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Brylev VA, Ustinov AV, Tsvetkov VB, Barinov NA, Aparin IO, Sapozhnikova KA, Berlina YY, Kokin EA, Klinov DV, Zatsepin TS, Korshun VA. Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:15119-15127. [PMID: 33264013 DOI: 10.1021/acs.langmuir.0c02696] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.
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Affiliation(s)
- Vladimir A Brylev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexey V Ustinov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Department of Biology and Biotechnology, Higher School of Economics, Vavilova 7, 117312 Moscow, Russia
| | - Vladimir B Tsvetkov
- Federal Research and Clinical Center of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
- Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, 119146 Moscow, Russia
- A.V. Topchiev Institute of Petrochemical Synthesis of Russian Academy of Sciences, Leninsky Prospect str. 29, 119991 Moscow, Russia
| | - Nikolay A Barinov
- Federal Research and Clinical Center of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Ilya O Aparin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Ksenia A Sapozhnikova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Yana Y Berlina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Department of Chemistry, Moscow State University, 1-3 Leninskiye Gory, 119991 Moscow, Russia
| | - Egor A Kokin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Department of Biology, Moscow State University, 1-12 Leninskie Gory, 119991 Moscow, Russia
| | - Dmitry V Klinov
- Federal Research and Clinical Center of Physico-Chemical Medicine, Malaya Pirogovskaya 1a, 119435 Moscow, Russia
| | - Timofei S Zatsepin
- Department of Chemistry, Moscow State University, 1-3 Leninskiye Gory, 119991 Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143026 Moscow, Russia
| | - Vladimir A Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Department of Biology and Biotechnology, Higher School of Economics, Vavilova 7, 117312 Moscow, Russia
- Gause Institute of New Antibiotics, Bolshaya Pirogovskaya 11, 119021 Moscow, Russia
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Etkind SI, Vander Griend DA, Swager TM. Electroactive Anion Receptor with High Affinity for Arsenate. J Org Chem 2020; 85:10050-10061. [PMID: 32790360 DOI: 10.1021/acs.joc.0c01206] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Herein, we present the synthesis and characterization of a macrocyclic polyamide cage that incorporates redox-active 1,4-dithiin units. UV/vis titration experiments with eight anions in acetonitrile revealed high affinity for H2AsO4- (log β2 = 10.4-0.4+0.4) and HCO3- (log β2 = 8.3-0.4+0.3) over other common anionic guests, such as Cl- (log K1:1 = 3.20-0.02+0.03), HSO4- (log K1:1 = 3.57-0.03+0.02), and H2PO4- (log K1:1 = 4.24-0.04+0.05), by the selective formation of HG2 complexes. The recognition of arsenate over phosphate is rare among both proteins and synthetic receptors, and though the origin of selectivity is not known, exploiting the difference in the binding stoichiometry represents an underexplored avenue toward developing receptors that can differentiate between the two anions. Additional analysis by 1H NMR in 1:3 CD2Cl2/MeCN-d3 found a strong dependence of anion binding stoichiometry with the solvent employed. Finally, titration experiments with cyclic voltammetry provided varying and complex responses for each anion tested, though reaction between the anion and receptors was observed in most cases. These results implicate 1,4-dithiins as interesting recognition moieties in the construction of supramolecular receptors.
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Affiliation(s)
- Samuel I Etkind
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Douglas A Vander Griend
- Department of Chemistry and Biochemistry, Calvin University, Grand Rapids, Michigan 49546, United States
| | - Timothy M Swager
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Dong Y, Yao C, Zhu Y, Yang L, Luo D, Yang D. DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications. Chem Rev 2020; 120:9420-9481. [DOI: 10.1021/acs.chemrev.0c00294] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuhang Dong
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Chi Yao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Yi Zhu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Lu Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
| | - Dan Luo
- Department of Biological & Environmental Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
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Khandelwal P, Poddar P. Fluorescent metal quantum clusters: an updated overview of the synthesis, properties, and biological applications. J Mater Chem B 2017; 5:9055-9084. [DOI: 10.1039/c7tb02320k] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A brief history of metal quantum clusters, their synthesis methods, physical properties, and an updated overview of their applications is provided.
