1
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Diaferia C, Avitabile C, Leone M, Gallo E, Saviano M, Accardo A, Romanelli A. Diphenylalanine Motif Drives Self-Assembling in Hybrid PNA-Peptide Conjugates. Chemistry 2021; 27:14307-14316. [PMID: 34314536 PMCID: PMC8597081 DOI: 10.1002/chem.202102481] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 11/12/2022]
Abstract
Peptides and nucleic acids can self-assemble to give supramolecular structures that find application in different fields, ranging from the delivery of drugs to the obtainment of materials endowed with optical properties. Forces that stabilize the "suprastructures" typically are hydrogen bonds or aromatic interactions; in case of nucleic acids, Watson-Crick pairing drives self-assembly while, in case of peptides, backbone hydrogen bonds and interactions between aromatic side chains trigger the formation of structures, such as nanotubes or ribbons. Molecules containing both aromatic peptides and nucleic acids could in principle exploit different forces to self-assemble. In this work we meant to investigate the self-assembly of mixed systems, with the aim to understand which forces play a major role and determine formation/structure of aggregates. We therefore synthesized conjugates of the peptide FF to the peptide nucleic acid dimer "gc" and characterized their aggregates by different spectroscopic techniques, including NMR, CD and fluorescence.
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Affiliation(s)
- Carlo Diaferia
- Department of PharmacyResearch Centre on Bioactive Peptides (CIRPeB)University of Naples “Federico II”Via Mezzocannone 1680134NaplesItaly
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging (CNR)Via Mezzocannone 1680134NaplesItaly
| | | | - Michele Saviano
- Institute of Crystallography (CNR)Via Amendola 12270126BariItaly
| | - Antonella Accardo
- Department of PharmacyResearch Centre on Bioactive Peptides (CIRPeB)University of Naples “Federico II”Via Mezzocannone 1680134NaplesItaly
| | - Alessandra Romanelli
- Department of Pharmaceutical SciencesUniversity of MilanVia Venezian 2120133MilanItaly
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2
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Damakoudi V, Feldner T, Dilji E, Belkin A, Richert C. Hybridization Networks of mRNA and Branched RNA Hybrids. Chembiochem 2021; 22:924-930. [PMID: 33105062 PMCID: PMC7984269 DOI: 10.1002/cbic.202000678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/21/2020] [Indexed: 12/28/2022]
Abstract
Messenger RNA (mRNA) is emerging as an attractive biopolymer for therapy and vaccination. To become suitable for vaccination, mRNA is usually converted to a biomaterial, using cationic peptides, polymers or lipids. An alternative form of converting mRNA into a material is demonstrated that uses branched oligoribonucleotide hybrids with the ability to hybridize with one or more regions of the mRNA sequence. Two such hybrids with hexamer arms and adamantane tetraol as branching element were prepared by solution-phase synthesis. When a rabies mRNA was treated with the branched hybrids at 1 M NaCl concentration, biomaterials formed that contained both of the nucleic acids. These results show that branched oligoribonucleotides are an alternative to the often toxic reagents commonly used to formulate mRNA for medical applications.
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Affiliation(s)
| | - Tobias Feldner
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Edina Dilji
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Andrey Belkin
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
| | - Clemens Richert
- Institute of Organic ChemistryUniversity of Stuttgart70569StuttgartGermany
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3
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Cheng HF, Wang S, Mirkin CA. Electron-Equivalent Valency through Molecularly Well-Defined Multivalent DNA. J Am Chem Soc 2021; 143:1752-1757. [DOI: 10.1021/jacs.0c11843] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Ho Fung Cheng
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Shunzhi Wang
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Chad A. Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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4
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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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5
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Feldner T, Wolfrum M, Richert C. Turning DNA Binding Motifs into a Material for Flow Cells. Chemistry 2019; 25:15288-15294. [PMID: 31483908 PMCID: PMC6916365 DOI: 10.1002/chem.201903631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/03/2019] [Indexed: 01/18/2023]
Abstract
Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine-containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.
