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Dore MD, Rafique MG, Yang TP, Zorman M, Platnich CM, Xu P, Trinh T, Rizzuto FJ, Cosa G, Li J, Guarné A, Sleiman HF. Heat-activated growth of metastable and length-defined DNA fibers expands traditional polymer assembly. Nat Commun 2024; 15:4384. [PMID: 38782917 PMCID: PMC11116425 DOI: 10.1038/s41467-024-48722-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
Biopolymers such as nucleic acids and proteins exhibit dynamic backbone folding, wherein site-specific intramolecular interactions determine overall structure. Proteins then hierarchically assemble into supramolecular polymers such as microtubules, that are robust yet dynamic, constantly growing or shortening to adjust to cellular needs. The combination of dynamic, energy-driven folding and growth with structural stiffness and length control is difficult to achieve in synthetic polymer self-assembly. Here we show that highly charged, monodisperse DNA-oligomers assemble via seeded growth into length-controlled supramolecular fibers during heating; when the temperature is lowered, these metastable fibers slowly disassemble. Furthermore, the specific molecular structures of oligomers that promote fiber formation contradict the typical theory of block copolymer self-assembly. Efficient curling and packing of the oligomers - or 'curlamers' - determine morphology, rather than hydrophobic to hydrophilic ratio. Addition of a small molecule stabilises the DNA fibers, enabling temporal control of polymer lifetime and underscoring their potential use in nucleic-acid delivery, stimuli-responsive biomaterials, and soft robotics.
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Affiliation(s)
- Michael D Dore
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | | | - Tianxiao Peter Yang
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Marlo Zorman
- Department of Chemistry, University of Vermont, Burlington, VT, 05405, USA
| | - Casey M Platnich
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Pengfei Xu
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Tuan Trinh
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
| | - Felix J Rizzuto
- School of Chemistry, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Gonzalo Cosa
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Jianing Li
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, 47906, USA
| | - Alba Guarné
- Department of Biochemistry and Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St W, Montréal, QC, H3A 08B, Canada.
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, QC, Canada.
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2
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Design, Synthesis and Actual Applications of the Polymers Containing Acidic P-OH Fragments: Part 1. Polyphosphodiesters. Int J Mol Sci 2022; 23:ijms232314857. [PMID: 36499185 PMCID: PMC9738169 DOI: 10.3390/ijms232314857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 12/03/2022] Open
Abstract
Among natural and synthetic polymers, main-chain phosphorus-containing polyacids (PCPAs) (polyphosphodiesters), stand in a unique position at the intersection of chemistry, physics, biology and medicine. The structural similarity of polyphosphodiesters PCPAs to natural nucleic and teichoic acids, their biocompatibility, mimicking to biomolecules providing the 'stealth effect', high bone mineral affinity of polyphosphodiesters resulting in biomineralization at physiological conditions, and adjustable hydrolytic stability of polyphosphodiesters are the basis for various biomedical, industrial and household applications of this type of polymers. In the present review, we discuss the synthesis, properties and actual applications of polyphosphodiesters.
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Rothenbühler S, Gonzalez A, Iacovache I, Langenegger SM, Zuber B, Häner R. Tetraphenylethylene-DNA conjugates: influence of sticky ends and DNA sequence length on the supramolecular assembly of AIE-active vesicles. Org Biomol Chem 2022; 20:3703-3707. [PMID: 35262542 PMCID: PMC9092531 DOI: 10.1039/d2ob00357k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The supramolecular assembly of DNA conjugates, functionalized with tetraphenylethylene (TPE) sticky ends, into vesicular structures is described. The aggregation-induced emission (AIE) active TPE units allow monitoring the assembly process by fluorescence spectroscopy. The number of TPE modifications in the overhangs of the conjugates influences the supramolecular assembly behavior. A minimum of two TPE residues on each end are required to ensure a well-defined assembly process. The design of the presented DNA-based nanostructures offers tailored functionalization with applications in DNA nanotechnology. The supramolecular assembly of tetraphenylethylene (TPE)–DNA conjugates is presented. The length of the TPE sticky ends exerts a pronounced effect on the formation of aggregation-induced emission (AIE)-active vesicles.![]()
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Affiliation(s)
- Simon Rothenbühler
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Adrian Gonzalez
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Ioan Iacovache
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Simon M Langenegger
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
| | - Benoît Zuber
- Institute of Anatomy, University of Bern, Baltzerstrasse 2, CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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Appukutti N, de Vries AH, Gudeangadi PG, Claringbold BR, Garrett MD, Reithofer MR, Serpell CJ. Sequence-complementarity dependent co-assembly of phosphodiester-linked aromatic donor–acceptor trimers. Chem Commun (Camb) 2022; 58:12200-12203. [DOI: 10.1039/d2cc00239f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sequence-defined trimers of phosphodiester-linked aromatic donor–acceptors self-assemble according to monomer order, and co-assemble into new structures with their complementary sequence.