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Affiliation(s)
- Puneet Khandelwal
- Physical & Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune – 411008
- India
| | - Pankaj Poddar
- Physical & Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune – 411008
- India
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Ponomarenko AI, Brylev VA, Sapozhnikova KA, Ustinov AV, Prokhorenko IA, Zatsepin TS, Korshun VA. Tetrahedral DNA conjugates from pentaerythritol-based polyazides. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.03.051] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Javani S, Lorca R, Latorre A, Flors C, Cortajarena AL, Somoza Á. Antibacterial Activity of DNA-Stabilized Silver Nanoclusters Tuned by Oligonucleotide Sequence. ACS APPLIED MATERIALS & INTERFACES 2016; 8:10147-10154. [PMID: 27058628 DOI: 10.1021/acsami.6b00670] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Silver nanoclusters (AgNCs) stabilized by DNA are promising materials with tunable fluorescent properties, which have been employed in a plethora of sensing systems. In this report, we explore their antimicrobial properties in Gram-positive and Gram-negative bacteria. After testing 9 oligonucleotides with different sequence and length, we found that the antibacterial activity depends on the sequence of the oligonucleotide employed. The sequences tested yielded fluorescent AgNCs, which can be grouped in blue, yellow, and red emitters. Interestingly, blue emitters yielded poor antibacterial activity, whereas yellow and red emitters afforded an activity similar to silver nitrate. Furthermore, structural studies using circular dichroism indicate the formation of complexes with different stability and structure, which might be one of the factors that modulate their activity. Finally, we prepared a trimeric structure containing the sequence that afforded the best antimicrobial activity, which inhibited the growth of Gram-positive and negative bacteria in the submicromolar range.
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Affiliation(s)
- Siamak Javani
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 Madrid, Spain
| | - Romina Lorca
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 Madrid, Spain
| | - Alfonso Latorre
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 Madrid, Spain
| | - Cristina Flors
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 Madrid, Spain
| | - Aitziber L Cortajarena
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 Madrid, Spain
| | - Álvaro Somoza
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia), & Nanobiotecnología (IMDEA-Nanociencia), Unidad Asociada al Centro Nacional de Biotecnología (CSIC) , 28049 Madrid, Spain
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Formation of Silver Nanoclusters from a DNA Template Containing Ag(I)-Mediated Base Pairs. Bioinorg Chem Appl 2016; 2016:7485125. [PMID: 27034627 PMCID: PMC4791510 DOI: 10.1155/2016/7485125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/22/2015] [Accepted: 12/27/2015] [Indexed: 11/18/2022] Open
Abstract
A series of DNA double helices containing different numbers of silver(I)-mediated base pairs involving the artificial nucleobases imidazole or 2-methylimidazole has been applied for the generation of DNA-templated silver nanoclusters. The original Ag(I)-containing nucleic acids as well as the resulting nanoclusters and nanoparticles have been characterized by means of UV/Vis spectroscopy, circular dichroism (CD) spectroscopy, fluorescence spectroscopy, and transmission electron microscopy (TEM). The results show for the first time that metal-mediated base pairs can be used for the templated growth of metal nanoclusters.
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Zhou Z, Dong S. Protein-DNA interactions: a novel approach to improve the fluorescence stability of DNA/Ag nanoclusters. NANOSCALE 2015; 7:1296-1300. [PMID: 25502467 DOI: 10.1039/c4nr04889j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein-DNA interactions are known to play an important role in a variety of biological processes. We have shown here that protein-DNA binding events can also be used to greatly improve the fluorescence stability of DNA-templated Ag nanoclusters (Ag NCs), which would be highly beneficial for Ag NCs in applications of biosensing/imaging.
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Affiliation(s)
- Zhixue Zhou
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, People's Republic of China.
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