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Affiliation(s)
- Tobias Feldner
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Manpreet Wolfrum
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Clemens Richert
- Institut für Organische ChemieUniversität StuttgartPfaffenwaldring 5570569StuttgartGermany
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6
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Trinh T, Saliba D, Liao C, de Rochambeau D, Prinzen AL, Li J, Sleiman HF. “Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence. Angew Chem Int Ed Engl 2019; 58:3042-3047. [PMID: 30290048 DOI: 10.1002/anie.201809251] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Indexed: 01/17/2023]
Affiliation(s)
- Tuan Trinh
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Chenyi Liao
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Donatien de Rochambeau
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Alexander Lee Prinzen
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Jianing Li
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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7
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Trinh T, Saliba D, Liao C, de Rochambeau D, Prinzen AL, Li J, Sleiman HF. “Printing” DNA Strand Patterns on Small Molecules with Control of Valency, Directionality, and Sequence. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201809251] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tuan Trinh
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Daniel Saliba
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Chenyi Liao
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Donatien de Rochambeau
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Alexander Lee Prinzen
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
| | - Jianing Li
- Deparment of ChemistryThe University of Vermont Burlington VT 05405 USA
| | - Hanadi F. Sleiman
- Department of ChemistryMcGill University 801 rue Sherbrooke West Montreal QC H3A 0B8 Canada
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8
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Schwenger A, Jurkowski TP, Richert C. Capturing and Stabilizing Folded Proteins in Lattices Formed with Branched Oligonucleotide Hybrids. Chembiochem 2018; 19:1523-1530. [DOI: 10.1002/cbic.201800145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Tomasz P. Jurkowski
- Institut für Biochemie und Technische BiochemieUniversität Stuttgart Allmandring 31 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart Pfaffenwaldring 55 70569 Stuttgart Germany
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9
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Wenz NL, Piasecka S, Kalinowski M, Schneider A, Richert C, Wege C. Building expanded structures from tetrahedral DNA branching elements, RNA and TMV protein. NANOSCALE 2018; 10:6496-6510. [PMID: 29569670 DOI: 10.1039/c7nr07743b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
By combining both chemical and enzymatic ligation with procedures guiding the self-assembly of nanotubular tobacco mosaic virus (TMV)-like particles (TLPs), novel nucleoprotein structures based on DNA-terminated branching elements, RNA scaffolds and TMV coat protein (CP) are made accessible. Tetrahedral tetrakis(hydroxybiphenyl)adamantane cores with four 5'-phosphorylated dinucleotide arms were coupled to DNA linkers by chemical ligation. The resulting three-dimensional (3D) branching elements were enzymatically ligated to the 3' termini of RNA scaffolds either prior to or after the RNAs' incorporation into TLPs. Thus, architectures with interconnected nanotube domains in two different length classes were generated, each containing 70 CP subunits per 10 nm length. Short TMV origin-of-assembly-containing RNA scaffolds ligated to the DNA allowed the growth of protein-coated 34 nm tubes on the terminal RNA strands in situ. Alternatively, 290 nm pre-fabricated tubes with accessible RNA 3' termini, attained by DNA blocking elements hybridized to the RNAs, were ligated with the branched cores. Both approaches resulted in four-armed nanoobjects, demonstrating a so far unique combination of organic synthesis of branching elements, enzymatic modifications, nucleic acid-based scaffolding and RNA-guided and DNA-controlled assembly of tubular RNA-encapsidating protein domains, yielding a novel class of 3D nucleoprotein architectures with polyvalent protein elements. In the long term, the production route might give rise to supramolecular systems with complex functionalities, installed via the orthogonal coupling of effector molecules to TLP domains.
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Affiliation(s)
- Nana L Wenz
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Sylwia Piasecka
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Matthäus Kalinowski
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Angela Schneider
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Christina Wege
- Department of Molecular Biology and Plant Virology, Institute of Biomaterials and Biomolecular Systems, University of Stuttgart, Pfaffenwaldring 57, 70569 Stuttgart, Germany.
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10
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He S, Richert C. A Three‐State System Based on Branched DNA Hybrids. Chemistry 2018; 24:4562-4572. [DOI: 10.1002/chem.201705941] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Shiliang He
- Institut für Organische ChemieUniversität Stuttgart 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische ChemieUniversität Stuttgart 70569 Stuttgart Germany
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11
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Efthymiou T, Krishnamurthy R. Microwave‐Assisted Phosphitylation of DNA and RNA Nucleosides and Their Analogs. ACTA ACUST UNITED AC 2018; 60:2.19.1-2.19.20. [DOI: 10.1002/0471142700.nc0219s60] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Tim Efthymiou
- Department of Chemistry, The Scripps Research Institute La Jolla California
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12
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Griesser H, Schwenger A, Richert C. Encapsulating Active Pharmaceutical Ingredients in Self-Assembling Adamantanes with Short DNA Zippers. ChemMedChem 2017; 12:1759-1767. [PMID: 28914989 PMCID: PMC5698727 DOI: 10.1002/cmdc.201700466] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/06/2017] [Indexed: 11/23/2022]
Abstract
Formulating pharmaceutically active ingredients for drug delivery is a challenge. There is a need for new drug delivery systems that take up therapeutic molecules and release them into biological systems. We propose a novel mode of encapsulation that involves matrices formed through co-assembly of drugs with adamantane hybrids that feature four CG dimers as sticky ends. Such adamantanes are accessible via inexpensive solution-phase syntheses, and the resulting materials show attractive properties for controlled release. This is demonstrated for two different hybrids and a series of drugs, including anticancer drugs, antibiotics, and cyclosporin. Up to 20 molar equivalents of active pharmaceutical ingredients (APIs) are encapsulated in hybrid materials. Encapsulation is demonstrated for DNA-binding and several non-DNA binding compounds. Nanoparticles were detected that range in size from 114-835 nm average diameter, and ζ potentials were found to be between -29 and +28 mV. Release of doxorubicin into serum at near-constant rates for 10 days was shown, demonstrating the potential for slow release. The encapsulation and release in self-assembling matrices of dinucleotide-bearing adamantanes appears to be broadly applicable and may thus lead to new drug delivery systems for APIs.
