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Garrido E, Climent E, Marcos MD, Sancenón F, Rurack K, Martínez-Máñez R. Dualplex lateral flow assay for simultaneous scopolamine and "cannibal drug" detection based on receptor-gated mesoporous nanoparticles. NANOSCALE 2022; 14:13505-13513. [PMID: 36102017 DOI: 10.1039/d2nr03325a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We report herein the design of a strip-based rapid test utilizing bio-inspired hybrid nanomaterials for the in situ and at site detection of the drug scopolamine (SCP) using a smartphone for readout, allowing SCP identification in diluted saliva down to 40 nM in less than 15 min. For this purpose, we prepared a nanosensor based on mesoporous silica nanoparticles loaded with a fluorescent reporter (rhodamine B) and functionalized with bethanechol, a potent agonist of recombinant human muscarinic acetylcholine receptor M2 (M2-AChR). M2-AChR interaction with the anchored bethanechol derivative leads to capping of the pores. The sensing mechanism relies on binding of SCP to M2-AChR resulting in pore opening and delivery of the entrapped rhodamine B reporter. Moreover, the material was incorporated into strips for lateral-flow assays coupled to smartphone readout, giving fast response time, good selectivity, and exceptional sensitivity. In an attempt to a mobile analytical test system for law enforcement services, we have also developed a dualplex lateral flow assay for SCP and 3,4-methylenedioxypyrovalerone (MDPV) also known as the so-called "cannibal drug".
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Affiliation(s)
- Eva Garrido
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, Pabellón 11, Planta 0 28029 Madrid
- Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Estela Climent
- Chemical and Optical Sensing Division, Bundesanstalt für Materialforschung und -prüfung (BAM) Richard-Willstätter-Str. 11, 12489, Berlin, Germany.
| | - M Dolores Marcos
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, Pabellón 11, Planta 0 28029 Madrid
- Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Félix Sancenón
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, Pabellón 11, Planta 0 28029 Madrid
- Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Knut Rurack
- Chemical and Optical Sensing Division, Bundesanstalt für Materialforschung und -prüfung (BAM) Richard-Willstätter-Str. 11, 12489, Berlin, Germany.
| | - Ramón Martínez-Máñez
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Spain.
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Av. Monforte de Lemos, 3-5, Pabellón 11, Planta 0 28029 Madrid
- Unidad Mixta de Investigación en Nanomedicina y Sensores. Universitat Politècnica de València, Instituto de Investigación Sanitaria La Fe, Valencia, Spain
- Unidad Mixta UPV-CIPF de Investigación en Mecanismos de Enfermedades y Nanomedicina, Universitat Politècnica de València, Centro de Investigación Príncipe Felipe, Valencia, Spain
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2
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Jeon HJ, Lee W, Seo S, Chang S. N-Chloro- N-sodio-carbamates as a Practical Amidating Reagent for Scalable and Sustainable Amidation of Aldehydes under Visible Light. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hyun Ji Jeon
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Wongyu Lee
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Sangwon Seo
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
| | - Sukbok Chang
- Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, South Korea
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, South Korea
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Liang Y, Miao S, Mao J, DeSantis C, Bong D. Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs. Biochemistry 2020; 59:2410-2418. [PMID: 32519542 DOI: 10.1021/acs.biochem.0c00362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we demonstrate context-dependent molecular recognition of DNA by synthetic bPNA iron and copper complexes, using oxidative backbone cleavage as a chemical readout for binding. Oligoethylenimine bPNAs displaying iron·EDTA or copper·phenanthroline sites were found to be efficient chemical nucleases for designed and native structured DNAs with T-rich single-stranded domains. Cleavage reactivity depends strongly on structural context, as strikingly demonstrated with DNA substrates of the form (GGGTTA)n. This repeat sequence from the human telomere is known to switch between parallel and antiparallel G-quadruplex (G4) topologies with a change from potassium to sodium buffer: notably, bPNA-copper complexes efficiently cleave long repeat sequences into ∼22-nucleotide portions in sodium, but not potassium, buffer. We hypothesize preferential cleavage of the antiparallel topology (Na+) over the parallel topology (K+) due to the greater accessibility of the TTA loop to bPNA in the antiparallel (Na+) form. Similar ion-sensitive telomere shortening upon treatment with bPNA nucleases can be observed in both isolated and intracellular DNA from PC3 cells by quantitative polymerase chain reaction. Live cell treatment was accompanied by accelerated cellular senescence, as expected for significant telomere shortening. Taken together, the loop-targeting approach of bPNA chemical nucleases complements prior intercalation strategies targeting duplex and quadruplex DNA. Structurally sensitive loop targeting enables discrimination between similar target sequences, thus expanding bPNA targeting beyond simple oligo-T sequences. In addition, bPNA nucleases are cell membrane permeable and therefore may be used to target native intracellular substrates. In addition, these data indicate that bPNA scaffolds can be a platform for new synthetic binders to particular nucleic acid structural motifs.