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Affiliation(s)
- Nadeema Appukutti
- School of Chemistry and Forensic Science, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Alex H. de Vries
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Prashant G. Gudeangadi
- School of Chemistry and Forensic Science, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Bini R. Claringbold
- School of Chemistry and Forensic Science, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK
| | - Michelle D. Garrett
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent, CT2 7NJ, UK
| | - Michael R. Reithofer
- Dept. of Inorganic Chemistry, University of Vienna, Wahringer Strabe. 42, 1090 Vienna, Austria
| | - Christopher J. Serpell
- School of Chemistry and Forensic Science, Ingram Building, University of Kent, Canterbury, Kent, CT2 7NH, UK
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5
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Dore MD, Trinh T, Zorman M, de Rochambeau D, Platnich CM, Xu P, Luo X, Remington JM, Toader V, Cosa G, Li J, Sleiman HF. Thermosetting supramolecular polymerization of compartmentalized DNA fibers with stereo sequence and length control. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Abstract
In biological systems, the storage and transfer of genetic information rely on sequence-controlled nucleic acids such as DNA and RNA. It has been realized for quite some time that this property is not only crucial for life but could also be very useful in human applications. For instance, DNA has been actively investigated as a digital storage medium over the past decade. Indeed, the "hard-disk of life" is an obvious choice and a highly optimized material for storing data. Through decades of nucleic acids research, technological tools for parallel synthesis and sequencing of DNA have been readily available. Consequently, it has already been demonstrated that different types of documents (e.g., texts, images, videos, and industrial data) can be stored in chemically synthesized DNA libraries. However, DNA is subject to biological constraints, and its molecular structure cannot be easily varied to match technological needs. In fact, DNA is not the only macromolecule that enables data storage. In recent years, it has been demonstrated that a wide variety of synthetic polymers can also be used for such a purpose. Indeed, modern polymer synthesis allows the preparation of synthetic macromolecules with precisely controlled monomer sequences. Altogether, about a dozens of synthetic digital polymers have already been described, and many more can be foreseen. Among them, sequence-defined poly(phosphodiester)s are one of the most promising options. These polymers are prepared by stepwise phosphoramidite chemistry like chemically synthesized oligonucleotides. However, they are constructed with non-natural building blocks and therefore share almost no structural characteristics with nucleic acids, except phosphate repeat units. Still, they contain readable digital messages that can be deciphered by nanopore sequencing or mass spectrometry sequencing. In this Account, we describe our recent research efforts in synthesizing and sequencing optimal abiological digital poly(phosphodiester)s. A major advantage of these polymers over DNA is that their molecular structure can easily be varied to tune their properties. During the last 5 years, we have engineered the molecular structure of these polymers to adjust crucial parameters such as the storage density, storage capacity, erasability, and readability. Consequently, high-capacity PPDE chains, containing hundreds of bits per chains, can now be synthesized and efficiently sequenced using a routine mass spectrometer. Furthermore, sequencing data can be automatically decrypted with the help of decoding software. This new type of coded matter can also be edited using practical physical triggers such as light and organized in space by programmed self-assembly. All of these recent improvements are summarized and discussed herein.
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Affiliation(s)
- Laurence Charles
- Aix Marseille Université, CNRS, Institute for Radical Chemistry, UMR 7273, 23 Av Escadrille Nomandie-Niemen, 13397 Marseille Cedex 20, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
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7
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Fadler RE, Al Ouahabi A, Qiao B, Carta V, König NF, Gao X, Zhao W, Zhang Y, Lutz JF, Flood AH. Chain Entropy Beats Hydrogen Bonds to Unfold and Thread Dialcohol Phosphates inside Cyanostar Macrocycles To Form [3]Pseudorotaxanes. J Org Chem 2021; 86:4532-4546. [PMID: 33636075 PMCID: PMC8063573 DOI: 10.1021/acs.joc.0c02887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The recognition of substituted phosphates underpins many processes including DNA binding, enantioselective catalysis, and recently template-directed rotaxane synthesis. Beyond ATP and a few commercial substrates, however, little is known about how substituents effect organophosphate recognition. Here, we examined alcohol substituents and their impact on recognition by cyanostar macrocycles. The organophosphates were disubstituted by alcohols of various chain lengths, dipropanol, dihexanol, and didecanol phosphate, each accessed using modular solid-phases syntheses. Based on the known size-selective binding of phosphates by π-stacked dimers of cyanostars, threaded [3]pseudorotaxanes were anticipated. While seen with butyl substituents, pseudorotaxane formation was disrupted by competitive OH···O- hydrogen bonding between both terminal hydroxyls and the anionic phosphate unit. Crystallography also showed formation of a backfolded propanol conformation resulting in an 8-membered ring and a perched cyanostar assembly. Motivated by established entropic penalties accompanying ring formation, we reinstated [3]pseudorotaxanes by extending the size of the substituent to hexanol and decanol. Chain entropy overcomes the enthalpically favored OH···O- contacts to favor random-coil conformations required for seamless, high-fidelity threading of dihexanol and didecanol phosphates inside cyanostars. These studies highlight how chain length and functional groups on phosphate's substituents can be powerful design tools to regulate binding and control assembly formation during phosphate recognition.
