, 3000 Leuven, Belgium
| | - Marcel Hollenstein
- Institut Pasteur, 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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