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Affiliation(s)
- Helmut Griesser
- Institute of Organic ChemistryUniversity of StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Alexander Schwenger
- Institute of Organic ChemistryUniversity of StuttgartPfaffenwaldring 5570569StuttgartGermany
| | - Clemens Richert
- Institute of Organic ChemistryUniversity of StuttgartPfaffenwaldring 5570569StuttgartGermany
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13
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Cho VY, Hong BJ, Kohlstedt KL, Schatz GC, Nguyen ST. The competing effects of core rigidity and linker flexibility in the nanoassembly of trivalent small molecule-DNA hybrids (SMDH 3s)-a synergistic experimental-modeling study. NANOSCALE 2017; 9:12652-12663. [PMID: 28825749 PMCID: PMC5804500 DOI: 10.1039/c7nr01931a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The nanoassembly behavior of trivalent small molecule-DNA hybrids (SMDH3s) was investigated as a function of core geometry and supramolecular flexibility through a synergistic experimental-modeling study. While complementary SMDH3s possessing a highly flexible tetrahedral trivalent core primarily assemble into nanoscale caged dimers, the nanoassemblies of SMDH3 comonomers with rigid pyramidal and trigonal cores yield fewer caged dimers and more large-oligomer networks. Specifically, the rigid pyramidal SMDH3 comonomers tend to form smaller nanosized aggregates (dimers, tetramers, and hexamers) upon assembly, attributable to the small (<109°) branch-core-branch angle of the pyramidal core. In contrast, the more-rigid trigonal planar SMDH3 comonomers have a larger (∼120°) branch-core-branch angle, which spaces their DNA arms farther apart, facilitating the formation of larger nanoassemblies (≥nonamers). The population distributions of these nanoassemblies were successfully captured by coarse-grained molecular dynamics (CGMD) simulations over a broad range of DNA concentrations. CGMD simulations can also forecast the effect of incorporating Tn spacer units between the hydridizing DNA arms and the rigid organic cores to increase the overall flexibility of the SMDH3 comonomers. Such "decoupling" of the DNA arms from the organic core was found to result in preferential formation of nanoscale dimers up to an optimal spacer length, beyond which network formation takes over due to entropic factors. This excellent agreement between the simulation and experimental results confirms the versatility of the CGMD model as a useful and reliable tool for elucidating the nanoassembly of SMDH-based building blocks.
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Affiliation(s)
- Vincent Y Cho
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA.
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14
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Schwenger A, Birchall N, Richert C. Solution-Phase Synthesis of Branched Oligonucleotides with up to 32 Nucleotides and the Reversible Formation of Materials. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700686] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Nicholas Birchall
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
| | - Clemens Richert
- Institut für Organische Chemie; Universität Stuttgart; 70569 Stuttgart Germany
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15
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Kalinowski M, Haug R, Said H, Piasecka S, Kramer M, Richert C. Phosphoramidate Ligation of Oligonucleotides in Nanoscale Structures. Chembiochem 2016; 17:1150-5. [PMID: 27225865 DOI: 10.1002/cbic.201600061] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Indexed: 01/25/2023]
Abstract
The folding of long DNA strands into designed nanostructures has evolved into an art. Being based on linear chains only, the resulting nanostructures cannot readily be transformed into covalently linked frameworks. Covalently linking strands in the context of folded DNA structures requires a robust method that avoids sterically demanding reagents or enzymes. Here we report chemical ligation of the 3'-amino termini of oligonucleotides and 5'-phosphorylated partner strands in templated reactions that produce phosphoramidate linkages. These reactions produce inter-nucleotide linkages that are isoelectronic and largely isosteric to phosphodiesters. Ligations were performed at three levels of complexity, including the extension of branched DNA hybrids and the ligation of six scaffold strands in a small origami.