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Affiliation(s)
- Rachel E Fadler
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Bo Qiao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Veronica Carta
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Niklas F König
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Xinfeng Gao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Wei Zhao
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Yankai Zhang
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, Strasbourg, 67034, France
| | - Amar H Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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Roszak I, Oswald L, Al Ouahabi A, Bertin A, Laurent E, Felix O, Carvin-Sergent I, Charles L, Lutz JF. Synthesis and sequencing of informational poly(amino phosphodiester)s. Polym Chem 2021. [DOI: 10.1039/d1py01052b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inclusion of main-chain tertiary amines in digital poly(phosphodiester)s allows synthesis of molecularly-defined achiral polymers and simplifies tandem mass spectrometry sequencing.
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Affiliation(s)
- Ian Roszak
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Laurence Oswald
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Abdelaziz Al Ouahabi
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Annabelle Bertin
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
- BAM Federal Institute for Materials Research and Testing, Unter den Eichen 87, 12205 Berlin, Germany
- Institute of Chemistry and Biochemistry − Organic Chemistry, Free University Berlin, Takustraße 3, 14195 Berlin, Germany
| | - Eline Laurent
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Olivier Felix
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Isaure Carvin-Sergent
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Laurence Charles
- Aix Marseille Université, CNRS, UMR 7273, Institute of Radical Chemistry, 13397, Marseille Cedex 20, France
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
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9
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Markova L, Probst M, Häner R. Assembly and functionalization of supramolecular polymers from DNA-conjugated squaraine oligomers. RSC Adv 2020; 10:44841-44845. [PMID: 35516236 PMCID: PMC9058661 DOI: 10.1039/d0ra10117f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
DNA conjugated oligomers of organic molecules are candidates for applications in the materials and medical sciences, in diagnostics, in optical devices, for delivery or for the design of complex molecular architectures. Herein, we describe the synthesis and properties of DNA-conjugated squaraine (Sq) oligomers. The oligomers self-assemble into supramolecular polymers that are amenable to further functionalization via DNA hybridization, as shown by the attachment of gold nanoparticles (AuNPs). The assembly of supramolecular polymers of DNA-linked squaraine oligomers and their subsequent derivatization is described.![]()
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Affiliation(s)
- Larysa Markova
- Department of Chemistry and Biochemistry, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Markus Probst
- Department of Chemistry and Biochemistry, University of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry, University of Bern Freiestrasse 3 3012 Bern Switzerland
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10
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Synthesis and applications of anisotropic nanoparticles with precisely defined dimensions. Nat Rev Chem 2020; 5:21-45. [PMID: 37118104 DOI: 10.1038/s41570-020-00232-7] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 02/07/2023]
Abstract
Shape and size play powerful roles in determining the properties of a material; controlling these aspects with precision is therefore an important, fundamental goal of the chemical sciences. In particular, the introduction of shape anisotropy at the nanoscale has emerged as a potent way to access new properties and functionality, enabling the exploration of complex nanomaterials across a range of applications. Recent advances in DNA and protein nanotechnology, inorganic crystallization techniques, and precision polymer self-assembly are now enabling unprecedented control over the synthesis of anisotropic nanoparticles with a variety of shapes, encompassing one-dimensional rods, dumbbells and wires, two-dimensional and three-dimensional platelets, rings, polyhedra, stars, and more. This has, in turn, enabled much progress to be made in our understanding of how anisotropy and particle dimensions can be tuned to produce materials with unique and optimized properties. In this Review, we bring these recent developments together to critically appraise the different methods for the bottom-up synthesis of anisotropic nanoparticles enabling exquisite control over morphology and dimensions. We highlight the unique properties of these materials in arenas as diverse as electron transport and biological processing, illustrating how they can be leveraged to produce devices and materials with otherwise inaccessible functionality. By making size and shape our focus, we aim to identify potential synergies between different disciplines and produce a road map for future research in this crucial area.
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