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Affiliation(s)
- Yufeng Liang
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shiqin Miao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Chris DeSantis
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry and Center for RNA Biology, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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4
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Theoretical study of hydrogen bonds and electronic properties in hexagonal arrangements composed of self-assembled DNA analogues. Struct Chem 2020. [DOI: 10.1007/s11224-020-01545-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Kashida H, Hattori Y, Tazoe K, Inoue T, Nishikawa K, Ishii K, Uchiyama S, Yamashita H, Abe M, Kamiya Y, Asanuma H. Bifacial Nucleobases for Hexaplex Formation in Aqueous Solution. J Am Chem Soc 2018; 140:8456-8462. [PMID: 29886741 DOI: 10.1021/jacs.8b02807] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Although DNA can form triplex and quadruplex structures through hydrogen bonds, design and preparation of structures with more than five strands is difficult even when artificial nucleic acids are used. Herein we report a hexaplex formed by oligomers of artificial nucleic acids bearing bifacial molecules on d-threoninol. Aminopyrimidine and cyanuric acid derivatives were selected as bases because they have complementary hydrogen bonding patterns. The complex formed by aminopyrimidine and cyanuric acid decamers melted with large hysteresis. Hexaplex formation was indicated by gel electrophoresis, size exclusion chromatography and atomic force microscopy imaging, and proven directly through native mass spectrometry. CD measurements and molecular dynamics simulations indicated that the hexaplex adopts a helical structure. The hexaplex formation was highly dependent on pH and the presence of divalent cations. The hexaplex was stable in aqueous solution, and its unique structure and properties may lead to novel nanostructures, molecular assemblies, metal sensors, and ion channels.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan.,PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi , Saitama 332-0012 , Japan
| | - Yuhei Hattori
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Kaho Tazoe
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Tadashi Inoue
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Keiji Nishikawa
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Kentaro Ishii
- Okazaki Institute for Integrative Bioscience , National Institutes of Natural Sciences, Okazaki 444-8787 , Japan
| | - Susumu Uchiyama
- Okazaki Institute for Integrative Bioscience , National Institutes of Natural Sciences, Okazaki 444-8787 , Japan.,Graduate School of Engineering , Osaka University , Suita , Osaka 565-0871 , Japan
| | - Hayato Yamashita
- PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho, Kawaguchi , Saitama 332-0012 , Japan.,Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - Masayuki Abe
- Graduate School of Engineering Science , Osaka University , Toyonaka , Osaka 560-8531 , Japan
| | - Yukiko Kamiya
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering , Nagoya University , Furo-cho, Chikusa-ku , Nagoya 464-8603 , Japan
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6
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Tateishi-Karimata H, Sugimoto N. Expansion of the DNA Alphabet beyond Natural DNA Recognition. Chembiochem 2016; 17:1301-3. [PMID: 27061868 DOI: 10.1002/cbic.201600181] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 11/05/2022]
Abstract
Simple and inexpensive DNA fibres: New, stable DNA structures are created by the binding of a small molecule to poly(A). Because these DNA fibres are formed from inexpensive materials by using very simple methods, DNA materials suitable for practical use such as information storage should be possible in the near future.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan. .,Graduate School of Frontier of Innovative Research in Science and Technology (FIRST), Konan University, 7-1-20, Minatojima-minamimachi, Chuo-ku, Kobe, 650-0047, Japan.
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Avakyan N, Greschner AA, Aldaye F, Serpell CJ, Toader V, Petitjean A, Sleiman HF. Reprogramming the assembly of unmodified DNA with a small molecule. Nat Chem 2016; 8:368-76. [PMID: 27001733 DOI: 10.1038/nchem.2451] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 01/07/2016] [Indexed: 02/08/2023]
Abstract
The ability of DNA to store and encode information arises from base pairing of the four-letter nucleobase code to form a double helix. Expanding this DNA 'alphabet' by synthetic incorporation of new bases can introduce new functionalities and enable the formation of novel nucleic acid structures. However, reprogramming the self-assembly of existing nucleobases presents an alternative route to expand the structural space and functionality of nucleic acids. Here we report the discovery that a small molecule, cyanuric acid, with three thymine-like faces, reprogrammes the assembly of unmodified poly(adenine) (poly(A)) into stable, long and abundant fibres with a unique internal structure. Poly(A) DNA, RNA and peptide nucleic acid (PNA) all form these assemblies. Our studies are consistent with the association of adenine and cyanuric acid units into a hexameric rosette, which brings together poly(A) triplexes with a subsequent cooperative polymerization. Fundamentally, this study shows that small hydrogen-bonding molecules can be used to induce the assembly of nucleic acids in water, which leads to new structures from inexpensive and readily available materials.
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Affiliation(s)
- Nicole Avakyan
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Andrea A Greschner
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.,INRS: Centre Énergie Matériaux Télécommunications, 1650 Boul. Lionel-Boulet, Varennes Quebec J3X 1S2, Canada
| | - Faisal Aldaye
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Christopher J Serpell
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.,School of Physical Sciences, Ingram Building, University of Kent, Canterbury CT2 7NH, Kent, UK
| | - Violeta Toader
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
| | - Anne Petitjean
- Department of Chemistry, Queen's University, Chernoff Hall, 90 Bader Lane, Kingston Ontario K7L 3N6, Canada
| | - Hanadi F Sleiman
- Department of Chemistry and Centre for Self-assembled Chemical Structures, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada
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Takezawa Y, Nishiyama K, Mashima T, Katahira M, Shionoya M. Bifacial Base-Pairing Behaviors of 5-Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination. Chemistry 2015; 21:14713-6. [DOI: 10.1002/chem.201502772] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 11/11/2022]
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9
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Piao X, Xia X, Mao J, Bong D. Peptide Ligation and RNA Cleavage via an Abiotic Template Interface. J Am Chem Soc 2015; 137:3751-4. [PMID: 25747470 DOI: 10.1021/jacs.5b00236] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Xijun Piao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Xin Xia
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jie Mao
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry and
Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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Largy E, Liu W, Hasan A, Perrin DM. A Pyrimidopyrimidine Janus-AT Nucleoside with Improved Base-Pairing Properties to both A and T within a DNA Duplex: The Stabilizing Effect of a Second Endocyclic Ring Nitrogen. Chemistry 2014; 20:1495-9. [DOI: 10.1002/chem.201303867] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Indexed: 12/18/2022]
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