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Affiliation(s)
- Matthäus Kalinowski
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Rüdiger Haug
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Hassan Said
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Sylwia Piasecka
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Markus Kramer
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569, Stuttgart, Germany.
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16
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Thaner RV, Eryazici I, Macfarlane RJ, Brown KA, Lee B, Nguyen ST, Mirkin CA. The Significance of Multivalent Bonding Motifs and "Bond Order" in DNA-Directed Nanoparticle Crystallization. J Am Chem Soc 2016; 138:6119-22. [PMID: 27148838 DOI: 10.1021/jacs.6b02479] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Multivalent oligonucleotide-based bonding elements have been synthesized and studied for the assembly and crystallization of gold nanoparticles. Through the use of organic branching points, divalent and trivalent DNA linkers were readily incorporated into the oligonucleotide shells that define DNA-nanoparticles and compared to monovalent linker systems. These multivalent bonding motifs enable the change of "bond strength" between particles and therefore modulate the effective "bond order." In addition, the improved accessibility of strands between neighboring particles, either due to multivalency or modifications to increase strand flexibility, gives rise to superlattices with less strain in the crystallites compared to traditional designs. Furthermore, the increased availability and number of binding modes also provide a new variable that allows previously unobserved crystal structures to be synthesized, as evidenced by the formation of a thorium phosphide superlattice.
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Affiliation(s)
- Ryan V Thaner
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Ibrahim Eryazici
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Robert J Macfarlane
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Keith A Brown
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Byeongdu Lee
- X-ray Science Division, Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - SonBinh T Nguyen
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States
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17
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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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18
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Hong BJ, Cho VY, Bleher R, Schatz GC, Nguyen ST. Enhancing DNA-Mediated Assemblies of Supramolecular Cage Dimers through Tuning Core Flexibility and DNA Length—A Combined Experimental–Modeling Study. J Am Chem Soc 2015; 137:13381-8. [DOI: 10.1021/jacs.5b08678] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Bong Jin Hong
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Vincent Y. Cho
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Reiner Bleher
- NUANCE
Center and Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208-3108, United States
| | - George C. Schatz
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - SonBinh T. Nguyen
- Department
of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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19
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Tashiro R, Iwamoto M, Morinaga H, Emura T, Hidaka K, Endo M, Sugiyama H. Linking two DNA duplexes with a rigid linker for DNA nanotechnology. Nucleic Acids Res 2015; 43:6692-700. [PMID: 26130712 PMCID: PMC4538841 DOI: 10.1093/nar/gkv662] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 11/14/2022] Open
Abstract
DNA has recently emerged as a promising material for the construction of nanosized architectures. Chemically modified DNA has been suggested to be an important component of such architectural building blocks. We have designed and synthesized a novel H-shaped DNA oligonucleotide dimer that is cross-linked with a structurally rigid linker composed of phenylene and ethynylene groups. A rotatable DNA unit was constructed through the self-assembly of this H-shaped DNA component and two complementary DNA oligonucleotides. In addition to the rotatable unit, a locked DNA unit containing two H-shaped DNA components was also constructed. As an example of an extended locked structure, a hexagonal DNA origami dimer and oligomer were constructed by using H-shaped DNA as linkers.
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Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
| | - Masahiro Iwamoto
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-cho, Suzuka-shi, Mie 513-8670, Japan
| | - Hironobu Morinaga
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Tomoko Emura
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwakecho, Sakyo-ku, Kyoto, 606-8502, Japan Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto, 606-8501, Japan
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20
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Hong BJ, Eryazici I, Bleher R, Thaner RV, Mirkin CA, Nguyen ST. Directed Assembly of Nucleic Acid-Based Polymeric Nanoparticles from Molecular Tetravalent Cores. J Am Chem Soc 2015; 137:8184-91. [PMID: 25980315 PMCID: PMC5493157 DOI: 10.1021/jacs.5b03485] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complementary tetrahedral small molecule-DNA hybrid (SMDH) building blocks have been combined to form nucleic acid-based polymeric nanoparticles without the need for an underlying template or scaffold. The sizes of these particles can be tailored in a facile fashion by adjusting assembly conditions such as SMDH concentration, assembly time, and NaCl concentration. Notably, these novel particles can be stabilized and transformed into functionalized spherical nucleic acid (SNA) structures through the incorporation of capping DNA strands conjugated with functional groups. These results demonstrate a systematic, efficient strategy for the construction and surface functionalization of well-defined, size-tunable nucleic acid particles from readily accessible molecular building blocks. Furthermore, because these nucleic acid-based polymeric nanoparticles exhibited enhanced cellular internalization and resistance to DNase I compared to free synthetic nucleic acids, they should have a plethora of applications in diagnostics and therapeutics.
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Affiliation(s)
- Bong Jin Hong
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Ibrahim Eryazici
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Reiner Bleher
- Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208-3108, United States
- NUANCE Center, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208-3108, United States
| | - Ryan V. Thaner
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Chad A. Mirkin
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - SonBinh T. Nguyen
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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21
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Schwenger A, Frey W, Richert C. Tetrakis(dimethoxyphenyl)adamantane (TDA) and Its Inclusion Complexes in the Crystalline State: A Versatile Carrier for Small Molecules. Chemistry 2015; 21:8781-9. [PMID: 25925766 DOI: 10.1002/chem.201406568] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Alexander Schwenger
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-608-64321
| | - Wolfgang Frey
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-608-64321
| | - Clemens Richert
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany), Fax: (+49) 711-608-64321.
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22
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Schwenger A, Gerlach C, Griesser H, Richert C. Synthesis of eight-arm, branched oligonucleotide hybrids and studies on the limits of DNA-driven assembly. J Org Chem 2014; 79:11558-66. [PMID: 25407332 DOI: 10.1021/jo5022053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Oligonucleotide hybrids with organic cores as rigid branching elements and four or six CG dimer strands have been shown to form porous materials from dilute aqueous solution. In order to explore the limits of this form of DNA-driven assembly, we prepared hybrids with three or eight DNA arms via solution-phase syntheses, using H-phosphonates of protected dinucleoside phosphates. This included the synthesis of (CG)8TREA, where TREA stands for the tetrakis[4-(resorcin-5-ylethynyl)phenyl]adamantane core. The ability of the new compounds to assemble in a DNA-driven fashion was studied by UV-melting analysis and NMR, using hybrids with self-complementary CG zipper arms or non-self-complementary TC dimer arms. The three-arm hybrid failed to form a material under conditions where four-arm hybrids did so. Further, the assembly of TREA hybrids appears to be dominated by hydrophobic interactions, not base pairing of the DNA arms. These results help in the design of materials forming by multivalent DNA-DNA interactions.
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Affiliation(s)
- Alexander Schwenger
- Institute for Organic Chemistry, University of Stuttgart , 70569 Stuttgart, Germany
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23
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24
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Aghebat Rafat A, Pirzer T, Scheible MB, Kostina A, Simmel FC. Surface-Assisted Large-Scale Ordering of DNA Origami Tiles. Angew Chem Int Ed Engl 2014; 53:7665-8. [DOI: 10.1002/anie.201403965] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Indexed: 11/09/2022]
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25
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Bußkamp H, Keller S, Robotta M, Drescher M, Marx A. A new building block for DNA network formation by self-assembly and polymerase chain reaction. Beilstein J Org Chem 2014; 10:1037-1046. [PMID: 24991255 PMCID: PMC4077517 DOI: 10.3762/bjoc.10.104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 04/10/2014] [Indexed: 12/23/2022] Open
Abstract
The predictability of DNA self-assembly is exploited in many nanotechnological approaches. Inspired by naturally existing self-assembled DNA architectures, branched DNA has been developed that allows self-assembly to predesigned architectures with dimensions on the nanometer scale. DNA is an attractive material for generation of nanostructures due to a plethora of enzymes which modify DNA with high accuracy, providing a toolbox for many different manipulations to construct nanometer scaled objects. We present a straightforward synthesis of a rigid DNA branching building block successfully used for the generation of DNA networks by self-assembly and network formation by enzymatic DNA synthesis. The Y-shaped 3-armed DNA construct, bearing 3 primer strands is accepted by Taq DNA polymerase. The enzyme uses each arm as primer strand and incorporates the branched construct into large assemblies during PCR. The networks were investigated by agarose gel electrophoresis, atomic force microscopy, dynamic light scattering, and electron paramagnetic resonance spectroscopy. The findings indicate that rather rigid DNA networks were formed. This presents a new bottom-up approach for DNA material formation and might find applications like in the generation of functional hydrogels.
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Affiliation(s)
- Holger Bußkamp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Sascha Keller
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Marta Robotta
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Malte Drescher
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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26
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Yildirim I, Eryazici I, Nguyen ST, Schatz GC. Hydrophobic organic linkers in the self-assembly of small molecule-DNA hybrid dimers: a computational-experimental study of the role of linkage direction in product distributions and stabilities. J Phys Chem B 2014; 118:2366-76. [PMID: 24494718 PMCID: PMC3954456 DOI: 10.1021/jp501041m] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Detailed computational and experimental studies reveal the crucial role that hydrophobic interactions play in the self-assembly of small molecule-DNA hybrids (SMDHs) into cyclic nanostructures. In aqueous environments, the distribution of the cyclic structures (dimers or higher-order structures) greatly depends on how well the hydrophobic surfaces of the organic cores in these nanostructures are minimized. Specifically, when the cores are attached to the 3'-ends of the DNA component strands, they can insert into the minor groove of the duplex that forms upon self-assembly, favoring the formation of cyclic dimers. However, when the cores are attached to the 5'-ends of the DNA component strands, such insertion is hindered, leading to the formation of higher-order cyclic structures. These computational insights are supported by experimental results that show clear differences in product distributions and stabilities for a broad range of organic core-linked DNA hybrids with different linkage directions and flexibilities.
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Affiliation(s)
- Ilyas Yildirim
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208
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27
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Meher G, Efthymiou T, Stoop M, Krishnamurthy R. Microwave-assisted preparation of nucleoside-phosphoramidites. Chem Commun (Camb) 2014; 50:7463-5. [DOI: 10.1039/c4cc03092c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Microwave-assisted phosphitylation of nucleosides is an efficient method for the preparation of phosphoramidites.
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Affiliation(s)
- G. Meher
- Department of Chemistry
- The Scripps Research Institute
- La Jolla, USA
| | - T. Efthymiou
- Department of Chemistry
- The Scripps Research Institute
- La Jolla, USA
| | - M. Stoop
- Department of Chemistry
- The Scripps Research Institute
- La Jolla, USA
| | - R. Krishnamurthy
- Department of Chemistry
- The Scripps Research Institute
- La Jolla, USA
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28
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Muller T, Bräse S. Tetrahedral organic molecules as components in supramolecular architectures and in covalent assemblies, networks and polymers. RSC Adv 2014. [DOI: 10.1039/c3ra46951d] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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29
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Minuth M, Richert C. A nucleobase analogue that pairs strongly with adenine. Angew Chem Int Ed Engl 2013; 52:10874-7. [PMID: 24038815 DOI: 10.1002/anie.201305555] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Indexed: 12/28/2022]
Affiliation(s)
- Marco Minuth
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart (Germany)
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30
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31
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Li S, Langenegger SM, Häner R. Control of aggregation-induced emission by DNA hybridization. Chem Commun (Camb) 2013; 49:5835-7. [PMID: 23702589 DOI: 10.1039/c3cc42706d] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aggregation-induced emission (AIE) was studied by hybridization of dialkynyl-tetraphenylethylene (DATPE) modified DNA strands. Molecular aggregation and fluorescence of DATPEs are controlled by duplex formation.
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Affiliation(s)
- Shaoguang Li
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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32
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Plietzsch O, Schade A, Hafner A, Huuskonen J, Rissanen K, Nieger M, Muller T, Bräse S. Synthesis and Topological Determination of Hexakis-Substituted 1,4-Ditritylbenzene and Nonakis-Substituted 1,3,5-Tritritylbenzene Derivatives: Building Blocks for Higher Supramolecular Assemblies. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201162] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Haug R, Richert C. A porphycene-DNA hybrid and its DNA-templated interactions with a porphyrin. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424612500575] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A porphycene with a hydroxyethyl side chain was coupled to the 3′-terminus of an oligodeoxynucleotide via solid-phase synthesis. The resulting porphycene-DNA hybrid binds to a complementary region of a DNA target strand with greater affinity than the unmodified control oligonucleotide, resulting in an increase of the UV-melting point of 12.7 °C. Duplex formation is accompanied by an increase in porphycene fluorescence at 640 nm by 18%. When a tetrakis(p-hydroxyphenyl)porphyrin appended to the 5′-terminus of another DNA-strand is brought into close proximity of the porphycene by hybridizing it to the downstream-region of the template strand, 94% of the porphycene fluorescence is quenched. By quenching each others fluorescence to different degrees, porphycene and porphyrin, together, report on local DNA structure in a fashion reminiscent of that of molecular beacons. The introduction of porphycenes and the porphycene-porphyrin "two hybrid system'' to DNA-based structuring may open up new avenues to designed functional materials.
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Affiliation(s)
- Rüdiger Haug
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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34
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Haug R, Griesser H, Sabirov T, Richert C. DNA-porphyrin hybrids as reaction centers for photosensitized ene reactions with singlet oxygen. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424612500484] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recent developments in DNA-mediated nanostructuring have paved the way for the development of novel reaction centers. As part of a project focused on nanostructured reaction centers for reactions catalyzed by porphyrins, we have developed a solid-phase synthesis of tetrakis(p-hydroxyphenyl)porphyrin-oligonucleotide hybrids. In these hybrids, up to four nucleic acid chains are linked to the phenolic substituents of the porphyrin via phosphodiester linkages. A representative hybrid with one oligonucleotide chain of the sequence TTAA was found to survive light irradiation under aerobic conditions for 2 h with less than 35% oxidation of the DNA chain. An assay measuring the diastereo- and enantioselectivity of the photosensitized ene reaction of mesitylol with singlet oxygen was set up that provides diastereomeric ratios via NMR of aliquots of the reaction solution. Enantiomers were separated gas chromatographically on a chiral stationary phase and were assigned based on the product distribution obtained with an enantiomerically enriched starting material. Our results are a starting point for the exploration of nanostructured reaction media based on DNA and porphyrins.
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Affiliation(s)
- Rüdiger Haug
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Helmut Griesser
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Thomas Sabirov
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Clemens Richert
- Universität Stuttgart, Institut für Organische Chemie, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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35
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Eryazici I, Yildirim I, Schatz GC, Nguyen ST. Enhancing the Melting Properties of Small Molecule-DNA Hybrids through Designed Hydrophobic Interactions: An Experimental-Computational Study. J Am Chem Soc 2012; 134:7450-8. [DOI: 10.1021/ja300322a] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Ibrahim Eryazici
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
| | - Ilyas Yildirim
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
| | - George C. Schatz
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
| | - SonBinh T. Nguyen
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208,
United States
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36
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Griesser H, Tolev M, Singh A, Sabirov T, Gerlach C, Richert C. Solution-phase synthesis of branched DNA hybrids based on dimer phosphoramidites and phenolic or nucleosidic cores. J Org Chem 2012; 77:2703-17. [PMID: 22369351 DOI: 10.1021/jo202505h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Branched oligonucleotides with "CG zippers" as DNA arms assemble into materials from micromolar solutions. Their synthesis has been complicated by low yields in solid-phase syntheses. Here we present a solution-phase synthesis based on phosphoramidites of dimers and phenolic cores that produces six-arm or four-arm hybrids in up to 61% yield. On the level of hybrids, only the final product has to be purified by precipitation or chromatography. A total of five different hybrids were prepared via the solution-phase route, including new hybrid (TCG)(4)TTPA with a tetrakis(triazolylphenyl)adamantane core and trimer DNA arms. The new method is more readily scaled up than solid-phase syntheses, uses no more than 4 equiv of phosphoramidite per phenolic alcohol, and provides routine access to novel materials that assemble via predictable base-pairing interactions.
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Affiliation(s)
- Helmut Griesser
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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37
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Singh A, Tolev M, Schilling CI, Bräse S, Griesser H, Richert C. Solution-phase synthesis of branched DNA hybrids via H-phosphonate dimers. J Org Chem 2012; 77:2718-28. [PMID: 22369428 DOI: 10.1021/jo202508n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A method for the solution-phase synthesis of branched oligonucleotides with tetrahedral or pseudo-octahedral geometry is described that involves the coupling of 3'-H-phosphonates of protected dinucleoside phosphates and organic core molecules. The dimer building blocks are produced by a synthesis that requires no chromatographic purification and that produces the dimer H-phosphonates in up to 44% yield in less than three days of laboratory work. A total of seven different branched hybrids were prepared, including a new hybrid of the sequence (CG)(4)TBA, where TBA stands for tetrakis(p-hydroxybiphenyl)adamantane that assembles into a material from micromolar aqueous solution upon addition of MgCl(2).
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Affiliation(s)
- Arunoday Singh
- Institute for Organic Chemistry, University of Stuttgart, 70569 Stuttgart, Germany
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38
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Bhatia D, Sharma S, Krishnan Y. Synthetic, biofunctional nucleic acid-based molecular devices. Curr Opin Biotechnol 2011; 22:475-84. [PMID: 21652202 DOI: 10.1016/j.copbio.2011.05.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2011] [Revised: 05/10/2011] [Accepted: 05/15/2011] [Indexed: 02/05/2023]
Abstract
Structural DNA nanotechnology seeks to create architectures of highly precise dimensions using the physical property that short lengths of DNA behave as rigid rods and the chemical property of Watson-Crick base-pairing that acts as a specific molecular glue with which such rigid rods may be joined. Thus DNA has been used as a molecular scale construction material to make molecular devices that can be broadly classified under two categories (i) rigid scaffolds and (ii) switchable architectures. This review details the growing impact of such synthetic nucleic acid based molecular devices in biology and biotechnology. Notably, a significant trend is emerging that integrates morphology-rich nucleic acid motifs and alternative molecular glues into DNA and RNA architectures to achieve biological functionality.
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Affiliation(s)
- Dhiraj Bhatia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK, Bellary Road, Bangalore 560065, India
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39
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Pathak R, Marx A. An adamantane-based building block for DNA networks. Chem Asian J 2011; 6:1450-5. [PMID: 21500357 DOI: 10.1002/asia.201000887] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 11/10/2022]
Abstract
DNA governs the storage and transfer of genetic information through generations in all living systems with the exception of some viruses. Its physicochemical nature and the Watson-Crick base pairing properties allow molecular constructions at nanometer length, thereby enabling the design of desired structural motifs, which can self-assemble to form large supramolecular arrays and scaffolds. The tailor-made DNAs have been an interesting material for such designed nanoscale constructions. However, the synthesis of specific structures with a desired molecular function is still in its infancy and therefore has to be further explored. To add a new dimension to this approach, we have synthesized a rigid three-way branched adamantane motif, which is capable of forming highly stable DNA networks. The moiety generated could serve as a useful building block for DNA-based nanoconstructions.
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Affiliation(s)
- Richa Pathak
- Department of Chemistry and Konstanz Research School of Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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40
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41
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Singh A, Tolev M, Meng M, Klenin K, Plietzsch O, Schilling CI, Muller T, Nieger M, Bräse S, Wenzel W, Richert C. Branched DNA that forms a solid at 95 °C. Angew Chem Int Ed Engl 2011; 50:3227-31. [PMID: 21374767 DOI: 10.1002/anie.201006992] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 12/18/2010] [Indexed: 11/08/2022]
Affiliation(s)
- Arunoday Singh
- Institut für Organische Chemie, Universität Stuttgart, 70569 Stuttgart, Germany
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42
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Schilling CI, Plietzsch O, Nieger M, Muller T, Bräse S. Fourfold Suzuki-Miyaura and Sonogashira Cross-Coupling Reactions on Tetrahedral Methane and Adamantane Derivatives. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001567] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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43
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Plietzsch O, Schilling CI, Grab T, Grage SL, Ulrich AS, Comotti A, Sozzani P, Muller T, Bräse S. Click chemistry produces hyper-cross-linked polymers with tetrahedral cores. NEW J CHEM 2011. [DOI: 10.1039/c1nj20370c] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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45
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Asymmetric synthesis of chiral tectons with tetrapodal symmetry: fourfold asymmetric reactions. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.05.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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Boer D, Kerckhoffs J, Parajo Y, Pascu M, Usón I, Lincoln P, Hannon M, Coll M. Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders. Angew Chem Int Ed Engl 2010; 49:2336-9. [DOI: 10.1002/anie.200906742] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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47
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Boer D, Kerckhoffs J, Parajo Y, Pascu M, Usón I, Lincoln P, Hannon M, Coll M. Self-Assembly of Functionalizable Two-Component 3D DNA Arrays through the Induced Formation of DNA Three-Way-Junction Branch Points by Supramolecular Cylinders. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200906742] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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48
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Müller K, Malik S, Richert C. Sequence-specifically addressable hairpin DNA-single-walled carbon nanotube complexes for nanoconstruction. ACS NANO 2010; 4:649-656. [PMID: 20085346 DOI: 10.1021/nn900886q] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) are attractive building blocks for molecular electronics and novel materials. Generating functional architectures with SWCNTs requires methodologies for dispersing, purifying, and binding these highly insoluble quasi one-dimensional molecules. We have previously shown that unstructured DNA strands bind to carbon nanotubes so tightly that it is difficult to address them with complementary strands. Here we show that hairpin oligonucleotides give SWCNT suspensions more concentrated than those obtainable with previously optimized DNA sequences. Further, hairpin-forming oligonucleotides and (6,5)-SWCNTs form complexes that are addressable with complementary, triplex-forming oligonucleotides. As proof of principle, we show that DNA-SWCNT complexes can be bound sequence-specifically with oligonucleotides featuring fluorophores or quantum dots. The new method brings SWCNTs of exquisite purity into the realm of DNA-based nanostructuring.
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Richert C, Meng M, Singh A. Designed DNA crystals: triangles with short sticky ends. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2782-2783. [PMID: 20014216 DOI: 10.1002/smll.200902108] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Clemens Richert
- Institute for Organic Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany.
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Plietzsch O, Schilling CI, Tolev M, Nieger M, Richert C, Muller T, Bräse S. Four-fold click reactions: Generation of tetrahedral methane- and adamantane-based building blocks for higher-order molecular assemblies. Org Biomol Chem 2009; 7:4734-43. [DOI: 10.1039/b912189g] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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